Daily Papers

Deep learning models have driven significant progress in predicting protein function and interactions at the protein level. While these advancements have been invaluable for many biological applications such as enzyme engineering and function annotation, a more detailed perspective is essential for understanding protein functional mechanisms and evaluating the biological knowledge captured by models. To address this demand, we introduce VenusX, the first large-scale benchmark for fine-grained functional annotation and function-based protein pairing at the residue, fragment, and domain levels. VenusX comprises three major task categories across six types of annotations, including residue-level binary classification, fragment-level multi-class classification, and pairwise functional similarity scoring for identifying critical active sites, binding sites, conserved sites, motifs, domains, and epitopes. The benchmark features over 878,000 samples curated from major open-source databases such as InterPro, BioLiP, and SAbDab. By providing mixed-family and cross-family splits at three sequence identity thresholds, our benchmark enables a comprehensive assessment of model performance on both in-distribution and out-of-distribution scenarios. For baseline evaluation, we assess a diverse set of popular and open-source models, including pre-trained protein language models, sequence-structure hybrids, structure-based methods, and alignment-based techniques. Their performance is reported across all benchmark datasets and evaluation settings using multiple metrics, offering a thorough comparison and a strong foundation for future research. Code and data are publicly available at https://github.com/ai4protein/VenusX.

Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks. However, their ability to reliably reason from gene-level knowledge to functional understanding, a core requirement for knowledge-enhanced cell atlas interpretation, remains largely underexplored. To address this gap, we introduce SciHorizon-GENE, a large-scale gene-centric benchmark constructed from authoritative biological databases. The benchmark integrates curated knowledge for over 190K human genes and comprises more than 540K questions covering diverse gene-to-function reasoning scenarios relevant to cell type annotation, functional interpretation, and mechanism-oriented analysis. Motivated by behavioral patterns observed in preliminary examinations, SciHorizon-GENE evaluates LLMs along four biologically critical perspectives: research attention sensitivity, hallucination tendency, answer completeness, and literature influence, explicitly targeting failure modes that limit the safe adoption of LLMs in biological interpretation pipelines. We systematically evaluate a wide range of state-of-the-art general-purpose and biomedical LLMs, revealing substantial heterogeneity in gene-level reasoning capabilities and persistent challenges in generating faithful, complete, and literature-grounded functional interpretations. Our benchmark establishes a systematic foundation for analyzing LLM behavior at the gene scale and offers insights for model selection and development, with direct relevance to knowledge-enhanced biological interpretation.

Autonomous agents capable of navigating Graphical User Interfaces (GUIs) hold the potential to revolutionize digital productivity. However, achieving true digital autonomy extends beyond reactive element matching; it necessitates a predictive mental model of interface dynamics and the ability to foresee the "digital world state" resulting from interactions. Despite the perceptual capabilities of modern Vision-Language Models (VLMs), existing benchmarks remain bifurcated (focusing either on black-box task completion or static, shallow grounding), thereby failing to assess whether agents truly comprehend the implicit functionality and transition logic of GUIs. To bridge this gap, we introduce AutoGUI-v2, a comprehensive benchmark designed to evaluate deep GUI functionality understanding and interaction outcome prediction. We construct the benchmark using a novel VLM-human collaborative pipeline that recursively parses multi-platform screenshots into hierarchical functional regions to generate diverse evaluation tasks. Providing 2,753 tasks across six operating systems, AutoGUI-v2 rigorously tests agents on region and element-level semantics, grounding, and dynamic state prediction. Our evaluation reveals a striking dichotomy in VLMs: while open-source models fine-tuned on agent data (e.g., Qwen3-VL) excel at functional grounding, commercial models (e.g., Gemini-2.5-Pro-Thinking) dominate in functionality captioning. Crucially, all models struggle with complex interaction logic of uncommon actions, highlighting that deep functional understanding remains a significant hurdle. By systematically measuring these foundational capabilities, AutoGUI-v2 offers a new lens for advancing the next generation of GUI agents.

Understanding the structure and function of circuits is crucial for electronic design automation (EDA). Circuits can be formulated as And-Inverter graphs (AIGs), enabling efficient implementation of representation learning through graph neural networks (GNNs). Masked modeling paradigms have been proven effective in graph representation learning. However, masking augmentation to original circuits will destroy their logical equivalence, which is unsuitable for circuit representation learning. Moreover, existing masked modeling paradigms often prioritize structural information at the expense of abstract information such as circuit function. To address these limitations, we introduce MGVGA, a novel constrained masked modeling paradigm incorporating masked gate modeling (MGM) and Verilog-AIG alignment (VGA). Specifically, MGM preserves logical equivalence by masking gates in the latent space rather than in the original circuits, subsequently reconstructing the attributes of these masked gates. Meanwhile, large language models (LLMs) have demonstrated an excellent understanding of the Verilog code functionality. Building upon this capability, VGA performs masking operations on original circuits and reconstructs masked gates under the constraints of equivalent Verilog codes, enabling GNNs to learn circuit functions from LLMs. We evaluate MGVGA on various logic synthesis tasks for EDA and show the superior performance of MGVGA compared to previous state-of-the-art methods. Our code is available at https://github.com/wuhy68/MGVGA.

Understanding functional representations within higher visual cortex is a fundamental question in computational neuroscience. While artificial neural networks pretrained on large-scale datasets exhibit striking representational alignment with human neural responses, learning image-computable models of visual cortex relies on individual-level, large-scale fMRI datasets. The necessity for expensive, time-intensive, and often impractical data acquisition limits the generalizability of encoders to new subjects and stimuli. BraInCoRL uses in-context learning to predict voxelwise neural responses from few-shot examples without any additional finetuning for novel subjects and stimuli. We leverage a transformer architecture that can flexibly condition on a variable number of in-context image stimuli, learning an inductive bias over multiple subjects. During training, we explicitly optimize the model for in-context learning. By jointly conditioning on image features and voxel activations, our model learns to directly generate better performing voxelwise models of higher visual cortex. We demonstrate that BraInCoRL consistently outperforms existing voxelwise encoder designs in a low-data regime when evaluated on entirely novel images, while also exhibiting strong test-time scaling behavior. The model also generalizes to an entirely new visual fMRI dataset, which uses different subjects and fMRI data acquisition parameters. Further, BraInCoRL facilitates better interpretability of neural signals in higher visual cortex by attending to semantically relevant stimuli. Finally, we show that our framework enables interpretable mappings from natural language queries to voxel selectivity.

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.

Spatial intelligence is a critical component of embodied AI, promoting robots to understand and interact with their environments. While recent advances have enhanced the ability of VLMs to perceive object locations and positional relationships, they still lack the capability to precisely understand object orientations-a key requirement for tasks involving fine-grained manipulations. Addressing this limitation not only requires geometric reasoning but also an expressive and intuitive way to represent orientation. In this context, we propose that natural language offers a more flexible representation space than canonical frames, making it particularly suitable for instruction-following robotic systems. In this paper, we introduce the concept of semantic orientation, which defines object orientations using natural language in a reference-frame-free manner (e.g., the ''plug-in'' direction of a USB or the ''handle'' direction of a knife). To support this, we construct OrienText300K, a large-scale dataset of 3D models annotated with semantic orientations that link geometric understanding to functional semantics. By integrating semantic orientation into a VLM system, we enable robots to generate manipulation actions with both positional and orientational constraints. Extensive experiments in simulation and real world demonstrate that our approach significantly enhances robotic manipulation capabilities, e.g., 48.7% accuracy on Open6DOR and 74.9% accuracy on SIMPLER.

In this paper, we propose to use the general L^2-based Sobolev norms, i.e., H^s norms where sin R, to measure the data discrepancy due to noise in image processing tasks that are formulated as optimization problems. As opposed to a popular trend of developing regularization methods, we emphasize that an implicit regularization effect can be achieved through the class of Sobolev norms as the data-fitting term. Specifically, we analyze that the implicit regularization comes from the weights that the H^s norm imposes on different frequency contents of an underlying image. We further analyze the underlying noise assumption of using the Sobolev norm as the data-fitting term from a Bayesian perspective, build the connections with the Sobolev gradient-based methods and discuss the preconditioning effects on the convergence rate of the gradient descent algorithm, leading to a better understanding of functional spaces/metrics and the optimization process involved in image processing. Numerical results in full waveform inversion, image denoising and deblurring demonstrate the implicit regularization effects.

Large language models (LLMs) have significantly advanced protein representation learning. However, their capacity to interpret and design antibodies through natural language remains limited. To address this challenge, we present AFD-Instruction, the first large-scale instruction dataset with functional annotations tailored to antibodies. This dataset encompasses two key components: antibody understanding, which infers functional attributes directly from sequences, and antibody design, which enables de novo sequence generation under functional constraints. These components provide explicit sequence-function alignment and support antibody design guided by natural language instructions. Extensive instruction-tuning experiments on general-purpose LLMs demonstrate that AFD-Instruction consistently improves performance across diverse antibody-related tasks. By linking antibody sequences with textual descriptions of function, AFD-Instruction establishes a new foundation for advancing antibody modeling and accelerating therapeutic discovery.

Affordance understanding bridges visual perception and physical action, serving as an explainable interface for robot manipulation in open and unstructured real-world environments. Yet, building an affordance foundation model that not only understands where and how the interaction should happen, but also generalizes across diverse environments, objects, and tasks, remains a long-standing research challenge. Existing methods typically address only part of this challenge, either localizing task-relevant regions without specifying executable motion, or predicting motion but with limited scalability. In this paper, we present ourmodel, a step towards an affordance foundation model for functionality understanding. From a single RGB-D observation and a language task description, ourmodel predicts a task-conditional functional mask (where to interact) and a 3D post-contact motion curve (how to interact). To support open-world generalization, we build a large-scale standardized data pipeline that converts heterogeneous robot, human, simulation, and real-world scan data into a shared affordance schema with language, masks, and object-centric 3D motion labels. We evaluate ourmodel from three aspects: for affordance segmentation, ourmodel outperforms all baselines by a large margin across 8 test sets from 4 benchmarks, improving mean gIoU/cIoU by +23.9/+26.3; for contact-point prediction, it predicts substantially more accurate points, with a 12.7--61.3% hit-rate gain over the best baseline; and for 3D motion, it achieves the best performance on all three test sets. ourmodel can be deployed for real-world robot manipulation without finetuning for robot embodiment or using task-specific heuristics, demonstrating the ability to adapt to open-world affordance tasks. Project page: https://www.zhaoningwang.com/AFUN

Reinforcement Learning with Verifiable Rewards (RLVR) is highly effective for enhancing LLM reasoning, yet recent evidence shows models like Qwen 2.5 achieve significant gains even with spurious or incorrect rewards. We investigate this phenomenon and identify a "Perplexity Paradox": spurious RLVR triggers a divergence where answer-token perplexity drops while prompt-side coherence degrades, suggesting the model is bypassing reasoning in favor of memorization. Using Path Patching, Logit Lens, JSD analysis, and Neural Differential Equations, we uncover a hidden Anchor-Adapter circuit that facilitates this shortcut. We localize a Functional Anchor in the middle layers (L18-20) that triggers the retrieval of memorized solutions, followed by Structural Adapters in later layers (L21+) that transform representations to accommodate the shortcut signal. Finally, we demonstrate that scaling specific MLP keys within this circuit allows for bidirectional causal steering-artificially amplifying or suppressing contamination-driven performance. Our results provide a mechanistic roadmap for identifying and mitigating data contamination in RLVR-tuned models. Code is available at https://github.com/idwts/How-RLVR-Activates-Memorization-Shortcuts.

Large Language Models (LLMs) have demonstrated notable proficiency in both code generation and comprehension across multiple programming languages. However, the mechanisms underlying this proficiency remain underexplored, particularly with respect to whether distinct programming languages are processed independently or within a shared parametric region. Drawing an analogy to the specialized regions of the brain responsible for distinct cognitive functions, we introduce the concept of Coding Spot, a specialized parametric region within LLMs that facilitates coding capabilities. Our findings identify this Coding Spot and show that targeted modifications to this subset significantly affect performance on coding tasks, while largely preserving non-coding functionalities. This compartmentalization mirrors the functional specialization observed in cognitive neuroscience, where specific brain regions are dedicated to distinct tasks, suggesting that LLMs may similarly employ specialized parameter regions for different knowledge domains.

Field evaporation from ionic or covalently bonded materials often leads to the emission of molecular ions. The metastability of these molecular ions, particularly under the influence of the intense electrostatic field (1010 Vm-1), makes them prone to dissociation with or without an exchange of energy amongst them. These processes can affect the analytical performance of atom probe tomography (APT). For instance, neutral species formed through dissociation may not be detected at all or with a time of flight no longer related to their mass, causing their loss from the analysis. Here, we evaluated the changes in the measured composition of FeO, Fe2O3 and Fe3O4 across a wide range of analysis conditions. Possible dissociation reactions are predicted by density-functional theory (DFT) calculations considering the spin states of the molecules. The energetically favoured reactions are traced on to the multi-hit ion correlation histograms, to confirm their existence within experiments, using an automated Python-based routine. The detected reactions are carefully analysed to reflect upon the influence of these neutrals from dissociation reactions on the performance of APT for analysing iron oxides.

Task arithmetic provides an efficient, training-free way to edit pre-trained models, yet lacks a fundamental theoretical explanation for its success. The existing concept of ``weight disentanglement" describes the ideal outcome of non-interfering task composition but does not reveal its underlying cause. Crucially, what intrinsic properties of the pre-trained model (θ_0) or the task vectors (τ_t) enable this disentanglement remains underexplored. In this paper, we introduce Task-Feature Specialization (TFS), a model's ability to allocate distinct internal features to different tasks, as the fundamental principle. We first prove that TFS is a sufficient condition for weight disentanglement. More importantly, we find that TFS also gives rise to an observable geometric consequence: weight vector orthogonality. This positions TFS as the common cause for both the desired functional outcome (disentanglement) and a measurable geometric property (orthogonality). This relationship provides the key insight for our method: since the abstract TFS property is intractable to enforce directly, we can instead promote weight disentanglement by shaping its concrete geometric consequence, orthogonality. Therefore, we propose OrthoReg, a simple and effective regularization method that actively enforces an internal orthogonal structure on weight updates (ΔW) that constitute τ_t during fine-tuning. And we theoretically prove that OrthoReg promotes disentanglement. Extensive experiments demonstrate that OrthoReg consistently and significantly enhances the performance of various task arithmetic methods. Code is available at https://github.com/RL-MIND/OrthoReg{https://github.com/RL-MIND/OrthoReg}.

