The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Synthetic tabular data enables microdata sharing in regulated domains, yet deploying continuous-time generative models requires balancing analytical utility, disclosure risk, and computational cost. Latent-space flow models are flexible, but theoretical equivalences across learning targets, probability paths, and sampling dynamics can translate into different behaviour under finite-step integration and explicit compute budgets. We present an empirical study of tabular latent flow models across seven datasets, evaluating velocity, score, noise, and posterior matching objectives under optimal transport (OT) and variance-preserving (VP) paths, ODE and SDE sampling, and varying integration budgets. Our contributions are threefold: (1) we show that the learning target largely determines the utility-risk operating regime, with velocity and posterior matching tending to yield higher utility, while score and noise matching tend to achieve lower disclosure risk; (2) we demonstrate that configuration and sampling choices shift performance, with midpoint often improving distributional fidelity and OT paths often tolerating earlier stopping than VP, enabling compute savings under fixed budgets or risk thresholds; and (3) we distil these findings into actionable defaults and practical configuration guidance to support pre-release model selection under disclosure risk and resource constraints. The code implementation and supplementary materials can be accessed in https://github.com/rulnasution/tabular-latent-flow/.

However, their widespread adoption is hindered by critical limitations, such as low information transfer rates and extensive user-specific calibration. To overcome these challenges, recent research has explored the integration of Large Language Models (LLMs), extending the focus from simple command decoding to understanding complex cognitive states. Despite these advancements, deploying agentic AI faces technical hurdles and ethical concerns. Due to the lack of comprehensive discussion on this emerging direction, this position paper argues that the field is poised for a paradigm extension from BCI to Brain-Agent Collaboration (BAC). We emphasize reframing agents as active and collaborative partners for intelligent assistance rather than passive brain signal data processors, demanding a focus on ethical data handling, model reliability, and a robust human-agent collaboration framework to ensure these systems are safe, trustworthy, and effective.

Understanding cellular responses to chemical interventions is critical to the discovery of effective therapeutics. Because individual biological techniques often measure only one axis of cellular response at a time, high-quality multimodal datasets are needed to unlock a holistic understanding of how cells respond to treatments and to advance computational methods that integrate modalities. However, many techniques destroy cells and thus preclude paired measurements, and attempts to match disparate unimodal datasets are often confounded by data being generated in incompatible experimental settings. Here we introduce scGeneScope, a multimodal single-cell RNA sequencing (scRNA-seq) and Cell Painting microscopy image dataset conditionally paired by chemical treatment, designed to facilitate the development and benchmarking of unimodal, multimodal, and multiple profile machine learning methods for cellular profiling.

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 the 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 symmetries, whereas connectomes omit key cellular parameters such as synaptic gains, neuronal thresholds, and time constants, and reveal that biological wiring can be heterogeneous. We introduce a method that combines selfsupervised and unsupervised learning objectives to estimate unknown parameters at the level of cell types, rather than individual neurons and synapses. Starting from the raw connectivity matrix, our approach recovers a network that exhibits continuous attractor dynamics and accurately integrates a range of velocity inputs, despite minimal parameter tuning on a connectome that 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.

Designing optimal Bayes filters for nonlinear non-Gaussian systems is a challenging task. The main difficulties are: 1) representing complex beliefs, 2) handling non-Gaussian noise, and 3) marginalizing past states. To address these challenges, we focus on polynomial systems and propose the Max Entropy Moment Kalman Filter (MEM-KF). To address 1), we represent arbitrary beliefs by a MomentConstrained Max-Entropy Distribution (MED). The MED can asymptotically approximate almost any distribution given an increasing number of moment constraints. To address 2), we model the noise in the process and observation model as MED. To address 3), we propagate the moments through the process model and recover the distribution as MED, thus avoiding symbolic integration, which is generally intractable. All the steps in MEM-KF, including the extraction of a point estimate, can be solved via convex optimization.

Testing hypotheses on how representational changes occur in biological systems is challenging, but large language models (LLMs) offer a scalable alternative. Building on LLMs' in-context learning, we adapt a cognitive neuroscience associative learning paradigm and investigate how representations evolve across six models. Our initial findings reveal a non-monotonic pattern consistent with the Non-Monotonic Plasticity Hypothesis, with moderately similar items differentiating after learning. Leveraging the controllability of LLMs, we further show that this differentiation is modulated by the overlap of associated items with the broader vocabulary-a factor we term vocabulary interference, capturing how new associations compete with prior knowledge. We find that higher vocabulary interference amplifies differentiation, suggesting that representational change is influenced by both item similarity and global competition.

Sparse inertial measurement units (IMUs) provide a portable, low-cost solution for human motion tracking but struggle with error accumulation from drift and sensor noise when estimating joint position through time-based linear acceleration integration (i.e., indirect measurement). To address this, we propose ToF-IP, a novel 3D full-body pose estimation system that integrates Time-of-Flight (ToF) sensors with sparse IMUs. The distinct advantage of our approach is that ToF sensors provide direct distance measurements, effectively mitigating error accumulation without relying on indirect time-based integration. From a hardware perspective, we maintain the portability of existing solutions by attaching ToF sensors to selected IMUs with a negligible volume increase of just 3%. On the software side, we introduce two novel techniques to enhance multi-sensor integration: (i) a NodeCentric Data Integration strategy that leverages a Transformer encoder to explicitly model both intra-node and inter-node data integration by treating each sensing node as a token; and (ii) a Dynamic Spatial Positional Encoding scheme that encodes the continuously changing spatial positions of wearable nodes as motion-conditioned functions, enabling the model to better capture human body dynamics in the embedding space. Additionally, we contribute a 208-minute human motion dataset from 10 participants, including synchronized IMU-ToF measurements and groundtruth from optical tracking. Extensive experiments demonstrate that our method outperforms state-of-the-art approaches such as PNP, achieving superior accuracy in tracking complex and slow motions like Tai Chi, which remains challenging for inertial-only methods.

Contextual Markov Decision Processes (cMDP) model this challenge, but existing methods often require explicit context variables (e.g., friction, gravity), limiting their use when contexts are latent or hard to measure. We introduce Dynamics-Aligned Latent Imagination (DALI), a framework integrated within the Dreamer architecture that infers latent context representations from agent-environment interactions. By training a self-supervised encoder to predict forward dynamics, DALI generates actionable representations conditioning the world model and policy, bridging perception and control. We theoretically prove this encoder is essential for efficient context inference and robust generalization. DALI's latent space enables counterfactual consistency: Perturbing a gravity-encoding dimension alters imagined rollouts in physically plausible ways. On challenging cMDP benchmarks, DALI achieves significant gains over contextunaware baselines, often surpassing context-aware baselines in extrapolation tasks, enabling zero-shot generalization to unseen contextual variations.

Audio-visual understanding is a rapidly evolving field that seeks to integrate and interpret information from both auditory and visual modalities. Despite recent advances in multi-modal learning, existing benchmarks often suffer from strong visual bias - when answers can be inferred from visual data alone - and provide only aggregate scores that conflate multiple sources of error. This makes it difficult to determine whether models struggle with visual understanding, audio interpretation, or audio-visual alignment. In this work, we introduce DAVE (Diagnostic Audio Visual Evaluation), a novel benchmark dataset designed to systematically evaluate audio-visual models across controlled settings. DAVE alleviates existing limitations by (i) ensuring both modalities are necessary to answer correctly and (ii) decoupling evaluation into atomic subcategories. Our detailed analysis of state-of-the-art models reveals specific failure modes and provides targeted insights for improvement. By offering this standardized diagnostic framework, we aim to facilitate more robust development of audio-visual models.