Mechanisms of AI Protein Folding in ESMFold

How do protein structure prediction models fold proteins? We investigate this question by tracing how ESMFold folds a beta hairpin, a prevalent structural motif. Through counterfactual interventions on model latents, we identify two computational stages in the folding trunk. In the first stage, early blocks initialize pairwise biochemical signals: residue identities and associated biochemical features such as charge flow from sequence representations into pairwise representations. In the second stage, late blocks develop pairwise spatial features: distance and contact information accumulate in the pairwise representation. We demonstrate that the mechanisms underlying structural decisions of ESMFold can be localized, traced through interpretable representations, and manipulated with strong causal effects.

Optimism Stabilizes Thompson Sampling for Adaptive Inference

Thompson sampling (TS) is widely used for stochastic multi-armed bandits, yet its inferential properties under adaptive data collection are subtle. Classical asymptotic theory for sample means can fail because arm-specific sample sizes are random and coupled with the rewards through the action-selection rule. We study this phenomenon in the $K$-armed Gaussian bandit and identify \emph{optimism} as a key mechanism for restoring \emph{stability}, a sufficient condition for valid asymptotic inference requiring each arm's pull count to concentrate around a deterministic scale. First, we prove that variance-inflated TS \citep{halder2025stable} is stable for any $K \ge 2$, including the challenging regime where multiple arms are optimal. This resolves the open question raised by \citet{halder2025stable} through extending their results from the two-armed setting to the general $K$-armed setting. Second, we analyze an alternative optimistic modification that keeps the posterior variance unchanged but adds an explicit mean bonus to posterior mean, and establish the same stability conclusion. In summary, suitably implemented optimism stabilizes Thompson sampling and enables asymptotically valid inference in multi-armed bandits, while incurring only a mild additional regret cost.

Learning Compact Boolean Networks

Floating-point neural networks dominate modern machine learning but incur substantial inference cost, motivating interest in Boolean networks for resource-constrained settings. However, learning compact and accurate Boolean networks is challenging due to their combinatorial nature. In this work, we address this challenge from three different angles: learned connections, compact convolutions and adaptive discretization. First, we propose a novel strategy to learn efficient connections with no additional parameters and negligible computational overhead. Second, we introduce a novel convolutional Boolean architecture that exploits the locality with reduced number of Boolean operations than existing methods. Third, we propose an adaptive discretization strategy to reduce the accuracy drop when converting a continuous-valued network into a Boolean one. Extensive results on standard vision benchmarks demonstrate that the Pareto front of accuracy vs. computation of our method significantly outperforms prior state-of-the-art, achieving better accuracy with up to 37x fewer Boolean operations.

Mining Generalizable Activation Functions

The choice of activation function is an active area of research, with different proposals aimed at improving optimization, while maintaining expressivity. Additionally, the activation function can significantly alter the implicit inductive bias of the architecture, controlling its non-linear behavior. In this paper, in line with previous work, we argue that evolutionary search provides a useful framework for finding new activation functions, while we also make two novel observations. The first is that modern pipelines, such as AlphaEvolve, which relies on frontier LLMs as a mutator operator, allows for a much wider and flexible search space; e.g., over all possible python functions within a certain FLOP budget, eliminating the need for manually constructed search spaces. In addition, these pipelines will be biased towards meaningful activation functions, given their ability to represent common knowledge, leading to a potentially more efficient search of the space. The second observation is that, through this framework, one can target not only performance improvements but also activation functions that encode particular inductive biases. This can be done by using performance on out-of-distribution data as a fitness function, reflecting the degree to which the architecture respects the inherent structure in the data in a manner independent of distribution shifts. We carry an empirical exploration of this proposal and show that relatively small scale synthetic datasets can be sufficient for AlphaEvolve to discover meaningful activations.