With the development of large language models (LLMs), particularly with the introduction of the long reasoning chain technique, the reasoning ability of LLMs in complex problem-solving has been significantly enhanced. While acknowledging the power of long reasoning chains, we cannot help but wonder: Why do different reasoning chains perform differently in reasoning? What components of the reasoning chains play a key role? Existing studies mainly focus on evaluating reasoning chains from a functional perspective, with little attention paid to their structural mechanisms. To address this gap, this work is the first to analyze and evaluate the quality of the reasoning chain from a structural perspective. We apply persistent homology from Topological Data Analysis (TDA) to map reasoning steps into semantic space, extract topological features, and analyze structural changes. These changes reveal semantic coherence, logical redundancy, and identify logical breaks and gaps. By calculating homology groups, we assess connectivity and redundancy at various scales, using barcode and persistence diagrams to quantify stability and consistency. Our results show that the topological structural complexity of reasoning chains correlates positively with accuracy. More complex chains identify correct answers sooner, while successful reasoning exhibits simpler topologies, reducing redundancy and cycles, enhancing efficiency and interpretability. This work provides a new perspective on reasoning chain quality assessment and offers guidance for future optimization.

Code clone detection is a critical task in software engineering, aimed at identifying duplicated or similar code fragments within or across software systems. Traditional methods often fail to capture functional equivalence, particularly for semantic clones (Type 4), where code fragments implement identical functionality despite differing syntactic structures. Recent advances in large language models (LLMs) have shown promise in understanding code semantics. However, directly applying LLMs to code clone detection yields suboptimal results due to their sensitivity to syntactic differences. To address these challenges, we propose a novel two-stage framework that combines LLM-based screening with execution-based validation for detecting semantic clones in Python programs. In the first stage, an LLM evaluates code pairs to filter out obvious non-clones based on semantic analysis. For pairs not identified as clones, the second stage employs an execution-based validation approach, utilizing LLM-generated test inputs to assess functional equivalence through cross-execution validation. Our experimental evaluation demonstrates significant improvements in precision, recall, and F1-score compared to direct LLM-based detection, highlighting the framework's effectiveness in identifying semantic clones. Future work includes exploring cross-language clone detection and optimizing the framework for large-scale applications.

Understanding the inner workings of neural networks is essential for enhancing model performance and interpretability. Current research predominantly focuses on examining the connection between individual neurons and the model's final predictions. Which suffers from challenges in interpreting the internal workings of the model, particularly when neurons encode multiple unrelated features. In this paper, we propose a novel framework that transitions the focus from analyzing individual neurons to investigating groups of neurons, shifting the emphasis from neuron-output relationships to functional interaction between neurons. Our automated framework, NeurFlow, first identifies core neurons and clusters them into groups based on shared functional relationships, enabling a more coherent and interpretable view of the network's internal processes. This approach facilitates the construction of a hierarchical circuit representing neuron interactions across layers, thus improving interpretability while reducing computational costs. Our extensive empirical studies validate the fidelity of our proposed NeurFlow. Additionally, we showcase its utility in practical applications such as image debugging and automatic concept labeling, thereby highlighting its potential to advance the field of neural network explainability.

Understanding functionalities in 3D scenes involves interpreting natural language descriptions to locate functional interactive objects, such as handles and buttons, in a 3D environment. Functionality understanding is highly challenging, as it requires both world knowledge to interpret language and spatial perception to identify fine-grained objects. For example, given a task like 'turn on the ceiling light', an embodied AI agent must infer that it needs to locate the light switch, even though the switch is not explicitly mentioned in the task description. To date, no dedicated methods have been developed for this problem. In this paper, we introduce Fun3DU, the first approach designed for functionality understanding in 3D scenes. Fun3DU uses a language model to parse the task description through Chain-of-Thought reasoning in order to identify the object of interest. The identified object is segmented across multiple views of the captured scene by using a vision and language model. The segmentation results from each view are lifted in 3D and aggregated into the point cloud using geometric information. Fun3DU is training-free, relying entirely on pre-trained models. We evaluate Fun3DU on SceneFun3D, the most recent and only dataset to benchmark this task, which comprises over 3000 task descriptions on 230 scenes. Our method significantly outperforms state-of-the-art open-vocabulary 3D segmentation approaches. Project page: https://jcorsetti.github.io/fun3du

Despite superior reasoning prowess demonstrated by Large Language Models (LLMs) with Chain-of-Thought (CoT) prompting, a lack of understanding prevails around the internal mechanisms of the models that facilitate CoT generation. This work investigates the neural sub-structures within LLMs that manifest CoT reasoning from a mechanistic point of view. From an analysis of Llama-2 7B applied to multistep reasoning over fictional ontologies, we demonstrate that LLMs deploy multiple parallel pathways of answer generation for step-by-step reasoning. These parallel pathways provide sequential answers from the input question context as well as the generated CoT. We observe a functional rift in the middle layers of the LLM. Token representations in the initial half remain strongly biased towards the pretraining prior, with the in-context prior taking over in the later half. This internal phase shift manifests in different functional components: attention heads that write the answer token appear in the later half, attention heads that move information along ontological relationships appear in the initial half, and so on. To the best of our knowledge, this is the first attempt towards mechanistic investigation of CoT reasoning in LLMs.

The performance differential of large language models (LLM) between languages hinders their effective deployment in many regions, inhibiting the potential economic and societal value of generative AI tools in many communities. However, the development of functional LLMs in many languages (\ie, multilingual LLMs) is bottlenecked by the lack of high-quality evaluation resources in languages other than English. Moreover, current practices in multilingual benchmark construction often translate English resources, ignoring the regional and cultural knowledge of the environments in which multilingual systems would be used. In this work, we construct an evaluation suite of 197,243 QA pairs from local exam sources to measure the capabilities of multilingual LLMs in a variety of regional contexts. Our novel resource, INCLUDE, is a comprehensive knowledge- and reasoning-centric benchmark across 44 written languages that evaluates multilingual LLMs for performance in the actual language environments where they would be deployed.

Code-LLMs, LLMs pre-trained on large code corpora, have shown great progress in learning rich representations of the structure and syntax of code, successfully using it to generate or classify code fragments. At the same time, understanding if they are able to do so because they capture code semantics, and how well, is still an open question. In this paper, we tackle this problem by introducing SeqCoBench, a benchmark for systematically assessing how Code-LLMs can capture code functional equivalence. SeqCoBench contains over 20 code transformations that either preserve or alter the semantics of Python programs. We conduct extensive evaluations in different settings, including zero-shot and parameter-efficient finetuning methods on state-of-the-art (Code)-LLMs to see if they can discern semantically equivalent or different pairs of programs in SeqCoBench. We find that the performance gap between these LLMs and classical match-based retrieval scores is minimal, with both approaches showing a concerning lack of depth in understanding code semantics.

AI systems increasingly produce fluent, correct, end-to-end outcomes. Over time, this erodes users' ability to explain, verify, or intervene. We define this divergence as the Capability-Comprehension Gap: a decoupling where assisted performance improves while users' internal models deteriorate. This paper argues that prevailing approaches to transparency, user control, literacy, and governance do not define the foundational understanding humans must retain for oversight under sustained AI delegation. To formalize this, we define the Cognitive Integrity Threshold (CIT) as the minimum comprehension required to preserve oversight, autonomy, and accountable participation under AI assistance. CIT does not require full reasoning reconstruction, nor does it constrain automation. It identifies the threshold beyond which oversight becomes procedural and contestability fails. We operatinalize CIT through three functional dimensions: (i) verification capacity, (ii) comprehension-preserving interaction, and (iii) institutional scaffolds for governance. This motivates a design and governance agenda that aligns human-AI interaction with cognitive sustainability in responsibility-critical settings.

While prior work has examined the generation capabilities of Agentic AI systems, little is known about how reviewers respond to AI-authored code in practice. In this paper, we present a large-scale empirical study of code review dynamics in agent-generated PRs. Using a curated subset of the AIDev dataset, we analyze 19,450 inline review comments spanning 3,177 agent-authored PRs from real-world GitHub repositories. We first derive a taxonomy of 12 review comment themes using topic modeling combined with large language model (LLM)-assisted semantic clustering and consolidation. According to this taxonomy, we then investigate whether zero-shot prompts to LLM can reliably annotate review comments. Our evaluation against human annotations shows that open-source LLM achieves reasonably high exact match (78.63%), macro F1 score (0.78), and substantial agreement with human annotators at the review comment level. At the PR level, the LLM also correctly identifies the dominant review theme with 78% Top-1 accuracy and achieves an average Jaccard similarity of 0.76, indicating strong alignment with human judgments. Applying this annotation pipeline at scale, we find that apart from functional correctness and logical changes, reviews of agent-authored PRs predominantly focus on documentation gaps, refactoring needs, styling and formatting issues, with testing and security-related concerns. These findings suggest that while AI agents can accelerate code production, there remain gaps requiring targeted human review oversight.

Unlike human-engineered systems such as aeroplanes, where each component's role and dependencies are well understood, the inner workings of AI models remain largely opaque, hindering verifiability and undermining trust. This paper introduces SemanticLens, a universal explanation method for neural networks that maps hidden knowledge encoded by components (e.g., individual neurons) into the semantically structured, multimodal space of a foundation model such as CLIP. In this space, unique operations become possible, including (i) textual search to identify neurons encoding specific concepts, (ii) systematic analysis and comparison of model representations, (iii) automated labelling of neurons and explanation of their functional roles, and (iv) audits to validate decision-making against requirements. Fully scalable and operating without human input, SemanticLens is shown to be effective for debugging and validation, summarizing model knowledge, aligning reasoning with expectations (e.g., adherence to the ABCDE-rule in melanoma classification), and detecting components tied to spurious correlations and their associated training data. By enabling component-level understanding and validation, the proposed approach helps bridge the "trust gap" between AI models and traditional engineered systems. We provide code for SemanticLens on https://github.com/jim-berend/semanticlens and a demo on https://semanticlens.hhi-research-insights.eu.

In recent years, cancer genome sequencing and other high-throughput studies of cancer genomes have generated many notable discoveries. In this review, Novel genomic alteration mechanisms, such as chromothripsis (chromosomal crisis) and kataegis (mutation storms), and their implications for cancer are discussed. Genomic alterations spur cancer genome evolution. Thus, the relationship between cancer clonal evolution and cancer stems cells is commented. The key question in cancer biology concerns how these genomic alterations support cancer development and metastasis in the context of biological functioning. Thus far, efforts such as pathway analysis have improved the understanding of the functional contributions of genetic mutations and DNA copy number variations to cancer development, progression and metastasis. However, the known pathways correspond to a small fraction, plausibly 5-10%, of somatic mutations and genes with an altered copy number. To develop a comprehensive understanding of the function of these genomic alterations in cancer, an integrative network framework is proposed and discussed. Finally, the challenges and the directions of studying cancer omic data using an integrative network approach are commented.

Scientific Large Language Models (Sci-LLMs) have emerged as a promising frontier for accelerating biological discovery. However, these models face a fundamental challenge when processing raw biomolecular sequences: the tokenization dilemma. Whether treating sequences as a specialized language, risking the loss of functional motif information, or as a separate modality, introducing formidable alignment challenges, current strategies fundamentally limit their reasoning capacity. We challenge this sequence-centric paradigm by positing that a more effective strategy is to provide Sci-LLMs with high-level structured context derived from established bioinformatics tools, thereby bypassing the need to interpret low-level noisy sequence data directly. Through a systematic comparison of leading Sci-LLMs on biological reasoning tasks, we tested three input modes: sequence-only, context-only, and a combination of both. Our findings are striking: the context-only approach consistently and substantially outperforms all other modes. Even more revealing, the inclusion of the raw sequence alongside its high-level context consistently degrades performance, indicating that raw sequences act as informational noise, even for models with specialized tokenization schemes. These results suggest that the primary strength of existing Sci-LLMs lies not in their nascent ability to interpret biomolecular syntax from scratch, but in their profound capacity for reasoning over structured, human-readable knowledge. Therefore, we argue for reframing Sci-LLMs not as sequence decoders, but as powerful reasoning engines over expert knowledge. This work lays the foundation for a new class of hybrid scientific AI agents, repositioning the developmental focus from direct sequence interpretation towards high-level knowledge synthesis. The code is available at https://github.com/opendatalab-raiser/CoKE.

Multi-lingual competence in large language models is often evaluated via static data benchmarks such as Belebele, M-MMLU and M-GSM. However, these evaluations often fail to provide an adequate understanding of the practical performance and robustness of models across multi-lingual settings. In response, we create multi-lingual functional benchmarks -- Cross-Lingual Grade School Math Symbolic (CL-GSM Symbolic) and Cross-Lingual Instruction-Following Eval (CL-IFEval)-- by translating existing functional benchmark templates from English to five additional languages that span the range of resources available for NLP: French, Spanish, Hindi, Arabic and Yoruba. Our results reveal that some static multi-lingual benchmarks capture functional performance much more closely than others (i.e. across models, there is a 24%, 17% and 18% decrease in performance between M-GSM and CL-GSM Symbolic in English, French and Spanish respectively; similarly there's a 15 - 24% performance drop across languages between Belebele and CL-IFEval, and only a 0.5% to 3% performance drop between M-MMLU and CL-IFEval). Similarly, we find that model robustness across languages varies significantly, with certain languages (eg. Arabic, English) being the most consistently well performing across evaluation iterations.

Elucidating the functional effect of missense variants is of crucial importance, yet challenging. To understand the impact of such variants, we fine-tuned the ESM2 protein language model to classify 20 protein features at amino acid resolution. We used the resulting models to: 1) identify protein features that are enriched in either pathogenic or benign missense variants, 2) compare the characteristics of proteins with reference or alternate alleles to understand how missense variants affect protein functionality. We show that our model can be used to reclassify some variants of unknown significance. We also demonstrate the usage of our models for understanding the potential effect of variants on protein features.

We introduce Functional Group-Aware Representations for Small Molecules (FARM), a novel foundation model designed to bridge the gap between SMILES, natural language, and molecular graphs. The key innovation of FARM lies in its functional group-aware tokenization, which incorporates functional group information directly into the representations. This strategic reduction in tokenization granularity in a way that is intentionally interfaced with key drivers of functional properties (i.e., functional groups) enhances the model's understanding of chemical language, expands the chemical lexicon, more effectively bridging SMILES and natural language, and ultimately advances the model's capacity to predict molecular properties. FARM also represents molecules from two perspectives: by using masked language modeling to capture atom-level features and by employing graph neural networks to encode the whole molecule topology. By leveraging contrastive learning, FARM aligns these two views of representations into a unified molecular embedding. We rigorously evaluate FARM on the MoleculeNet dataset, where it achieves state-of-the-art performance on 10 out of 12 tasks. These results highlight FARM's potential to improve molecular representation learning, with promising applications in drug discovery and pharmaceutical research.

