Protein language models (PLMs) are often assumed to capture evolutionary information by training on large protein sequence datasets. Yet it remains unclear whether PLMs can reason about evolution--that is, infer evolutionary relationships between sequences. We test this capability by evaluating whether standard PLM usage, frozen or fine-tuned embeddings with distance-based comparison, supports evolutionary reasoning. Existing PLMs consistently fail to recover phylogenetic structure, despite strong performance on sequence-level tasks such as masked-token and contact prediction. We present Phyla, a hybrid state-space and transformer model that jointly processes multiple sequences and is trained using a tree-based objective across 3,000 phylogenies spanning diverse protein families.

Natural disasters cause devastating damage to communities and infrastructure every year. Effective disaster response is hampered by the difficulty of accessing affected areas during and after events. Remote sensing has allowed us to monitor natural disasters in a remote way. More recently there have been advances in computer vision and deep learning that help automate satellite imagery analysis, However, they remain limited by their narrow focus on specific disaster types, reliance on manual expert interpretation, and lack of datasets with sufficient temporal granularity or natural language annotations for tracking disaster progression. We present MONITRS, a novel multimodal dataset of $\sim$10,000 FEMA disaster events with temporal satellite imagery with natural language annotations from news articles, accompanied by geotagged locations, and question-answer pairs. We demonstrate that fine-tuning existing MLLMs on our dataset yields significant performance improvements for disaster monitoring tasks, establishing a new benchmark for machine learning-assisted disaster response systems.

Deep learning techniques have driven significant progress in various analytical tasks within 3D genomics in computational biology. However, a holistic understanding of 3D genomics knowledge remains underexplored.

Antimicrobial peptides have emerged as promising molecules to combat antimicrobial resistance. However, fragmented datasets, inconsistent annotations, and the lack of standardized benchmarks hinder computational approaches and slow down the discovery of new candidates. To address these challenges, we present the Expanded Standardized Collection for Antimicrobial Peptide Evaluation (ESCAPE), an experimental framework integrating over 80.000 peptides from 27 validated repositories. Our dataset separates antimicrobial peptides from negative sequences and incorporates their functional annotations into a biologically coherent multilabel hierarchy, capturing activities across antibacterial, antifungal, antiviral, and antiparasitic classes. Building on ESCAPE, we propose a transformer-based model that leverages sequence and structural information to predict multiple functional activities of peptides. Our method achieves up to a 2.56% relative average improvement in mean Average Precision over the second-best method adapted for this task, establishing a new state-of-the-art multilabel peptide classification. ESCAPE provides a comprehensive and reproducible evaluation framework to advance AI-driven antimicrobial peptide research.

Dynamic graph modeling aims to uncover evolutionary patterns in real-world systems, enabling accurate social recommendation and early detection of cancer cells. Inspired by the success of recent state space models in efficiently capturing long-term dependencies, we propose DyG-Mamba by translating dynamic graph modeling into a long-term sequence modeling problem. Specifically, inspired by Ebbinghaus' forgetting curve, we treat the irregular timespans between events as control signals, allowing DyG-Mamba to dynamically adjust the forgetting of historical information. This mechanism ensures effective usage of irregular timespans, thereby improving both model effectiveness and inductive capability. In addition, inspired by Ebbinghaus' review cycle, we redefine core parameters to ensure that DyG-Mamba selectively reviews historical information and filters out noisy inputs, further enhancing the model's robustness. Through exhaustive experiments on 12 datasets covering dynamic link prediction and node classification tasks, we show that DyG-Mamba achieves state-of-the-art performance on most datasets, while demonstrating significantly improved computational and memory efficiency.

How precisely does circuit wiring specify function? This fundamental question is particularly relevant for modern neuroscience, as large-scale electron microscopy now enables the reconstruction of neural circuits at single-synapse resolution across many organisms. To interpret circuit function from such datasets, we must understand the extent to which [measured] structure constrains dynamics. We investigate this question in the drosophila head direction (HD) circuit, which maintains an internal heading estimate through attractor dynamics that integrate self-motion velocity cues. This circuit serves as a sensitive assay for functional specification: continuous attractor networks are theoretically known to require finely tuned wiring, whereas connectomes reveal that biological wiring can be variable and omit key cellular parameters such as synaptic gains, neuronal thresholds, and time constants. We introduce a method that combines self-supervised and unsupervised learning objectives to estimate unknown parameters at the level of cell types, rather than individual neurons and synapses. Given the raw connectivity matrix, our approach recovers a network that robustly exhibits continuous attractor dynamics and accurately integrates a range of velocity inputs, despite minimal parameter tuning on a connectome which notably departs from the symmetric regularity of an idealized ring attractor. We characterize how deviations from the original connectome shape the space of viable solutions. We also perform in-silico ablation experiments to probe the distinct functional roles of specific cell types in the circuit, demonstrating how connectome-derived structure, when augmented with minimal, biologically grounded tuning, can replicate known physiology and elucidate circuit function.