Logical Guidance for the Exact Composition of Diffusion Models

We propose LOGDIFF (Logical Guidance for the Exact Composition of Diffusion Models), a guidance framework for diffusion models that enables principled constrained generation with complex logical expressions at inference time. We study when exact score-based guidance for complex logical formulas can be obtained from guidance signals associated with atomic properties. First, we derive an exact Boolean calculus that provides a sufficient condition for exact logical guidance. Specifically, if a formula admits a circuit representation in which conjunctions combine conditionally independent subformulas and disjunctions combine subformulas that are either conditionally independent or mutually exclusive, exact logical guidance is achievable. In this case, the guidance signal can be computed exactly from atomic scores and posterior probabilities using an efficient recursive algorithm. Moreover, we show that, for commonly encountered classes of distributions, any desired Boolean formula is compilable into such a circuit representation. Second, by combining atomic guidance scores with posterior probability estimates, we introduce a hybrid guidance approach that bridges classifierguidance and classifier-free guidance, applicable to both compositional logical guidance and standard conditional generation. We demonstrate the effectiveness of our framework on multiple image and protein structure generation tasks.

TaSA: Two-Phased Deep Predictive Learning of Tactile Sensory Attenuation for Improving In-Grasp Manipulation

Humans can achieve diverse in-hand manipulations, such as object pinching and tool use, which often involve simultaneous contact between the object and multiple fingers. This is still an open issue for robotic hands because such dexterous manipulation requires distinguishing between tactile sensations generated by their self-contact and those arising from external contact. Otherwise, object/robot breakage happens due to contacts/collisions. Indeed, most approaches ignore self-contact altogether, by constraining motion to avoid/ignore self-tactile information during contact. While this reduces complexity, it also limits generalization to real-world scenarios where self-contact is inevitable. Humans overcome this challenge through self-touch perception, using predictive mechanisms that anticipate the tactile consequences of their own motion, through a principle called sensory attenuation, where the nervous system differentiates predictable self-touch signals, allowing novel object stimuli to stand out as relevant. Deriving from this, we introduce TaSA, a two-phased deep predictive learning framework. In the first phase, TaSA explicitly learns self-touch dynamics, modeling how a robot's own actions generate tactile feedback. In the second phase, this learned model is incorporated into the motion learning phase, to emphasize object contact signals during manipulation. We evaluate TaSA on a set of insertion tasks, which demand fine tactile discrimination: inserting a pencil lead into a mechanical pencil, inserting coins into a slot, and fixing a paper clip onto a sheet of paper, with various orientations, positions, and sizes. Across all tasks, policies trained with TaSA achieve significantly higher success rates than baseline methods, demonstrating that structured tactile perception with self-touch based on sensory attenuation is critical for dexterous robotic manipulation.

Structured Context Engineering for File-Native Agentic Systems: Evaluating Schema Accuracy, Format Effectiveness, and Multi-File Navigation at Scale

Large Language Model agents increasingly operate external systems through programmatic interfaces, yet practitioners lack empirical guidance on how to structure the context these agents consume. Using SQL generation as a proxy for programmatic agent operations, we present a systematic study of context engineering for structured data, comprising 9,649 experiments across 11 models, 4 formats (YAML, Markdown, JSON, Token-Oriented Object Notation [TOON]), and schemas ranging from 10 to 10,000 tables. Our findings challenge common assumptions. First, architecture choice is model-dependent: file-based context retrieval improves accuracy for frontier-tier models (Claude, GPT, Gemini; +2.7%, p=0.029) but shows mixed results for open source models (aggregate -7.7%, p<0.001), with deficits varying substantially by model. Second, format does not significantly affect aggregate accuracy (chi-squared=2.45, p=0.484), though individual models, particularly open source, exhibit format-specific sensitivities. Third, model capability is the dominant factor, with a 21 percentage point accuracy gap between frontier and open source tiers that dwarfs any format or architecture effect. Fourth, file-native agents scale to 10,000 tables through domain-partitioned schemas while maintaining high navigation accuracy. Fifth, file size does not predict runtime efficiency: compact formats can consume significantly more tokens at scale due to format-unfamiliar search patterns. These findings provide practitioners with evidence-based guidance for deploying LLM agents on structured systems, demonstrating that architectural decisions should be tailored to model capability rather than assuming universal best practices.