Embodied AI depends on interactive 3D environments that support meaningful activities for diverse users, yet assessing their functional affordances remains a core challenge. We introduce SceneTeract, a framework that verifies 3D scene functionality under agent-specific constraints. Our core contribution is a grounded verification engine that couples high-level semantic reasoning with low-level geometric checks. SceneTeract decomposes complex activities into sequences of atomic actions and validates each step against accessibility requirements (e.g., reachability, clearance, and navigability) conditioned on an embodied agent profile, using explicit physical and geometric simulations. We deploy SceneTeract to perform an in-depth evaluation of (i) synthetic indoor environments, uncovering frequent functional failures that prevent basic interactions, and (ii) the ability of frontier Vision-Language Models (VLMs) to reason about and predict functional affordances, revealing systematic mismatches between semantic confidence and physical feasibility even for the strongest current models. Finally, we leverage SceneTeract as a reward engine for VLM post-training, enabling scalable distillation of geometric constraints into reasoning models. We release the SceneTeract verification suite and data to bridge perception and physical reality in embodied 3D scene understanding.

Multimodal models that jointly process audio and language hold great promise in audio understanding and are increasingly being adopted in the music domain. By allowing users to query via text and obtain information about a given audio input, these models have the potential to enable a variety of music understanding tasks via language-based interfaces. However, their evaluation poses considerable challenges, and it remains unclear how to effectively assess their ability to correctly interpret music-related inputs with current methods. Motivated by this, we introduce MuChoMusic, a benchmark for evaluating music understanding in multimodal language models focused on audio. MuChoMusic comprises 1,187 multiple-choice questions, all validated by human annotators, on 644 music tracks sourced from two publicly available music datasets, and covering a wide variety of genres. Questions in the benchmark are crafted to assess knowledge and reasoning abilities across several dimensions that cover fundamental musical concepts and their relation to cultural and functional contexts. Through the holistic analysis afforded by the benchmark, we evaluate five open-source models and identify several pitfalls, including an over-reliance on the language modality, pointing to a need for better multimodal integration. Data and code are open-sourced.

AI agents operating on user interfaces must understand how interfaces communicate state and feedback to act reliably. As a core communicative modality, animations are increasingly used in modern interfaces, serving critical functional purposes beyond mere aesthetics. Thus, understanding UI animation is essential for comprehensive interface interpretation. However, recent studies of Vision Language Models (VLMs) for UI understanding have focused primarily on static screenshots, leaving it unclear how well these models handle dynamic UI animations. To address this gap, we created AniMINT, a novel dataset of 300 densely annotated UI animation videos. We systematically evaluate state-of-the-art VLMs on UI animation understanding, including their abilities to perceive the animation effects, identify animation purposes, and interpret animation meaning. Our results show that VLMs can reliably detect primitive motion. However, their high-level animation interpretation remains inconsistent, with substantial gaps relative to human performance. Finally, we use Motion, Context, and Perceptual Cues (MCPC) to probe factors affecting VLM performance, revealing key bottlenecks and directions for future improvement.

The ability to conduct and learn from interaction and experience is a central challenge in robotics, offering a scalable alternative to labor-intensive human demonstrations. However, realizing such "play" requires (1) a policy robust to diverse, potentially out-of-distribution environment states, and (2) a procedure that continuously produces useful robot experience. To address these challenges, we introduce Tether, a method for autonomous functional play involving structured, task-directed interactions. First, we design a novel open-loop policy that warps actions from a small set of source demonstrations (<=10) by anchoring them to semantic keypoint correspondences in the target scene. We show that this design is extremely data-efficient and robust even under significant spatial and semantic variations. Second, we deploy this policy for autonomous functional play in the real world via a continuous cycle of task selection, execution, evaluation, and improvement, guided by the visual understanding capabilities of vision-language models. This procedure generates diverse, high-quality datasets with minimal human intervention. In a household-like multi-object setup, our method is the first to perform many hours of autonomous multi-task play in the real world starting from only a handful of demonstrations. This produces a stream of data that consistently improves the performance of closed-loop imitation policies over time, ultimately yielding over 1000 expert-level trajectories and training policies competitive with those learned from human-collected demonstrations.

The adaptation of large language models (LLMs) to chemistry has shown promising performance in molecular understanding tasks, such as generating a text description from a molecule. However, proper reasoning based on molecular structural information remains a significant challenge, e.g., even advanced LLMs such as GPT-4o struggle to identify functional groups which are crucial for inferring the molecular property of interest. To address this limitation, we propose StructCoT, a structure-aware chain-of-thought (CoT) that enhances LLMs' understanding of molecular structures by explicitly injecting the key structural features of molecules. Moreover, we introduce two fine-tuning frameworks for adapting the existing LLMs to use our StructCoT. Our experiments demonstrate that incorporating StructCoT with our fine-tuning frameworks leads to consistent improvements in both molecular understanding tasks.

Existing evaluation benchmarks of language models of code (code LMs) focus almost exclusively on whether the LMs can generate functionally-correct code. In real-world software engineering, developers think beyond functional correctness. They have requirements on "how" a functionality should be implemented to meet overall system design objectives like efficiency, security, and maintainability. They would also trust the code LMs more if the LMs demonstrate robust understanding of requirements and code semantics. We propose a new benchmark NoFunEval to evaluate code LMs on non-functional requirements and simple classification instances for both functional and non-functional requirements. We propose a prompting method, Coding Concepts (CoCo), as a way for a developer to communicate the domain knowledge to the LMs. We conduct an extensive evaluation of twenty-two code LMs. Our finding is that they generally falter when tested on our benchmark, hinting at fundamental blindspots in their training setups. Surprisingly, even the classification accuracy on functional-correctness instances derived from the popular HumanEval benchmark is low, calling in question the depth of their comprehension and the source of their success in generating functionally-correct code in the first place. We will release our benchmark and evaluation scripts publicly at https://aka.ms/NoFunEval.

Previous work has highlighted that existing post-hoc explanation methods exhibit disparities in explanation fidelity (across 'race' and 'gender' as sensitive attributes), and while a large body of work focuses on mitigating these issues at the explanation metric level, the role of the data generating process and black box model in relation to explanation disparities remains largely unexplored. Accordingly, through both simulations as well as experiments on a real-world dataset, we specifically assess challenges to explanation disparities that originate from properties of the data: limited sample size, covariate shift, concept shift, omitted variable bias, and challenges based on model properties: inclusion of the sensitive attribute and appropriate functional form. Through controlled simulation analyses, our study demonstrates that increased covariate shift, concept shift, and omission of covariates increase explanation disparities, with the effect pronounced higher for neural network models that are better able to capture the underlying functional form in comparison to linear models. We also observe consistent findings regarding the effect of concept shift and omitted variable bias on explanation disparities in the Adult income dataset. Overall, results indicate that disparities in model explanations can also depend on data and model properties. Based on this systematic investigation, we provide recommendations for the design of explanation methods that mitigate undesirable disparities.

Video understanding is being rapidly transformed by multimodal large language models (MLLMs), as research moves from short clips to long, multimodal, and knowledge-intensive video scenarios. These scenarios require models to handle sparse evidence, long-range dependencies, multimodal alignment, and reliable inference under limited computational budgets. This work presents a human-view perspective on LLM-based video understanding, organized around three functional abilities: watching, remembering, and reasoning. Rather than treating video tasks as isolated benchmarks, this view provides a unified structure for analyzing how video MLLMs acquire evidence, preserve context, and produce grounded outputs. We introduce a formulation that characterizes video understanding systems by their perceptual representations, memory states, reasoning traces, and final predictions. Based on this formulation, we identify challenges in spatio-temporal perception, efficient long-video processing, memory modeling, streaming understanding, and faithful reasoning. Representative methods are organized by their roles in video MLLM systems. Watching covers fine-grained, comprehensive, audio-visual, and efficient perception. Remembering includes offline and streaming memory, while reasoning covers text-only reasoning and thinking with videos. We further examine application domains such as egocentric, sports, instructional, medical, and narrative videos, and cover training datasets and evaluation benchmarks across task types, supervision formats, modalities, and capability dimensions. Finally, we outline open problems and future directions for scalable, memory-aware, and evidence-grounded video intelligence. Related works will be continuously traced at https://github.com/marinero4972/Awesome-HumanView-VideoUnderstanding.

We present WebMMU, a multilingual benchmark that evaluates three core web tasks: (1) website visual question answering, (2) code editing involving HTML/CSS/JavaScript, and (3) mockup-to-code generation. Unlike prior benchmarks that treat these tasks separately, WebMMU unifies them using expert-annotated, real-world web data to assess models' abilities in complex multi-step reasoning, precise element grounding, and functional UI comprehension and coding. Our evaluation shows that while multimodal large language models (MLLMs) perform well on basic information extraction, they struggle with reasoning and grounding, editing code to preserve functionality, and generating design-to-code that maintains hierarchy and supports multilingual content. These findings reveal key limitations in current MLLMs and underscore the need for improved multimodal and cross-lingual reasoning to build future web agents capable of automating diverse web development tasks.

Integrating large language models (LLMs) into automatic speech recognition (ASR) has become a dominant paradigm. Although recent LLM-based ASR models have shown promising performance on public benchmarks, it remains challenging to balance recognition quality with latency and overhead, while hallucinations further limit real-world deployment. In this study, we revisit LLM-based ASR from an entropy allocation perspective and introduce three metrics to characterize how training paradigms allocate entropy reduction between the speech encoder and the LLM. To remedy entropy-allocation inefficiencies in prevailing approaches, we propose a principled multi-stage training strategy grounded in capability-boundary awareness, optimizing parameter efficiency and hallucination robustness. Specifically, we redesign the pretraining strategy to alleviate the speech-text modality gap, and further introduce an iterative asynchronous SFT stage between alignment and joint SFT to preserve functional decoupling and constrain encoder representation drift. Experiments on Mandarin and English benchmarks show that our method achieves competitive performance with state-of-the-art models using only 2.3B parameters, while also effectively mitigating hallucinations through our decoupling-oriented design.

Genuine spatial reasoning relies on the capacity to construct and manipulate coherent internal spatial representations, often conceptualized as mental models, rather than merely processing surface linguistic associations. While large language models exhibit advanced capabilities across various domains, existing benchmarks fail to isolate this intrinsic spatial cognition from statistical language heuristics. Furthermore, multimodal evaluations frequently conflate genuine spatial reasoning with visual perception. To systematically investigate whether models construct flexible spatial mental models, we introduce SpatialText, a theory-driven diagnostic framework. Rather than functioning simply as a dataset, SpatialText isolates text-based spatial reasoning through a dual-source methodology. It integrates human-annotated descriptions of real 3D indoor environments, which capture natural ambiguities, perspective shifts, and functional relations, with code-generated, logically precise scenes designed to probe formal spatial deduction and epistemic boundaries. Systematic evaluation across state-of-the-art models reveals fundamental representational limitations. Although models demonstrate proficiency in retrieving explicit spatial facts and operating within global, allocentric coordinate systems, they exhibit critical failures in egocentric perspective transformation and local reference frame reasoning. These systematic errors provide strong evidence that current models rely heavily on linguistic co-occurrence heuristics rather than constructing coherent, verifiable internal spatial representations. SpatialText thus serves as a rigorous instrument for diagnosing the cognitive boundaries of artificial spatial intelligence.

Time series analysis is crucial in diverse scenarios. Beyond forecasting, considerable real-world tasks are categorized into classification, imputation, and anomaly detection, underscoring different capabilities termed time series understanding in this paper. While GPT-style models have been positioned as foundation models for time series forecasting, the BERT-style architecture, which has made significant advances in natural language understanding, has not been fully unlocked for time series understanding, possibly attributed to the undesirable dropout of essential elements of BERT. In this paper, inspired by the shared multi-granularity structure between multivariate time series and multisentence documents, we design TimesBERT to learn generic representations of time series including temporal patterns and variate-centric characteristics. In addition to a natural adaptation of masked modeling, we propose a parallel task of functional token prediction to embody vital multi-granularity structures. Our model is pre-trained on 260 billion time points across diverse domains. Leveraging multi-granularity representations, TimesBERT achieves state-of-the-art performance across four typical downstream understanding tasks, outperforming task-specific models and language pre-trained backbones, positioning it as a versatile foundation model for time series understanding.

The pre-trained language models have achieved great successes in various natural language understanding (NLU) tasks due to its capacity to capture the deep contextualized information in text by pre-training on large-scale corpora. In this technical report, we present our practice of pre-training language models named NEZHA (NEural contextualiZed representation for CHinese lAnguage understanding) on Chinese corpora and finetuning for the Chinese NLU tasks. The current version of NEZHA is based on BERT with a collection of proven improvements, which include Functional Relative Positional Encoding as an effective positional encoding scheme, Whole Word Masking strategy, Mixed Precision Training and the LAMB Optimizer in training the models. The experimental results show that NEZHA achieves the state-of-the-art performances when finetuned on several representative Chinese tasks, including named entity recognition (People's Daily NER), sentence matching (LCQMC), Chinese sentiment classification (ChnSenti) and natural language inference (XNLI).

While Vision-Language Models (VLMs) have demonstrated significant potential in chemical visual understanding, current models are predominantly optimized for direct visual question-answering tasks. This paradigm often results in "black-box" systems that fail to utilize the inherent capability of Large Language Models (LLMs) to infer underlying reaction mechanisms. In this work, we introduce ChemVLR, a chemical VLM designed to prioritize reasoning within the perception process. Unlike conventional chemical VLMs, ChemVLR analyzes visual inputs in a fine-grained manner by explicitly identifying granular chemical descriptors, such as functional groups, prior to generating answers. This approach ensures the production of explicit and interpretable reasoning paths for complex visual chemical problems. To facilitate this methodology, we implement a cross-modality reverse-engineering strategy, combined with a rigorous filtering pipeline, to curate a large-scale reasoning-and-captioning dataset comprising 760k high-quality samples across molecular and reaction tasks. Furthermore, we adopt a three-stage training framework that systemically builds model perception and reasoning capacity. Experiments demonstrate that ChemVLR achieves state-of-the-art (SOTA) performance, surpassing both leading proprietary models and domain-specific open-source baselines. We also provide comprehensive ablation studies to validate our training strategy and data generation designs. Code and model weights will be available at https://github.com/xxlllz/ChemVLR.