Clinical reasoning in medicine is a hypothesis-driven process where physicians refine diagnoses from limited information through targeted history, physical examination, and diagnostic investigations. In contrast, current medical benchmarks for large language models (LLMs) primarily assess knowledge recall through single-turn questions, where complete clinical information is provided upfront. To address this gap, we introduce VivaBench, a multi-turn benchmark that evaluates sequential clinical reasoning in LLM agents. Our dataset consists of 1762 physician-curated clinical vignettes structured as interactive scenarios that simulate a $ \textit{viva voce}$ (oral) examination in medical training, requiring agents to actively probe for relevant findings, select appropriate investigations, and synthesize information across multiple steps to reach a diagnosis. While current LLMs demonstrate competence in diagnosing conditions from well-described clinical presentations, their performance degrades significantly when required to navigate iterative diagnostic reasoning under uncertainty in our evaluation. Our analysis identified several failure modes that mirror common cognitive errors in clinical practice, including: (1) fixation on initial hypotheses, (2) inappropriate investigation ordering, (3) premature diagnostic closure, and (4) failing to screen for critical conditions. These patterns reveal fundamental limitations in how current LLMs reason and make decisions under uncertainty. Through VivaBench, we provide a standardized benchmark for evaluating conversational medical AI systems for real-world clinical decision support. Beyond medical applications, we contribute to the larger corpus of research on agentic AI by demonstrating how sequential reasoning trajectories can diverge in complex decision-making environments.

Generative diffusion models have achieved remarkable success in producing high-quality images. However, these models typically operate in continuous intensity spaces, diffusing independently across pixels and color channels. As a result, they are fundamentally ill-suited for applications involving inherently discrete quantities such as particle counts or material units, that are constrained by strict conservation laws like mass conservation, limiting their applicability in scientific workflows. To address this limitation, we propose Discrete Spatial Diffusion (DSD), a framework based on a continuous-time, discrete-state jump stochastic process that operates directly in discrete spatial domains while strictly preserving particle counts in both forward and reverse diffusion processes. By using spatial diffusion to achieve particle conservation, we introduce stochasticity naturally through a discrete formulation. We demonstrate the expressive flexibility of DSD by performing image synthesis, class conditioning, and image inpainting across standard image benchmarks, while exactly conditioning total image intensity. We validate DSD on two challenging scientific applications: porous rock microstructures and lithium-ion battery electrodes, demonstrating its ability to generate structurally realistic samples under strict mass conservation constraints, with quantitative evaluation using state-of-the-art metrics for transport and electrochemical performance.

Precise, generalizable subject-agnostic seizure prediction (SASP) remains a fundamental challenge due to the intrinsic complexity and significant spectral variability of electrophysiologial signals across individuals and recording modalities. We propose \model{FAPEX}, a novel architecture that introduces a learnable \emph{fractional neural frame operator} (FrNFO) for adaptive time-frequency decomposition. Unlike conventional models that exhibit spectral bias toward low frequencies, our FrNFO employs fractional-order convolutions to capture both high and low-frequency dynamics, achieving approximately $10\%$ improvement in F1-score and sensitivity over state-of-the-art baselines. The FrNFO enables the extraction of \emph{instantaneous phase and amplitude representations} that are particularly informative for preictal biomarker discovery and enhance out-of-distribution generalization.

Multi-Agent Reinforcement Learning (MARL) has achieved remarkable success in various real-world scenarios, but its high cost of online training makes it impractical to learn each task from scratch. To enable effective policy reuse, we consider the problem of zero-shot generalization from offline data across multiple tasks. While prior work focuses on transferring individual skills of agents, we argue that the effective policy transfer across tasks should also capture the team-level coordination knowledge. In this paper, we propose Bi-Level Knowledge Transfer (BiKT) for Multi-Task MARL, which performs knowledge transfer at both the individual and team levels. At the individual level, we extract transferable individual skill embeddings from offline MARL trajectories.