Disco: Densely-overlapping Cell Instance Segmentation via Adjacency-aware Collaborative Coloring

Accurate cell instance segmentation is foundational for digital pathology analysis. Existing methods based on contour detection and distance mapping still face significant challenges in processing complex and dense cellular regions. Graph coloring-based methods provide a new paradigm for this task, yet the effectiveness of this paradigm in real-world scenarios with dense overlaps and complex topologies has not been verified. Addressing this issue, we release a large-scale dataset GBC-FS 2025, which contains highly complex and dense sub-cellular nuclear arrangements. We conduct the first systematic analysis of the chromatic properties of cell adjacency graphs across four diverse datasets and reveal an important discovery: most real-world cell graphs are non-bipartite, with a high prevalence of odd-length cycles (predominantly triangles). This makes simple 2-coloring theory insufficient for handling complex tissues, while higher-chromaticity models would cause representational redundancy and optimization difficulties. Building on this observation of complex real-world contexts, we propose Disco (Densely-overlapping Cell Instance Segmentation via Adjacency-aware COllaborative Coloring), an adjacency-aware framework based on the "divide and conquer" principle. It uniquely combines a data-driven topological labeling strategy with a constrained deep learning system to resolve complex adjacency conflicts. First, "Explicit Marking" strategy transforms the topological challenge into a learnable classification task by recursively decomposing the cell graph and isolating a "conflict set." Second, "Implicit Disambiguation" mechanism resolves ambiguities in conflict regions by enforcing feature dissimilarity between different instances, enabling the model to learn separable feature representations.

Explainable Pathomics Feature Visualization via Correlation-aware Conditional Feature Editing

Pathomics is a recent approach that offers rich quantitative features beyond what black-box deep learning can provide, supporting more reproducible and explainable biomarkers in digital pathology. However, many derived features (e.g., "second-order moment") remain difficult to interpret, especially across different clinical contexts, which limits their practical adoption. Conditional diffusion models show promise for explainability through feature editing, but they typically assume feature independence**--**an assumption violated by intrinsically correlated pathomics features. Consequently, editing one feature while fixing others can push the model off the biological manifold and produce unrealistic artifacts. To address this, we propose a Manifold-Aware Diffusion (MAD) framework for controllable and biologically plausible cell nuclei editing. Unlike existing approaches, our method regularizes feature trajectories within a disentangled latent space learned by a variational auto-encoder (VAE). This ensures that manipulating a target feature automatically adjusts correlated attributes to remain within the learned distribution of real cells. These optimized features then guide a conditional diffusion model to synthesize high-fidelity images. Experiments demonstrate that our approach is able to navigate the manifold of pathomics features when editing those features. The proposed method outperforms baseline methods in conditional feature editing while preserving structural coherence.

MTPano: Multi-Task Panoramic Scene Understanding via Label-Free Integration of Dense Prediction Priors

Comprehensive panoramic scene understanding is critical for immersive applications, yet it remains challenging due to the scarcity of high-resolution, multi-task annotations. While perspective foundation models have achieved success through data scaling, directly adapting them to the panoramic domain often fails due to severe geometric distortions and coordinate system discrepancies. Furthermore, the underlying relations between diverse dense prediction tasks in spherical spaces are underexplored. To address these challenges, we propose MTPano, a robust multi-task panoramic foundation model established by a label-free training pipeline. First, to circumvent data scarcity, we leverage powerful perspective dense priors. We project panoramic images into perspective patches to generate accurate, domain-gap-free pseudo-labels using off-the-shelf foundation models, which are then re-projected to serve as patch-wise supervision. Second, to tackle the interference between task types, we categorize tasks into rotation-invariant (e.g., depth, segmentation) and rotation-variant (e.g., surface normals) groups. We introduce the Panoramic Dual BridgeNet, which disentangles these feature streams via geometry-aware modulation layers that inject absolute position and ray direction priors. To handle the distortion from equirectangular projections (ERP), we incorporate ERP token mixers followed by a dual-branch BridgeNet for interactions with gradient truncation, facilitating beneficial cross-task information sharing while blocking conflicting gradients from incompatible task attributes. Additionally, we introduce auxiliary tasks (image gradient, point map, etc.) to fertilize the cross-task learning process. Extensive experiments demonstrate that MTPano achieves state-of-the-art performance on multiple benchmarks and delivers competitive results against task-specific panoramic specialist foundation models.