LLMs demonstrate promising performance in software vulnerability detection after fine-tuning. However, it remains unclear whether these gains reflect a genuine understanding of vulnerability root causes or merely an exploitation of functional patterns. In this paper, we identify a critical failure mode termed the "semantic trap," where fine-tuned LLMs achieve high detection scores by associating certain functional domains with vulnerability likelihood rather than reasoning about the underlying security semantics. To systematically evaluate this phenomenon, we propose TrapEval, a comprehensive evaluation framework designed to disentangle vulnerability root cause from functional pattern. TrapEval introduces two complementary datasets derived from real-world open-source projects: V2N, which pairs vulnerable code with unrelated benign code, and V2P, which pairs vulnerable code with its corresponding patched version, forcing models to distinguish near-identical code that differs only in subtle security-critical logic. Using TrapEval, we fine-tune five representative state-of-the-art LLMs across three model families and evaluate them under cross-dataset testing, semantic-preserving perturbations, and varying degrees of semantic gap measured by CodeBLEU. Our empirical results reveal that, despite improvements in metrics, fine-tuned LLMs consistently struggle to distinguish vulnerable code from its patched counterpart, exhibit severe robustness degradation under minor semantic-preserving transformations, and rely heavily on functional-context shortcuts when the semantic gap is small. These findings provide strong evidence that current fine-tuning practices often fail to impart true vulnerability reasoning. Our findings serve as a wake-up call: high benchmark scores on traditional datasets may be illusory, masking the model's inability to understand the true causal logic of vulnerabilities.

Proteins, as essential biomolecules, play a central role in biological processes, including metabolic reactions and DNA replication. Accurate prediction of their properties and functions is crucial in biological applications. Recent development of protein language models (pLMs) with supervised fine tuning provides a promising solution to this problem. However, the fine-tuned model is tailored for particular downstream prediction task, and achieving general-purpose protein understanding remains a challenge. In this paper, we introduce Structure-Enhanced Protein Instruction Tuning (SEPIT) framework to bridge this gap. Our approach integrates a noval structure-aware module into pLMs to inform them with structural knowledge, and then connects these enhanced pLMs to large language models (LLMs) to generate understanding of proteins. In this framework, we propose a novel two-stage instruction tuning pipeline that first establishes a basic understanding of proteins through caption-based instructions and then refines this understanding using a mixture of experts (MoEs) to learn more complex properties and functional information with the same amount of activated parameters. Moreover, we construct the largest and most comprehensive protein instruction dataset to date, which allows us to train and evaluate the general-purpose protein understanding model. Extensive experimental results on open-ended generation and closed-set answer tasks demonstrate the superior performance of SEPIT over both closed-source general LLMs and open-source LLMs trained with protein knowledge.

Partially inspired by features of computation in visual cortex, deep neural networks compute hierarchical representations of their inputs. While these networks have been highly successful in machine learning, it remains unclear to what extent they can aid our understanding of cortical function. Several groups have developed metrics that provide a quantitative comparison between representations computed by networks and representations measured in cortex. At the same time, neuroscience is well into an unprecedented phase of large-scale data collection, as evidenced by projects such as the Allen Brain Observatory. Despite the magnitude of these efforts, in a given experiment only a fraction of units are recorded, limiting the information available about the cortical representation. Moreover, only a finite number of stimuli can be shown to an animal over the course of a realistic experiment. These limitations raise the question of how and whether metrics that compare representations of deep networks are meaningful on these datasets. Here, we empirically quantify the capabilities and limitations of these metrics due to limited image presentations and neuron samples. We find that the comparison procedure is robust to different choices of stimuli set and the level of subsampling that one might expect in a large-scale brain survey with thousands of neurons. Using these results, we compare the representations measured in the Allen Brain Observatory in response to natural image presentations to deep neural network. We show that the visual cortical areas are relatively high order representations (in that they map to deeper layers of convolutional neural networks). Furthermore, we see evidence of a broad, more parallel organization rather than a sequential hierarchy, with the primary area VISp(V1) being lower order relative to the other areas.

Current Large Language Models (LLMs) are unparalleled in their ability to generate grammatically correct, fluent text. LLMs are appearing rapidly, and debates on LLM capacities have taken off, but reflection is lagging behind. Thus, in this position paper, we first zoom in on the debate and critically assess three points recurring in critiques of LLM capacities: i) that LLMs only parrot statistical patterns in the training data; ii) that LLMs master formal but not functional language competence; and iii) that language learning in LLMs cannot inform human language learning. Drawing on empirical and theoretical arguments, we show that these points need more nuance. Second, we outline a pragmatic perspective on the issue of `real' understanding and intentionality in LLMs. Understanding and intentionality pertain to unobservable mental states we attribute to other humans because they have pragmatic value: they allow us to abstract away from complex underlying mechanics and predict behaviour effectively. We reflect on the circumstances under which it would make sense for humans to similarly attribute mental states to LLMs, thereby outlining a pragmatic philosophical context for LLMs as an increasingly prominent technology in society.

Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein engineering. Existing methods either construct a supervised learning scheme on small-scale datasets with manually processed physicochemical properties, or blindly apply pre-trained protein language models to extract amino acid interaction information. The scale and quality of available training datasets leave significant room for improvement in terms of accuracy and generalization. To address these research gaps, we propose \sol, a novel deep learning method that combines pre-training and fine-tuning schemes for protein solubility prediction. ProtSolM integrates information from multiple dimensions, including physicochemical properties, amino acid sequences, and protein backbone structures. Our model is trained using \data, the largest solubility dataset that we have constructed. PDBSol includes over 60,000 protein sequences and structures. We provide a comprehensive leaderboard of existing statistical learning and deep learning methods on independent datasets with computational and experimental labels. ProtSolM achieved state-of-the-art performance across various evaluation metrics, demonstrating its potential to significantly advance the accuracy of protein solubility prediction.

Understanding and interpreting dynamics of functional materials in situ is a grand challenge in physics and materials science due to the difficulty of experimentally probing materials at varied length and time scales. X-ray photon correlation spectroscopy (XPCS) is uniquely well-suited for characterizing materials dynamics over wide-ranging time scales, however spatial and temporal heterogeneity in material behavior can make interpretation of experimental XPCS data difficult. In this work we have developed an unsupervised deep learning (DL) framework for automated classification and interpretation of relaxation dynamics from experimental data without requiring any prior physical knowledge of the system behavior. We demonstrate how this method can be used to rapidly explore large datasets to identify samples of interest, and we apply this approach to directly correlate bulk properties of a model system to microscopic dynamics. Importantly, this DL framework is material and process agnostic, marking a concrete step towards autonomous materials discovery.

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

Large language models (LLMs) sometimes appear to exhibit emotional reactions. We investigate why this is the case in Claude Sonnet 4.5 and explore implications for alignment-relevant behavior. We find internal representations of emotion concepts, which encode the broad concept of a particular emotion and generalize across contexts and behaviors it might be linked to. These representations track the operative emotion concept at a given token position in a conversation, activating in accordance with that emotion's relevance to processing the present context and predicting upcoming text. Our key finding is that these representations causally influence the LLM's outputs, including Claude's preferences and its rate of exhibiting misaligned behaviors such as reward hacking, blackmail, and sycophancy. We refer to this phenomenon as the LLM exhibiting functional emotions: patterns of expression and behavior modeled after humans under the influence of an emotion, which are mediated by underlying abstract representations of emotion concepts. Functional emotions may work quite differently from human emotions, and do not imply that LLMs have any subjective experience of emotions, but appear to be important for understanding the model's behavior.

While Vision-Language-Action models (VLAs) have shown remarkable progress toward human-like generalist robotic policies through the versatile intelligence (i.e. broad scene understanding and language-conditioned generalization) inherited from pre-trained Vision-Language Models, they still struggle with complex real-world tasks requiring broader functional capabilities (e.g. motion awareness, memory-aware decision making, and physical sensing). To address this, we introduce RLDX-1, a general-purpose robotic policy for dexterous manipulation built on the Multi-Stream Action Transformer (MSAT), an architecture that unifies these capabilities by integrating heterogeneous modalities through modality-specific streams with cross-modal joint self-attention. RLDX-1 further combines this architecture with system-level design choices, including synthesizing training data for rare manipulation scenarios, learning procedures specialized for human-like manipulation, and inference optimizations for real-time deployment. Through empirical evaluation, we show that RLDX-1 consistently outperforms recent frontier VLAs (e.g. π_{0.5} and GR00T N1.6) across both simulation benchmarks and real-world tasks that require broad functional capabilities beyond general versatility. In particular, RLDX-1 shows superiority in ALLEX humanoid tasks by achieving success rates of 86.8% while π_{0.5} and GR00T N1.6 achieve around 40%, highlighting the ability of RLDX-1 to control a high-DoF humanoid robot under diverse functional demands. Together, these results position RLDX-1 as a promising step toward reliable VLAs for complex, contact-rich, and dynamic real-world dexterous manipulation.

Conversational image segmentation grounds abstract, intent-driven concepts into pixel-accurate masks. Prior work on referring image grounding focuses on categorical and spatial queries (e.g., "left-most apple") and overlooks functional and physical reasoning (e.g., "where can I safely store the knife?"). We address this gap and introduce Conversational Image Segmentation (CIS) and ConverSeg, a benchmark spanning entities, spatial relations, intent, affordances, functions, safety, and physical reasoning. We also present ConverSeg-Net, which fuses strong segmentation priors with language understanding, and an AI-powered data engine that generates prompt-mask pairs without human supervision. We show that current language-guided segmentation models are inadequate for CIS, while ConverSeg-Net trained on our data engine achieves significant gains on ConverSeg and maintains strong performance on existing language-guided segmentation benchmarks. Project webpage: https://glab-caltech.github.io/converseg/

The prediction of crystal properties is essential for understanding structure-property relationships and accelerating the discovery of functional materials. However, conventional approaches relying on experimental measurements or density functional theory (DFT) calculations are often resource-intensive, limiting their scalability. Machine learning (ML) models offer a promising alternative by learning complex structure-property relationships from data, enabling faster predictions. Yet, existing ML models often rely on labeled data, adopt representations that poorly capture essential structural characteristics, and lack integration with physical principles--factors that limit their generalizability and interpretability. Here, we introduce CLOUD (Crystal Language mOdel for Unified and Differentiable materials modeling), a transformer-based framework trained on a novel Symmetry-Consistent Ordered Parameter Encoding (SCOPE) that encodes crystal symmetry, Wyckoff positions, and composition in a compact, coordinate-free string representation. Pre-trained on over six million crystal structures, CLOUD is fine-tuned on multiple downstream tasks and achieves competitive performance in predicting a wide range of material properties, demonstrating strong scaling performance. Furthermore, as proof of concept of differentiable materials modeling, CLOUD is applied to predict the phonon internal energy and heat capacity, which integrates the Debye model to preserve thermodynamic consistency. The CLOUD-DEBYE framework enforces thermodynamic consistency and enables temperature-dependent property prediction without requiring additional data. These results demonstrate the potential of CLOUD as a scalable and physics-informed foundation model for crystalline materials, unifying symmetry-consistent representations with physically grounded learning for property prediction and materials discovery.

The issue of hallucinations in large language models (LLMs) remains a critical barrier to the adoption of AI in enterprise and other high-stakes applications. Despite advancements in retrieval-augmented generation (RAG) systems, current state-of-the-art methods fail to achieve more than 80% accuracy in generating faithful and factually correct outputs, even when provided with relevant and accurate context. In this work, we introduce Acurai, a novel systematic approach that achieves 100% hallucination-free responses in LLMs by reformatting queries and context data prior to input. Leveraging a deep understanding of LLM internal representations, the importance of noun-phrase dominance, and the role of discrete functional units (DFUs), Acurai ensures alignment between input context and generated output. We validate this method using the RAGTruth corpus, demonstrating its ability to eliminate 100% hallucinations for both GPT-4 and GPT-3.5 Turbo. Acurai sets a new standard for achieving consistent, accurate, and faithful AI responses, marking a significant step forward in the development of trustworthy AI systems.

Instruction tuning has recently been recognized as an effective way of aligning Large Language Models (LLMs) to enhance their generalization ability across various tasks. However, when tuning publicly accessible, centralized LLMs with private instruction data, privacy concerns are inevitable. While direct transfer of parameterized modules between models is a plausible approach to address this, its implications and effectiveness need further exploration. This paper focuses on Offsite-Tuning (OFT), a representative technique that transfers transformer blocks between centralized LLMs and downstream emulators. Given the limited understanding of the underlying mechanism of OFT, we perform an empirical analysis on LLMs from the perspectives of representation and functional similarity. Interestingly, our findings reveal a unique modular structure within the layers of LLMs that appears to emerge as the model size expands. Simultaneously, we note subtle but potentially significant changes in representation and intermediate predictions across the layers. Inspired by these observations, we propose CRaSh, involving Clustering, Removing, and Sharing, a training-free strategy to derive improved emulators from LLMs. CRaSh significantly boosts performance of OFT with billions of parameters. Furthermore, we investigate the optimal solutions yielded by fine-tuning with and without full model through the lens of loss landscape. Our findings demonstrate a linear connectivity among these optima falling over the same basin, thereby highlighting the effectiveness of CRaSh and OFT. The source code is publicly available at https://github.com/TsinghuaC3I/CRaSh.

This paper investigates how Transformer language models (LMs) fine-tuned for acceptability classification capture linguistic features. Our approach uses the best practices of topological data analysis (TDA) in NLP: we construct directed attention graphs from attention matrices, derive topological features from them, and feed them to linear classifiers. We introduce two novel features, chordality, and the matching number, and show that TDA-based classifiers outperform fine-tuning baselines. We experiment with two datasets, CoLA and RuCoLA in English and Russian, typologically different languages. On top of that, we propose several black-box introspection techniques aimed at detecting changes in the attention mode of the LMs during fine-tuning, defining the LM's prediction confidences, and associating individual heads with fine-grained grammar phenomena. Our results contribute to understanding the behavior of monolingual LMs in the acceptability classification task, provide insights into the functional roles of attention heads, and highlight the advantages of TDA-based approaches for analyzing LMs. We release the code and the experimental results for further uptake.

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

Unified multimodal models (UMMs) achieve strong performance in both understanding and generation by learning a shared latent space, yet they often exhibit functional inconsistency between these two capabilities. We observe that this issue does not stem from a lack of shared representations, but from the absence of explicit alignment between the transformations that map into and out of the latent space. As a result, generation and re-encoding can follow inconsistent trajectories, leading to semantic drift under modality transitions. In this work, we propose LatentUMM, a framework that constructs an enhanced shared latent space to explicitly align these transformations and improve cross-modal consistency. LatentUMM consists of two stages. First, dual latent alignment enforces consistency at both the modality and capacity levels: cross-modal alignment uses a stronger embedding model to impose structured cross-modal semantics, while dual capacity alignment enforces bidirectional consistency under generation and re-encoding. Second, latent dynamics stabilization improves robustness via stochastic latent rollouts and preference optimization, favoring trajectories that better preserve semantic consistency. Experiments show that LatentUMM consistently improves multimodal consistency across diverse architectures. Code is available at: https://github.com/AIFrontierLab/TorchUMM/tree/main/src/umm/post_training/LatentUMM.

We introduce iFlyBot-VLM, a general-purpose Vision-Language Model (VLM) used to improve the domain of Embodied Intelligence. The central objective of iFlyBot-VLM is to bridge the cross-modal semantic gap between high-dimensional environmental perception and low-level robotic motion control. To this end, the model abstracts complex visual and spatial information into a body-agnostic and transferable Operational Language, thereby enabling seamless perception-action closed-loop coordination across diverse robotic platforms. The architecture of iFlyBot-VLM is systematically designed to realize four key functional capabilities essential for embodied intelligence: 1) Spatial Understanding and Metric Reasoning; 2) Interactive Target Grounding; 3) Action Abstraction and Control Parameter Generation; 4) Task Planning and Skill Sequencing. We envision iFlyBot-VLM as a scalable and generalizable foundation model for embodied AI, facilitating the progression from specialized task-oriented systems toward generalist, cognitively capable agents. We conducted evaluations on 10 current mainstream embodied intelligence-related VLM benchmark datasets, such as Blink and Where2Place, and achieved optimal performance while preserving the model's general capabilities. We will publicly release both the training data and model weights to foster further research and development in the field of Embodied Intelligence.

Code Large Language Models (Code LLMs) have excelled at tasks like code completion but often miss deeper semantics such as execution effects and dynamic states. This paper aims to bridge the gap between Code LLMs' reliance on static text data and the need for semantic understanding for complex tasks like debugging and program repair. We introduce a novel strategy, monologue reasoning, to train Code LLMs to reason comprehensive semantics, encompassing high-level functional descriptions, local execution effects of individual statements, and overall input/output behavior, thereby linking static code text with dynamic execution states. We begin by collecting PyX, a clean Python corpus of fully executable code samples with functional descriptions and test cases. We propose training Code LLMs not only to write code but also to understand code semantics by reasoning about key properties, constraints, and execution behaviors using natural language, mimicking human verbal debugging, i.e., rubber-duck debugging. This approach led to the development of SemCoder, a Code LLM with only 6.7B parameters, which shows competitive performance with GPT-3.5-turbo on code generation and execution reasoning tasks. SemCoder achieves 79.3% on HumanEval (GPT-3.5-turbo: 76.8%), 63.6% on CRUXEval-I (GPT-3.5-turbo: 50.3%), and 63.9% on CRUXEval-O (GPT-3.5-turbo: 59.0%). We also study the effectiveness of SemCoder's monologue-style execution reasoning compared to concrete scratchpad reasoning, showing that our approach integrates semantics from multiple dimensions more smoothly. Finally, we demonstrate the potential of applying learned semantics to improve Code LLMs' debugging and self-refining capabilities. Our data, code, and models are available at: https://github.com/ARiSE-Lab/SemCoder.

Reliable evaluation of large language models (LLMs) is impeded by two key challenges: objective metrics often fail to reflect human perception of natural language, and exhaustive human labeling is prohibitively expensive. Here, we propose a sample-efficient human evaluation method for LLMs based on the principle of MAximum Discrepancy (MAD) Competition. Our method automatically and adaptively selects a compact set of input instructions that maximize semantic discrepancy between pairs of LLM responses. Human evaluators then perform three-alternative forced choices on these paired responses, which are aggregated into a global ranking using Elo rating. We apply our approach to compare eight widely used LLMs across four tasks: scientific knowledge understanding, mathematical reasoning, creative and functional writing, and code generation and explanation. Experimental results show that our sample-efficient evaluation method recovers "gold-standard" model rankings with a handful of MAD-selected instructions, reveals respective strengths and weaknesses of each LLM, and offers nuanced insights to guide future LLM development. Code is available at https://github.com/weiji-Feng/MAD-Eval .

Robotic manipulation and navigation are fundamental capabilities of embodied intelligence, enabling effective robot interactions with the physical world. Achieving these capabilities requires a cohesive understanding of the environment, including object recognition to localize target objects, object affordances to identify potential interaction areas and spatial affordances to discern optimal areas for both object placement and robot movement. While Vision-Language Models (VLMs) excel at high-level task planning and scene understanding, they often struggle to infer actionable positions for physical interaction, such as functional grasping points and permissible placement regions. This limitation stems from the lack of fine-grained annotations for object and spatial affordances in their training datasets. To tackle this challenge, we introduce RoboAfford++, a generative AI-enhanced dataset for multimodal affordance learning for both robotic manipulation and navigation. Our dataset comprises 869,987 images paired with 2.0 million question answering (QA) annotations, covering three critical tasks: object affordance recognition to identify target objects based on attributes and spatial relationships, object affordance prediction to pinpoint functional parts for manipulation, and spatial affordance localization to identify free space for object placement and robot navigation. Complementing this dataset, we propose RoboAfford-Eval, a comprehensive benchmark for assessing affordance-aware prediction in real-world scenarios, featuring 338 meticulously annotated samples across the same three tasks. Extensive experimental results reveal the deficiencies of existing VLMs in affordance learning, while fine-tuning on the RoboAfford++ dataset significantly enhances their ability to reason about object and spatial affordances, validating the dataset's effectiveness.

With the advancement of software rendering techniques, GUI pages in mobile apps now encompass a wealth of visual information, where the visual semantics of each page contribute to the overall app logic, presenting new challenges to software testing. Despite the progress in automated Graphical User Interface (GUI) testing, the absence of testing oracles has constrained its efficacy to identify only crash bugs with evident abnormal signals. Nonetheless, there are still a considerable number of non-crash bugs, ranging from unexpected behaviors to misalignments, often evading detection by existing techniques. While these bugs can exhibit visual cues that serve as potential testing oracles, they often entail a sequence of screenshots, and detecting them necessitates an understanding of the operational logic among GUI page transitions, which is challenging traditional techniques. Considering the remarkable performance of Multimodal Large Language Models (MLLM) in visual and language understanding, this paper proposes a vision-driven automated GUI testing approach VisionDroid to detect non-crash functional bugs with MLLM. It begins by extracting GUI text information and aligning it with screenshots to form a vision prompt, enabling MLLM to understand GUI context. The function-aware explorer then employs MLLM for deeper and function-oriented GUI page exploration, while the logic-aware bug detector segments the entire exploration history into logically cohesive parts and prompts the MLLM for bug detection. We evaluate VisionDroid on three datasets and compare it with 10 baselines, demonstrating its excellent performance. The ablation study further proves the contribution of each module. Moreover, VisionDroid identifies 29 new bugs on Google Play, of which 19 have been confirmed and fixed.

Large Language Models (LLMs) have demonstrated remarkable capabilities in code understanding and generation; however, their effectiveness on non-code Software Engineering (SE) tasks remains underexplored. We present the first comprehensive benchmark, which we name `Software Engineering Language Understanding' (SELU), for evaluating LLMs on 17 non-code tasks, spanning from identifying whether a requirement is functional or non-functional to estimating the effort and complexity of backlog items. SELU covers classification, regression, Named Entity Recognition (NER), and Masked Language Modeling (MLM) targets, with data drawn from diverse sources such as code repositories, issue tracking systems, and developer forums. We fine-tune 22 open-source LLMs, prompt two proprietary alternatives, and train two baselines. Performance is measured using metrics such as F1-macro, SMAPE, F1-micro, and accuracy, and compared via the Bayesian signed-rank test. Our results show that moderate-scale decoder-only models consistently form a top-tier, exhibiting high mean performance and low across-task variance, while domain adaptation via code-focused pre-training might yield only modest improvements. These insights guide model selection for non-code SE workflows and highlight directions for expanding SELU to generative and design-oriented scenarios.

Current computer vision models, unlike the human visual system, cannot yet achieve general-purpose visual understanding. Existing efforts to create a general vision model are limited in the scope of assessed tasks and offer no overarching framework to perform them holistically. We present a new comprehensive benchmark, General-purpose Visual Understanding Evaluation (G-VUE), covering the full spectrum of visual cognitive abilities with four functional domains x2014 Perceive, Ground, Reason, and Act. The four domains are embodied in 11 carefully curated tasks, from 3D reconstruction to visual reasoning and manipulation. Along with the benchmark, we provide a general encoder-decoder framework to allow for the evaluation of arbitrary visual representation on all 11 tasks. We evaluate various pre-trained visual representations with our framework and observe that (1) Transformer-based visual backbone generally outperforms CNN-based backbone on G-VUE, (2) visual representations from vision-language pre-training are superior to those with vision-only pre-training across visual tasks. With G-VUE, we provide a holistic evaluation standard to motivate research toward building general-purpose visual systems via obtaining more general-purpose visual representations.

Large Vision-Language Models (LVLMs) show promise for embodied planning tasks but struggle with complex scenarios involving unfamiliar environments and multi-step goals. Current approaches rely on environment-agnostic imitation learning that disconnects instructions from environmental contexts, causing models to struggle with context-sensitive instructions and rely on supplementary cues rather than visual reasoning during long-horizon interactions. In this work, we propose World-Aware Planning Narrative Enhancement (WAP), a framework that infuses LVLMs with comprehensive environmental understanding through four cognitive capabilities (visual appearance modeling, spatial reasoning, functional abstraction, and syntactic grounding) while developing and evaluating models using only raw visual observations through curriculum learning. Evaluations on the EB-ALFRED benchmark demonstrate substantial improvements, with Qwen2.5-VL achieving a 60.7 absolute improvement in task success rates, particularly in commonsense reasoning (+60.0) and long-horizon planning (+70.0). Notably, our enhanced open-source models outperform proprietary systems like GPT-4o and Claude-3.5-Sonnet by a large margin.

3D Scene Graphs (3DSGs) constitute a powerful representation of the physical world, distinguished by their abilities to explicitly model the complex spatial, semantic, and functional relationships between entities, rendering a foundational understanding that enables agents to interact intelligently with their environment and execute versatile behaviors. Embodied navigation, as a crucial component of such capabilities, leverages the compact and expressive nature of 3DSGs to enable long-horizon reasoning and planning in complex, large-scale environments. However, prior works rely on a static-world assumption, defining traversable space solely based on static spatial layouts and thereby treating interactable obstacles as non-traversable. This fundamental limitation severely undermines their effectiveness in real-world scenarios, leading to limited reachability, low efficiency, and inferior extensibility. To address these issues, we propose HERO, a novel framework for constructing Hierarchical Traversable 3DSGs, that redefines traversability by modeling operable obstacles as pathways, capturing their physical interactivity, functional semantics, and the scene's relational hierarchy. The results show that, relative to its baseline, HERO reduces PL by 35.1% in partially obstructed environments and increases SR by 79.4% in fully obstructed ones, demonstrating substantially higher efficiency and reachability.

In the field of urban planning, existing Vision-Language Models (VLMs) frequently fail to effectively analyze and evaluate planning maps, despite the critical importance of these visual elements for urban planners and related educational contexts. Planning maps, which visualize land use, infrastructure layouts, and functional zoning, require specialized understanding of spatial configurations, regulatory requirements, and multi-scale analysis. To address this challenge, we introduce PlanGPT-VL, the first domain-specific Vision-Language Model tailored specifically for urban planning maps. PlanGPT-VL employs three innovative approaches: (1) PlanAnno-V framework for high-quality VQA data synthesis, (2) Critical Point Thinking to reduce hallucinations through structured verification, and (3) comprehensive training methodology combining Supervised Fine-Tuning with frozen vision encoder parameters. Through systematic evaluation on our proposed PlanBench-V benchmark, we demonstrate that PlanGPT-VL significantly outperforms general-purpose state-of-the-art VLMs in specialized planning map interpretation tasks, offering urban planning professionals a reliable tool for map analysis, assessment, and educational applications while maintaining high factual accuracy. Our lightweight 7B parameter model achieves comparable performance to models exceeding 72B parameters, demonstrating efficient domain specialization without sacrificing performance.

Comics have long been a popular form of storytelling, offering visually engaging narratives that captivate audiences worldwide. However, the visual nature of comics presents a significant barrier for visually impaired readers, limiting their access to these engaging stories. In this work, we provide a pragmatic solution to this accessibility challenge by developing an automated system that generates text-based literary narratives from manga comics. Our approach aims to create an evocative and immersive prose that not only conveys the original narrative but also captures the depth and complexity of characters, their interactions, and the vivid settings in which they reside. To this end we make the following contributions: (1) We present a unified model, Magiv3, that excels at various functional tasks pertaining to comic understanding, such as localising panels, characters, texts, and speech-bubble tails, performing OCR, grounding characters etc. (2) We release human-annotated captions for over 3300 Japanese comic panels, along with character grounding annotations, and benchmark large vision-language models in their ability to understand comic images. (3) Finally, we demonstrate how integrating large vision-language models with Magiv3, can generate seamless literary narratives that allows visually impaired audiences to engage with the depth and richness of comic storytelling.

The human brain is a complex, dynamic network, which is commonly studied using functional magnetic resonance imaging (fMRI) and modeled as network of Regions of interest (ROIs) for understanding various brain functions. Recent studies utilize deep learning approaches to learn the brain network representation based on functional connectivity (FC) profile, broadly falling into two main categories. The Fixed-FC approaches, utilizing the FC profile which represents the linear temporal relation within the brain network, are limited by failing to capture informative brain temporal dynamics. On the other hand, the Dynamic-FC approaches, modeling the evolving FC profile over time, often exhibit less satisfactory performance due to challenges in handling the inherent noisy nature of fMRI data. To address these challenges, we propose Brain Masked Auto-Encoder (BrainMAE) for learning representations directly from fMRI time-series data. Our approach incorporates two essential components: a region-aware graph attention mechanism designed to capture the relationships between different brain ROIs, and a novel self-supervised masked autoencoding framework for effective model pre-training. These components enable the model to capture rich temporal dynamics of brain activity while maintaining resilience to inherent noise in fMRI data. Our experiments demonstrate that BrainMAE consistently outperforms established baseline methods by significant margins in four distinct downstream tasks. Finally, leveraging the model's inherent interpretability, our analysis of model-generated representations reveals findings that resonate with ongoing research in the field of neuroscience.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

Today's large language models (LLMs) routinely generate coherent, grammatical and seemingly meaningful paragraphs of text. This achievement has led to speculation that these networks are -- or will soon become -- "thinking machines", capable of performing tasks that require abstract knowledge and reasoning. Here, we review the capabilities of LLMs by considering their performance on two different aspects of language use: 'formal linguistic competence', which includes knowledge of rules and patterns of a given language, and 'functional linguistic competence', a host of cognitive abilities required for language understanding and use in the real world. Drawing on evidence from cognitive neuroscience, we show that formal competence in humans relies on specialized language processing mechanisms, whereas functional competence recruits multiple extralinguistic capacities that comprise human thought, such as formal reasoning, world knowledge, situation modeling, and social cognition. In line with this distinction, LLMs show impressive (although imperfect) performance on tasks requiring formal linguistic competence, but fail on many tests requiring functional competence. Based on this evidence, we argue that (1) contemporary LLMs should be taken seriously as models of formal linguistic skills; (2) models that master real-life language use would need to incorporate or develop not only a core language module, but also multiple non-language-specific cognitive capacities required for modeling thought. Overall, a distinction between formal and functional linguistic competence helps clarify the discourse surrounding LLMs' potential and provides a path toward building models that understand and use language in human-like ways.

Architectural spatial intelligence, the ability to recognize and infer architectural space, is fundamental to tasks such as robot navigation, embodied interaction, and 3D scene understanding and generation. Although extensive research has evaluated the basic spatial skills of Vision-Language Models (VLMs) such as relative orientation, distance comparison, and object counting, these tasks cover only the most elementary levels of spatial cognition and largely overlook higher-level cognition of architectural space, including layout understanding, circulation patterns, and functional zoning. In this work, we present ArchSIBench, a Benchmark for Architectural Spatial Intelligence based on the perspectives from architecture, cognitive science, and psychology. ArchSIBench covers five core dimensions: perception, reasoning, navigation, transformation, and configuration, comprising 17 fine-grained subtasks. Through careful manual annotation by experts with architectural backgrounds, we construct 3,000 question-answer pairs to enable comprehensive evaluation of architectural spatial intelligence. Based on ArchSIBench, we evaluate various VLMs and find that the architectural spatial intelligence of most models shows significant differences from human baselines; additionally, models exhibit substantial variability across capability dimensions. Some state-of-the-art models can approach the level of human evaluators without architectural training. However, a clear gap remains compared to human evaluators with architectural training, particularly in spatial transformation and configuration reasoning. We believe that ArchSIBench will provide important insights and systematic resources for measuring and advancing the architectural spatial intelligence of VLMs. The dataset and code are available at https://huggingface.co/datasets/ArchSIBench/ArchSIBench.

Large Language Models (LLMs) have transformed natural language processing, yet their internal mechanisms remain largely opaque. Recently, mechanistic interpretability has attracted significant attention from the research community as a means to understand the inner workings of LLMs. Among various mechanistic interpretability approaches, Sparse Autoencoders (SAEs) have emerged as a promising method due to their ability to disentangle the complex, superimposed features within LLMs into more interpretable components. This paper presents a comprehensive survey of SAEs for interpreting and understanding the internal workings of LLMs. Our major contributions include: (1) exploring the technical framework of SAEs, covering basic architecture, design improvements, and effective training strategies; (2) examining different approaches to explaining SAE features, categorized into input-based and output-based explanation methods; (3) discussing evaluation methods for assessing SAE performance, covering both structural and functional metrics; and (4) investigating real-world applications of SAEs in understanding and manipulating LLM behaviors.

Learning mappings between infinite-dimensional function spaces, or operator learning, is essential for many machine learning applications. Although transformer-based operators are popular, they often rely on token-wise attention. These methods treat continuous fields as discrete tokens and usually ignore the global functional structure. We introduce Functional Attention, which reinterprets attention as a functional correspondence between adaptive bases. Inspired by geometric functional maps, our method replaces softmax affinities with structured linear operators. This yields a compact, generalizable, resolution-invariant representation that explicitly captures global dependencies. Experiments demonstrate that Functional Attention can match state-of-the-art performance in many operator learning tasks, including solving PDEs, 3D segmentation, and regression, while remaining robust to varying discretizations. Project page is available at https://github.com/xjffff/FUNCATTN.

Despite their widespread success, the application of deep neural networks to functional data remains scarce today. The infinite dimensionality of functional data means standard learning algorithms can be applied only after appropriate dimension reduction, typically achieved via basis expansions. Currently, these bases are chosen a priori without the information for the task at hand and thus may not be effective for the designated task. We instead propose to adaptively learn these bases in an end-to-end fashion. We introduce neural networks that employ a new Basis Layer whose hidden units are each basis functions themselves implemented as a micro neural network. Our architecture learns to apply parsimonious dimension reduction to functional inputs that focuses only on information relevant to the target rather than irrelevant variation in the input function. Across numerous classification/regression tasks with functional data, our method empirically outperforms other types of neural networks, and we prove that our approach is statistically consistent with low generalization error. Code is available at: https://github.com/jwyyy/AdaFNN.

Functional data play a pivotal role across science and engineering, yet their infinite-dimensional nature makes representation learning challenging. Conventional statistical models depend on pre-chosen basis expansions or kernels, limiting the flexibility of data-driven discovery, while many deep-learning pipelines treat functions as fixed-grid vectors, ignoring inherent continuity. In this paper, we introduce Functional Attention with a Mixture-of-Experts (FAME), an end-to-end, fully data-driven framework for function-on-function regression. FAME forms continuous attention by coupling a bidirectional neural controlled differential equation with MoE-driven vector fields to capture intra-functional continuity, and further fuses change to inter-functional dependencies via multi-head cross attention. Extensive experiments on synthetic and real-world functional-regression benchmarks show that FAME achieves state-of-the-art accuracy, strong robustness to arbitrarily sampled discrete observations of functions.

Although large language models (LLMs) are increasingly capable, these capabilities are unevenly distributed: they excel at formal linguistic tasks, such as producing fluent, grammatical text, but struggle more with functional linguistic tasks like reasoning and consistent fact retrieval. Inspired by neuroscience, recent work suggests that to succeed on both formal and functional linguistic tasks, LLMs should use different mechanisms for each; such localization could either be built-in or emerge spontaneously through training. In this paper, we ask: do current models, with fast-improving functional linguistic abilities, exhibit distinct localization of formal and functional linguistic mechanisms? We answer this by finding and comparing the "circuits", or minimal computational subgraphs, responsible for various formal and functional tasks. Comparing 5 LLMs across 10 distinct tasks, we find that while there is indeed little overlap between circuits for formal and functional tasks, there is also little overlap between formal linguistic tasks, as exists in the human brain. Thus, a single formal linguistic network, unified and distinct from functional task circuits, remains elusive. However, in terms of cross-task faithfulness - the ability of one circuit to solve another's task - we observe a separation between formal and functional mechanisms, suggesting that shared mechanisms between formal tasks may exist.

Contemporary predictive models are hard to interpret as their deep nets exploit numerous complex relations between input elements. This work suggests a theoretical framework for model interpretability by measuring the contribution of relevant features to the functional entropy of the network with respect to the input. We rely on the log-Sobolev inequality that bounds the functional entropy by the functional Fisher information with respect to the covariance of the data. This provides a principled way to measure the amount of information contribution of a subset of features to the decision function. Through extensive experiments, we show that our method surpasses existing interpretability sampling-based methods on various data signals such as image, text, and audio.

We introduce the task of predicting functional 3D scene graphs for real-world indoor environments from posed RGB-D images. Unlike traditional 3D scene graphs that focus on spatial relationships of objects, functional 3D scene graphs capture objects, interactive elements, and their functional relationships. Due to the lack of training data, we leverage foundation models, including visual language models (VLMs) and large language models (LLMs), to encode functional knowledge. We evaluate our approach on an extended SceneFun3D dataset and a newly collected dataset, FunGraph3D, both annotated with functional 3D scene graphs. Our method significantly outperforms adapted baselines, including Open3DSG and ConceptGraph, demonstrating its effectiveness in modeling complex scene functionalities. We also demonstrate downstream applications such as 3D question answering and robotic manipulation using functional 3D scene graphs. See our project page at https://openfungraph.github.io

We propose a new class of generative diffusion models, called functional diffusion. In contrast to previous work, functional diffusion works on samples that are represented by functions with a continuous domain. Functional diffusion can be seen as an extension of classical diffusion models to an infinite-dimensional domain. Functional diffusion is very versatile as images, videos, audio, 3D shapes, deformations, \etc, can be handled by the same framework with minimal changes. In addition, functional diffusion is especially suited for irregular data or data defined in non-standard domains. In our work, we derive the necessary foundations for functional diffusion and propose a first implementation based on the transformer architecture. We show generative results on complicated signed distance functions and deformation functions defined on 3D surfaces.

Functional grasping is essential for humans to perform specific tasks, such as grasping scissors by the finger holes to cut materials or by the blade to safely hand them over. Enabling dexterous robot hands with functional grasping capabilities is crucial for their deployment to accomplish diverse real-world tasks. Recent research in dexterous grasping, however, often focuses on power grasps while overlooking task- and object-specific functional grasping poses. In this paper, we introduce FunGrasp, a system that enables functional dexterous grasping across various robot hands and performs one-shot transfer to unseen objects. Given a single RGBD image of functional human grasping, our system estimates the hand pose and transfers it to different robotic hands via a human-to-robot (H2R) grasp retargeting module. Guided by the retargeted grasping poses, a policy is trained through reinforcement learning in simulation for dynamic grasping control. To achieve robust sim-to-real transfer, we employ several techniques including privileged learning, system identification, domain randomization, and gravity compensation. In our experiments, we demonstrate that our system enables diverse functional grasping of unseen objects using single RGBD images, and can be successfully deployed across various dexterous robot hands. The significance of the components is validated through comprehensive ablation studies. Project page: https://hly-123.github.io/FunGrasp/ .

Explainability has become an important topic in computer science and artificial intelligence, leading to a subfield called Explainable Artificial Intelligence (XAI). The goal of providing or seeking explanations is to achieve (better) 'understanding' on the part of the explainee. However, what it means to 'understand' is still not clearly defined, and the concept itself is rarely the subject of scientific investigation. This conceptual article aims to present a model of forms of understanding for XAI-explanations and beyond. From an interdisciplinary perspective bringing together computer science, linguistics, sociology, philosophy and psychology, a definition of understanding and its forms, assessment, and dynamics during the process of giving everyday explanations are explored. Two types of understanding are considered as possible outcomes of explanations, namely enabledness, 'knowing how' to do or decide something, and comprehension, 'knowing that' -- both in different degrees (from shallow to deep). Explanations regularly start with shallow understanding in a specific domain and can lead to deep comprehension and enabledness of the explanandum, which we see as a prerequisite for human users to gain agency. In this process, the increase of comprehension and enabledness are highly interdependent. Against the background of this systematization, special challenges of understanding in XAI are discussed.

Deep functional maps have recently emerged as a powerful tool for solving non-rigid shape correspondence tasks. Methods that use this approach combine the power and flexibility of the functional map framework, with data-driven learning for improved accuracy and generality. However, most existing methods in this area restrict the learning aspect only to the feature functions and still rely on axiomatic modeling for formulating the training loss or for functional map regularization inside the networks. This limits both the accuracy and the applicability of the resulting approaches only to scenarios where assumptions of the axiomatic models hold. In this work, we show, for the first time, that both in-network regularization and functional map training can be replaced with data-driven methods. For this, we first train a generative model of functional maps in the spectral domain using score-based generative modeling, built from a large collection of high-quality maps. We then exploit the resulting model to promote the structural properties of ground truth functional maps on new shape collections. Remarkably, we demonstrate that the learned models are category-agnostic, and can fully replace commonly used strategies such as enforcing Laplacian commutativity or orthogonality of functional maps. Our key technical contribution is a novel distillation strategy from diffusion models in the spectral domain. Experiments demonstrate that our learned regularization leads to better results than axiomatic approaches for zero-shot non-rigid shape matching. Our code is available at: https://github.com/daidedou/diffumatch/

It is desirable for statistical models to detect signals of interest independently of their position. If the data is generated by some smooth process, this additional structure should be taken into account. We introduce a new class of neural networks that are shift invariant and preserve smoothness of the data: functional neural networks (FNNs). For this, we use methods from functional data analysis (FDA) to extend multi-layer perceptrons and convolutional neural networks to functional data. We propose different model architectures, show that the models outperform a benchmark model from FDA in terms of accuracy and successfully use FNNs to classify electroencephalography (EEG) data.

Language understanding entails not just extracting the surface-level meaning of the linguistic input, but constructing rich mental models of the situation it describes. Here we propose that because processing within the brain's core language system is fundamentally limited, deeply understanding language requires exporting information from the language system to other brain regions that compute perceptual and motor representations, construct mental models, and store our world knowledge and autobiographical memories. We review the existing evidence for this hypothesis, and argue that recent progress in cognitive neuroscience provides both the conceptual foundation and the methods to directly test it, thus opening up a new strategy to reveal what it means, cognitively and neurally, to understand language.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively explored, translating protein structure to function continues to present substantial challenges. Various models, particularly, CNN and graph-based deep learning approaches that integrate structural and functional data, have been proposed to address these challenges. However, these methods often fall short in elucidating the functional significance of key residues essential for protein functionality, as they predominantly adopt a retrospective perspective, leading to suboptimal performance. Inspired by region proposal networks in computer vision, we introduce the Protein Region Proposal Network (ProteinRPN) for accurate protein function prediction. Specifically, the region proposal module component of ProteinRPN identifies potential functional regions (anchors) which are refined through the hierarchy-aware node drop pooling layer favoring nodes with defined secondary structures and spatial proximity. The representations of the predicted functional nodes are enriched using attention mechanisms and subsequently fed into a Graph Multiset Transformer, which is trained with supervised contrastive (SupCon) and InfoNCE losses on perturbed protein structures. Our model demonstrates significant improvements in predicting Gene Ontology (GO) terms, effectively localizing functional residues within protein structures. The proposed framework provides a robust, scalable solution for protein function annotation, advancing the understanding of protein structure-function relationships in computational biology.

We present a new dataset, Functional Map of the World (fMoW), which aims to inspire the development of machine learning models capable of predicting the functional purpose of buildings and land use from temporal sequences of satellite images and a rich set of metadata features. The metadata provided with each image enables reasoning about location, time, sun angles, physical sizes, and other features when making predictions about objects in the image. Our dataset consists of over 1 million images from over 200 countries. For each image, we provide at least one bounding box annotation containing one of 63 categories, including a "false detection" category. We present an analysis of the dataset along with baseline approaches that reason about metadata and temporal views. Our data, code, and pretrained models have been made publicly available.

We present a smoothly broken power law functional form (that we refer to as a Broken Neural Scaling Law (BNSL)) that accurately models & extrapolates the scaling behaviors of deep neural networks (i.e. how the evaluation metric of interest varies as amount of compute used for training (or inference), number of model parameters, training dataset size, model input size, number of training steps, or upstream performance varies) for various architectures & for each of various tasks within a large & diverse set of upstream & downstream tasks, in zero-shot, prompted, & finetuned settings. This set includes large-scale vision, language, audio, video, diffusion, generative modeling, multimodal learning, contrastive learning, AI alignment, AI capabilities, robotics, out-of-distribution (OOD) generalization, continual learning, transfer learning, uncertainty estimation / calibration, OOD detection, adversarial robustness, distillation, sparsity, retrieval, quantization, pruning, fairness, molecules, computer programming/coding, math word problems, "emergent phase transitions", arithmetic, supervised learning, unsupervised/self-supervised learning, & reinforcement learning (single agent & multi-agent). When compared to other functional forms for neural scaling, this functional form yields extrapolations of scaling behavior that are considerably more accurate on this set. Moreover, this functional form accurately models & extrapolates scaling behavior that other functional forms are incapable of expressing such as the nonmonotonic transitions present in the scaling behavior of phenomena such as double descent & the delayed, sharp inflection points present in the scaling behavior of tasks such as arithmetic. Lastly, we use this functional form to glean insights about the limit of the predictability of scaling behavior. Code is available at https://github.com/ethancaballero/broken_neural_scaling_laws

Neurons in the brain are spatially organized such that neighbors on tissue often exhibit similar response profiles. In the human language system, experimental studies have observed clusters for syntactic and semantic categories, but the mechanisms underlying this functional organization remain unclear. Here, building on work from the vision literature, we develop TopoLM, a transformer language model with an explicit two-dimensional spatial representation of model units. By combining a next-token prediction objective with a spatial smoothness loss, representations in this model assemble into clusters that correspond to semantically interpretable groupings of text and closely match the functional organization in the brain's language system. TopoLM successfully predicts the emergence of the spatio-functional organization of a cortical language system as well as the organization of functional clusters selective for fine-grained linguistic features empirically observed in human cortex. Our results suggest that the functional organization of the human language system is driven by a unified spatial objective, and provide a functionally and spatially aligned model of language processing in the brain.

Transformers, and the attention mechanism in particular, have become ubiquitous in machine learning. Their success in modeling nonlocal, long-range correlations has led to their widespread adoption in natural language processing, computer vision, and time series problems. Neural operators, which map spaces of functions into spaces of functions, are necessarily both nonlinear and nonlocal if they are universal; it is thus natural to ask whether the attention mechanism can be used in the design of neural operators. Motivated by this, we study transformers in the function space setting. We formulate attention as a map between infinite dimensional function spaces and prove that the attention mechanism as implemented in practice is a Monte Carlo or finite difference approximation of this operator. The function space formulation allows for the design of transformer neural operators, a class of architectures designed to learn mappings between function spaces. In this paper, we state and prove the first universal approximation result for transformer neural operators, using only a slight modification of the architecture implemented in practice. The prohibitive cost of applying the attention operator to functions defined on multi-dimensional domains leads to the need for more efficient attention-based architectures. For this reason we also introduce a function space generalization of the patching strategy from computer vision, and introduce a class of associated neural operators. Numerical results, on an array of operator learning problems, demonstrate the promise of our approaches to function space formulations of attention and their use in neural operators.

Activation steering presupposes that task-relevant behaviors correspond to linear directions in activation space -- directions that should both steer the model and be readable along the unembedding. Function vectors (FVs), extracted as mean differences across ICL demonstrations, are the canonical test case; the prediction: steering and decoding succeed or fail together. Across 12 tasks, 6 models from 3 families, and 4,032 directed cross-template pairs, we find the opposite. FV steering routinely succeeds where the logit lens cannot decode the correct answer at any intermediate layer, while the converse -- decodable without steerable -- is nearly empty (3 of 72). The gap is not representational dialect. A diagonal tuned lens closes 1 of 14 steerable-not-decodable cases; a 2-layer MLP probe with a Hewitt \& Liang control closes 5 of 10 via nonlinearly encoded structure but leaves 5 invisible to every decoder tested. Even at > 0.90 steering accuracy, projecting the FV through the unembedding yields incoherent token distributions: FVs encode computational instructions, not answer directions. A model-family asymmetry sharpens the picture. Mistral FVs rewrite intermediate representations, while Llama and Gemma FVs steer the final output without leaving a logit-lens-visible trace, corroborated by three signals (post-steering deltas, activation-patching recovery, FV norm-transfer correlations). A previously reported negative cosine-transfer correlation dissolves at scale, adding at most ΔR^2 = 0.011 beyond task identity. These results decompose the linear representation hypothesis into linear decodability and linear steerability and show they come apart opposite to intuition, with implications for safety monitoring: vocabulary-projection tools are blind to FV-style interventions on widely deployed model families.

Modern life sciences research is increasingly relying on artificial intelligence approaches to model biological systems, primarily centered around the use of machine learning (ML) models. Although ML is undeniably useful for identifying patterns in large, complex data sets, its widespread application in biological sciences represents a significant deviation from traditional methods of scientific inquiry. As such, the interplay between these models and scientific understanding in biology is a topic with important implications for the future of scientific research, yet it is a subject that has received little attention. Here, we draw from an epistemological toolkit to contextualize recent applications of ML in biological sciences under modern philosophical theories of understanding, identifying general principles that can guide the design and application of ML systems to model biological phenomena and advance scientific knowledge. We propose that conceptions of scientific understanding as information compression, qualitative intelligibility, and dependency relation modelling provide a useful framework for interpreting ML-mediated understanding of biological systems. Through a detailed analysis of two key application areas of ML in modern biological research - protein structure prediction and single cell RNA-sequencing - we explore how these features have thus far enabled ML systems to advance scientific understanding of their target phenomena, how they may guide the development of future ML models, and the key obstacles that remain in preventing ML from achieving its potential as a tool for biological discovery. Consideration of the epistemological features of ML applications in biology will improve the prospects of these methods to solve important problems and advance scientific understanding of living systems.

Many recent datasets contain a variety of different data modalities, for instance, image, question, and answer data in visual question answering (VQA). When training deep net classifiers on those multi-modal datasets, the modalities get exploited at different scales, i.e., some modalities can more easily contribute to the classification results than others. This is suboptimal because the classifier is inherently biased towards a subset of the modalities. To alleviate this shortcoming, we propose a novel regularization term based on the functional entropy. Intuitively, this term encourages to balance the contribution of each modality to the classification result. However, regularization with the functional entropy is challenging. To address this, we develop a method based on the log-Sobolev inequality, which bounds the functional entropy with the functional-Fisher-information. Intuitively, this maximizes the amount of information that the modalities contribute. On the two challenging multi-modal datasets VQA-CPv2 and SocialIQ, we obtain state-of-the-art results while more uniformly exploiting the modalities. In addition, we demonstrate the efficacy of our method on Colored MNIST.

Mechanistic interpretability aims to understand model behaviors in terms of specific, interpretable features, often hypothesized to manifest as low-dimensional subspaces of activations. Specifically, recent studies have explored subspace interventions (such as activation patching) as a way to simultaneously manipulate model behavior and attribute the features behind it to given subspaces. In this work, we demonstrate that these two aims diverge, potentially leading to an illusory sense of interpretability. Counterintuitively, even if a subspace intervention makes the model's output behave as if the value of a feature was changed, this effect may be achieved by activating a dormant parallel pathway leveraging another subspace that is causally disconnected from model outputs. We demonstrate this phenomenon in a distilled mathematical example, in two real-world domains (the indirect object identification task and factual recall), and present evidence for its prevalence in practice. In the context of factual recall, we further show a link to rank-1 fact editing, providing a mechanistic explanation for previous work observing an inconsistency between fact editing performance and fact localization. However, this does not imply that activation patching of subspaces is intrinsically unfit for interpretability. To contextualize our findings, we also show what a success case looks like in a task (indirect object identification) where prior manual circuit analysis informs an understanding of the location of a feature. We explore the additional evidence needed to argue that a patched subspace is faithful.

Recent work has shown that feed-forward networks (FFNs) in pre-trained Transformers are a key component, storing various linguistic and factual knowledge. However, the computational patterns of FFNs are still unclear. In this work, we study the computational patterns of FFNs and observe that most inputs only activate a tiny ratio of neurons of FFNs. This phenomenon is similar to the sparsity of the human brain, which drives research on functional partitions of the human brain. To verify whether functional partitions also emerge in FFNs, we propose to convert a model into its MoE version with the same parameters, namely MoEfication. Specifically, MoEfication consists of two phases: (1) splitting the parameters of FFNs into multiple functional partitions as experts, and (2) building expert routers to decide which experts will be used for each input. Experimental results show that MoEfication can conditionally use 10% to 30% of FFN parameters while maintaining over 95% original performance for different models on various downstream tasks. Besides, MoEfication brings two advantages: (1) it significantly reduces the FLOPS of inference, i.e., 2x speedup with 25% of FFN parameters, and (2) it provides a fine-grained perspective to study the inner mechanism of FFNs. The source code of this paper can be obtained from https://github.com/thunlp/MoEfication.

Unsupervised learning with functional data is an emerging paradigm of machine learning research with applications to computer vision, climate modeling and physical systems. A natural way of modeling functional data is by learning operators between infinite dimensional spaces, leading to discretization invariant representations that scale independently of the sample grid resolution. Here we present Variational Autoencoding Neural Operators (VANO), a general strategy for making a large class of operator learning architectures act as variational autoencoders. For this purpose, we provide a novel rigorous mathematical formulation of the variational objective in function spaces for training. VANO first maps an input function to a distribution over a latent space using a parametric encoder and then decodes a sample from the latent distribution to reconstruct the input, as in classic variational autoencoders. We test VANO with different model set-ups and architecture choices for a variety of benchmarks. We start from a simple Gaussian random field where we can analytically track what the model learns and progressively transition to more challenging benchmarks including modeling phase separation in Cahn-Hilliard systems and real world satellite data for measuring Earth surface deformation.

We present a new dataset for form understanding in noisy scanned documents (FUNSD) that aims at extracting and structuring the textual content of forms. The dataset comprises 199 real, fully annotated, scanned forms. The documents are noisy and vary widely in appearance, making form understanding (FoUn) a challenging task. The proposed dataset can be used for various tasks, including text detection, optical character recognition, spatial layout analysis, and entity labeling/linking. To the best of our knowledge, this is the first publicly available dataset with comprehensive annotations to address FoUn task. We also present a set of baselines and introduce metrics to evaluate performance on the FUNSD dataset, which can be downloaded at https://guillaumejaume.github.io/FUNSD/.

Large Language Models (LLMs) are often described as being instances of foundation models - that is, models that transfer strongly across various tasks and conditions in few-show or zero-shot manner, while exhibiting scaling laws that predict function improvement when increasing the pre-training scale. These claims of excelling in different functions and tasks rely on measurements taken across various sets of standardized benchmarks showing high scores for such models. We demonstrate here a dramatic breakdown of function and reasoning capabilities of state-of-the-art models trained at the largest available scales which claim strong function, using a simple, short, conventional common sense problem formulated in concise natural language, easily solvable by humans. The breakdown is dramatic, as models also express strong overconfidence in their wrong solutions, while providing often non-sensical "reasoning"-like explanations akin to confabulations to justify and backup the validity of their clearly failed responses, making them sound plausible. Various standard interventions in an attempt to get the right solution, like various type of enhanced prompting, or urging the models to reconsider the wrong solutions again by multi step re-evaluation, fail. We take these initial observations to the scientific and technological community to stimulate urgent re-assessment of the claimed capabilities of current generation of LLMs, Such re-assessment also requires common action to create standardized benchmarks that would allow proper detection of such basic reasoning deficits that obviously manage to remain undiscovered by current state-of-the-art evaluation procedures and benchmarks. Code for reproducing experiments in the paper and raw experiments data can be found at https://github.com/LAION-AI/AIW

This position paper explores the rapid development of Foundation Models (FMs) in AI and their implications for intelligence and reasoning. It examines the characteristics of FMs, including their training on vast datasets and use of embedding spaces to capture semantic relationships. The paper discusses recent advancements in FMs' reasoning abilities which we argue cannot be attributed to increased model size but to novel training techniques which yield learning phenomena like grokking. It also addresses the challenges in benchmarking FMs and compares their structure to the human brain. We argue that while FMs show promising developments in reasoning and knowledge representation, understanding their inner workings remains a significant challenge, similar to ongoing efforts in neuroscience to comprehend human brain function. Despite having some similarities, fundamental differences between FMs and the structure of human brain warn us against making direct comparisons or expecting neuroscience to provide immediate insights into FM function.

We report the presence of a simple neural mechanism that represents an input-output function as a vector within autoregressive transformer language models (LMs). Using causal mediation analysis on a diverse range of in-context-learning (ICL) tasks, we find that a small number attention heads transport a compact representation of the demonstrated task, which we call a function vector (FV). FVs are robust to changes in context, i.e., they trigger execution of the task on inputs such as zero-shot and natural text settings that do not resemble the ICL contexts from which they are collected. We test FVs across a range of tasks, models, and layers and find strong causal effects across settings in middle layers. We investigate the internal structure of FVs and find while that they often contain information that encodes the output space of the function, this information alone is not sufficient to reconstruct an FV. Finally, we test semantic vector composition in FVs, and find that to some extent they can be summed to create vectors that trigger new complex tasks. Taken together, our findings suggest that LLMs contain internal abstractions of general-purpose functions that can be invoked in a variety of contexts.

The field of Automatic Machine Learning (AutoML) has recently attained impressive results, including the discovery of state-of-the-art machine learning solutions, such as neural image classifiers. This is often done by applying an evolutionary search method, which samples multiple candidate solutions from a large space and evaluates the quality of each candidate through a long training process. As a result, the search tends to be slow. In this paper, we show that large efficiency gains can be obtained by employing a fast unified functional hash, especially through the functional equivalence caching technique, which we also present. The central idea is to detect by hashing when the search method produces equivalent candidates, which occurs very frequently, and this way avoid their costly re-evaluation. Our hash is "functional" in that it identifies equivalent candidates even if they were represented or coded differently, and it is "unified" in that the same algorithm can hash arbitrary representations; e.g. compute graphs, imperative code, or lambda functions. As evidence, we show dramatic improvements on multiple AutoML domains, including neural architecture search and algorithm discovery. Finally, we consider the effect of hash collisions, evaluation noise, and search distribution through empirical analysis. Altogether, we hope this paper may serve as a guide to hashing techniques in AutoML.

In the rapidly evolving landscape of artificial intelligence, multi-modal large language models are emerging as a significant area of interest. These models, which combine various forms of data input, are becoming increasingly popular. However, understanding their internal mechanisms remains a complex task. Numerous advancements have been made in the field of explainability tools and mechanisms, yet there is still much to explore. In this work, we present a novel interactive application aimed towards understanding the internal mechanisms of large vision-language models. Our interface is designed to enhance the interpretability of the image patches, which are instrumental in generating an answer, and assess the efficacy of the language model in grounding its output in the image. With our application, a user can systematically investigate the model and uncover system limitations, paving the way for enhancements in system capabilities. Finally, we present a case study of how our application can aid in understanding failure mechanisms in a popular large multi-modal model: LLaVA.

Functional brain network (FBN) modeling often relies on local pairwise interactions, whose limitation in capturing high-order dependencies is theoretically analyzed in this paper. Meanwhile, the computational burden and heuristic nature of current hypergraph modeling approaches hinder end-to-end learning of FBN structures directly from data distributions. To address this, we propose to extract high-order FBN structures under global constraints, and implement this as a Global Constraints oriented Multi-resolution (GCM) FBN structure learning framework. It incorporates 4 types of global constraint (signal synchronization, subject identity, expected edge numbers, and data labels) to enable learning FBN structures for 4 distinct levels (sample/subject/group/project) of modeling resolution. Experimental results demonstrate that GCM achieves up to a 30.6% improvement in relative accuracy and a 96.3% reduction in computational time across 5 datasets and 2 task settings, compared to 9 baselines and 10 state-of-the-art methods. Extensive experiments validate the contributions of individual components and highlight the interpretability of GCM. This work offers a novel perspective on FBN structure learning and provides a foundation for interdisciplinary applications in cognitive neuroscience. Code is publicly available on https://github.com/lzhan94swu/GCM.

While Multimodal Large Language Models (MLLMs) have demonstrated remarkable proficiency in tasks such as abnormality detection and report generation for anatomical modalities, their capability in functional imaging remains largely unexplored. In this work, we identify and quantify a fundamental functional perception gap: the inability of current vision encoders to decode functional tracer biodistribution independent of morphological priors. Identifying Positron Emission Tomography (PET) as the quintessential modality to investigate this disconnect, we introduce PET-Bench, the first large-scale functional imaging benchmark comprising 52,308 hierarchical QA pairs from 9,732 multi-site, multi-tracer PET studies. Extensive evaluation of 19 state-of-the-art MLLMs reveals a critical safety hazard termed the Chain-of-Thought (CoT) hallucination trap. We observe that standard CoT prompting, widely considered to enhance reasoning, paradoxically decouples linguistic generation from visual evidence in PET, producing clinically fluent but factually ungrounded diagnoses. To resolve this, we propose Atomic Visual Alignment (AVA), a simple fine-tuning strategy that enforces the mastery of low-level functional perception prior to high-level diagnostic reasoning. Our results demonstrate that AVA effectively bridges the perception gap, transforming CoT from a source of hallucination into a robust inference tool and improving diagnostic accuracy by up to 14.83%. Code and data are available at https://github.com/yezanting/PET-Bench.

Large language models lack persistent, structured memory for long-term interaction and context-sensitive retrieval. Expanding context windows does not solve this: recent evidence shows that context length alone degrades reasoning by up to 85% - even with perfect retrieval. We propose a bio-inspired memory framework grounded in complementary learning systems theory, cognitive behavioral therapy's belief hierarchy, dual-process cognition, and fuzzy-trace theory, organized around three principles: (1) Memory has valence, not just content - pre-computed emotional-associative summaries (valence vectors) organized in an emergent belief hierarchy inspired by Beck's cognitive model enable instant orientation before deliberation; (2) Retrieval defaults to System 1 with System 2 escalation - automatic spreading activation and passive priming as default, with deliberate retrieval only when needed, and graded epistemic states that address hallucination structurally; and (3) Encoding is active, present, and feedback-dependent - a thalamic gateway tags and routes information between stores, while the executive forms gists through curiosity-driven investigation, not passive exposure. Seven functional properties specify what any implementation must satisfy. Over time, the system converges toward System 1 processing - the computational analog of clinical expertise - producing interactions that become cheaper, not more expensive, with experience.

Protein biology focuses on the intricate relationships among sequences, structures, and functions. Deciphering protein functions is crucial for understanding biological processes, advancing drug discovery, and enabling synthetic biology applications. Since protein sequences determine tertiary structures, which in turn govern functions, integrating sequence and structure information is essential for accurate prediction of protein functions. Traditional protein language models (pLMs) have advanced protein-related tasks by learning representations from large-scale sequence and structure data. However, pLMs are limited in integrating broader contextual knowledge, particularly regarding functional modalities that are fundamental to protein biology. In contrast, large language models (LLMs) have exhibited outstanding performance in contextual understanding, reasoning, and generation across diverse domains. Leveraging these capabilities, STELLA is proposed as a multimodal LLM integrating protein sequence-structure representations with general knowledge to address protein function prediction. Through multimodal instruction tuning (MMIT) using the proposed OPI-Struc dataset, STELLA achieves state-of-the-art performance in two function-related tasks-functional description prediction (FP) and enzyme-catalyzed reaction prediction (EP). This study highlights the potential of multimodal LLMs as an alternative paradigm to pLMs to advance protein biology research.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

We introduce Functional Diffusion Processes (FDPs), which generalize score-based diffusion models to infinite-dimensional function spaces. FDPs require a new mathematical framework to describe the forward and backward dynamics, and several extensions to derive practical training objectives. These include infinite-dimensional versions of Girsanov theorem, in order to be able to compute an ELBO, and of the sampling theorem, in order to guarantee that functional evaluations in a countable set of points are equivalent to infinite-dimensional functions. We use FDPs to build a new breed of generative models in function spaces, which do not require specialized network architectures, and that can work with any kind of continuous data. Our results on real data show that FDPs achieve high-quality image generation, using a simple MLP architecture with orders of magnitude fewer parameters than existing diffusion models.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating multimodal neuroimaging signals, such as EEG, MEG, and fMRI, remains a critical hurdle due to their inherent spatiotemporal misalignment. Current approaches often analyze these modalities in isolation, limiting a holistic view of neural representation. In this study, we introduce BrainFLORA, a unified framework for integrating cross-modal neuroimaging data to construct a shared neural representation. Our approach leverages multimodal large language models (MLLMs) augmented with modality-specific adapters and task decoders, achieving state-of-the-art performance in joint-subject visual retrieval task and has the potential to extend multitasking. Combining neuroimaging analysis methods, we further reveal how visual concept representations align across neural modalities and with real world object perception. We demonstrate that the brain's structured visual concept representations exhibit an implicit mapping to physical-world stimuli, bridging neuroscience and machine learning from different modalities of neural imaging. Beyond methodological advancements, BrainFLORA offers novel implications for cognitive neuroscience and brain-computer interfaces (BCIs). Our code is available at https://github.com/ncclab-sustech/BrainFLORA.

Labeling neural network submodules with human-legible descriptions is useful for many downstream tasks: such descriptions can surface failures, guide interventions, and perhaps even explain important model behaviors. To date, most mechanistic descriptions of trained networks have involved small models, narrowly delimited phenomena, and large amounts of human labor. Labeling all human-interpretable sub-computations in models of increasing size and complexity will almost certainly require tools that can generate and validate descriptions automatically. Recently, techniques that use learned models in-the-loop for labeling have begun to gain traction, but methods for evaluating their efficacy are limited and ad-hoc. How should we validate and compare open-ended labeling tools? This paper introduces FIND (Function INterpretation and Description), a benchmark suite for evaluating the building blocks of automated interpretability methods. FIND contains functions that resemble components of trained neural networks, and accompanying descriptions of the kind we seek to generate. The functions are procedurally constructed across textual and numeric domains, and involve a range of real-world complexities, including noise, composition, approximation, and bias. We evaluate new and existing methods that use language models (LMs) to produce code-based and language descriptions of function behavior. We find that an off-the-shelf LM augmented with only black-box access to functions can sometimes infer their structure, acting as a scientist by forming hypotheses, proposing experiments, and updating descriptions in light of new data. However, LM-based descriptions tend to capture global function behavior and miss local corruptions. These results show that FIND will be useful for characterizing the performance of more sophisticated interpretability methods before they are applied to real-world models.

Artificial intelligence has made great strides in the last decade but still falls short of the human brain, the best-known example of intelligence. Not much is known of the neural processes that allow the brain to make the leap to achieve so much from so little beyond its ability to create knowledge structures that can be flexibly and dynamically combined, recombined, and applied in new and novel ways. This paper proposes a mathematical approach using graph theory and spectral graph theory, to hypothesize how to constrain these neural clusters of information based on eigen-relationships. This same hypothesis is hierarchically applied to scale up from the smallest to the largest clusters of knowledge that eventually lead to model building and reasoning.

Advancements in LLMs have recently unveiled challenges tied to computational efficiency and continual scalability due to their requirements of huge parameters, making the applications and evolution of these models on devices with limited computation resources and scenarios requiring various abilities increasingly cumbersome. Inspired by modularity within the human brain, there is a growing tendency to decompose LLMs into numerous functional modules, allowing for inference with part of modules and dynamic assembly of modules to tackle complex tasks, such as mixture-of-experts. To highlight the inherent efficiency and composability of the modular approach, we coin the term brick to represent each functional module, designating the modularized structure as configurable foundation models. In this paper, we offer a comprehensive overview and investigation of the construction, utilization, and limitation of configurable foundation models. We first formalize modules into emergent bricks - functional neuron partitions that emerge during the pre-training phase, and customized bricks - bricks constructed via additional post-training to improve the capabilities and knowledge of LLMs. Based on diverse functional bricks, we further present four brick-oriented operations: retrieval and routing, merging, updating, and growing. These operations allow for dynamic configuration of LLMs based on instructions to handle complex tasks. To verify our perspective, we conduct an empirical analysis on widely-used LLMs. We find that the FFN layers follow modular patterns with functional specialization of neurons and functional neuron partitions. Finally, we highlight several open issues and directions for future research. Overall, this paper aims to offer a fresh modular perspective on existing LLM research and inspire the future creation of more efficient and scalable foundational models.

Large language models (LLMs) can reliably distinguish grammatical from ungrammatical sentences, but how grammatical knowledge is represented within the models remains an open question. We investigate whether different syntactic phenomena recruit shared or distinct components in LLMs. Using a functional localization approach inspired by cognitive neuroscience, we identify the LLM units most responsive to 67 English syntactic phenomena in seven open-weight models. These units are consistently recruited across sentences containing the phenomena and causally support the models' syntactic performance. Critically, different types of syntactic agreement (e.g., subject-verb, anaphor, determiner-noun) recruit overlapping sets of units, suggesting that agreement constitutes a meaningful functional category for LLMs. This pattern holds in English, Russian, and Chinese; and further, in a cross-lingual analysis of 57 diverse languages, structurally more similar languages share more units for subject-verb agreement. Taken together, these findings reveal that syntactic agreement-a critical marker of syntactic dependencies-constitutes a meaningful category within LLMs' representational spaces.

In this paper, we propose a real-world benchmark for studying robotic learning in the context of functional manipulation: a robot needs to accomplish complex long-horizon behaviors by composing individual manipulation skills in functionally relevant ways. The core design principles of our Functional Manipulation Benchmark (FMB) emphasize a harmonious balance between complexity and accessibility. Tasks are deliberately scoped to be narrow, ensuring that models and datasets of manageable scale can be utilized effectively to track progress. Simultaneously, they are diverse enough to pose a significant generalization challenge. Furthermore, the benchmark is designed to be easily replicable, encompassing all essential hardware and software components. To achieve this goal, FMB consists of a variety of 3D-printed objects designed for easy and accurate replication by other researchers. The objects are procedurally generated, providing a principled framework to study generalization in a controlled fashion. We focus on fundamental manipulation skills, including grasping, repositioning, and a range of assembly behaviors. The FMB can be used to evaluate methods for acquiring individual skills, as well as methods for combining and ordering such skills to solve complex, multi-stage manipulation tasks. We also offer an imitation learning framework that includes a suite of policies trained to solve the proposed tasks. This enables researchers to utilize our tasks as a versatile toolkit for examining various parts of the pipeline. For example, researchers could propose a better design for a grasping controller and evaluate it in combination with our baseline reorientation and assembly policies as part of a pipeline for solving multi-stage tasks. Our dataset, object CAD files, code, and evaluation videos can be found on our project website: https://functional-manipulation-benchmark.github.io

Large Language Models (LLMs) can generate reasoning tokens before their final answer to boost performance on complex tasks. While these sequences seem like human thought processes, empirical evidence reveals that they are not a faithful explanation of the model's actual reasoning process. To address this gap between appearance and function, we introduce the State over Tokens (SoT) conceptual framework. SoT reframes reasoning tokens not as a linguistic narrative, but as an externalized computational state -- the sole persistent information carrier across the model's stateless generation cycles. This explains how the tokens can drive correct reasoning without being a faithful explanation when read as text and surfaces previously overlooked research questions on these tokens. We argue that to truly understand the process that LLMs do, research must move beyond reading the reasoning tokens as text and focus on decoding them as state.