Spatial location and molecular interactions have long been linked to the connectivity patterns of neural circuits. Yet, at the macroscale of human brain networks, the interplay between spatial position, gene expression, and connectivity remains incompletely understood. Recent efforts to map the human transcriptome and connectome have yielded spatially resolved brain atlases, however modeling the relationship between high-dimensional transcriptomic data and connectivity while accounting for inherent spatial confounds presents a significant challenge. In this paper, we present the first deep learning approaches for predicting whole-brain functional connectivity from gene expression and regional spatial coordinates, including our proposed Spatiomolecular Transformer (SMT). SMT explicitly models biological context by tokenizing genes based on their transcription start site (TSS) order to capture multi-scale genomic organization, and incorporating regional 3D spatial location via a dedicated context [CLS] token within its multi-head self-attention mechanism. We rigorously benchmark context-aware neural networks, including SMT and a single-gene resolution Multilayer-Perceptron (MLP), to established rules-based and bilinear methods. Crucially, to ensure that learned relationships in any model are not mere artifacts of spatial proximity, we introduce novel spatiomolecular null maps preserving key transcriptomic autocorrelation structure. Context-aware neural networks outperform linear methods, significantly exceed our stringent null map estimates, and generalize across diverse connectomic datasets and parcellation resolutions. Together, these findings demonstrate a strong, predictable link between the spatial distributions of gene expression and functional brain network architecture, and establish a rigorously validated deep learning framework for decoding this relationship.

Recent advancements in video generation models have enabled the creation of diverse and realistic videos, with promising applications in advertising and film production. However, as one of the essential tasks of video generation models, video concept transfer remains significantly challenging.

Neural population activity exhibits complex, nonlinear dynamics, varying in time, over trials, and across experimental conditions. Here, we develop (CLDS) models as a general-purpose method to characterize these dynamics. These models use Gaussian Process priors to capture the nonlinear dependence of circuit dynamics on task and behavioral variables. Conditioned on these covariates, the data is modeled with linear dynamics. This allows for transparent interpretation and tractable Bayesian inference. We find that CLDS models can perform well even in severely data-limited regimes (e.g. one trial per condition) due to their Bayesian formulation and ability to share statistical power across nearby task conditions. In example applications, we apply CLDS to model thalamic neurons that nonlinearly encode heading direction and to model motor cortical neurons during a cued-reaching task.

Vision Transformers rely on fixed patch tokens that ignore the spatial and semantic structure of images. In this work, we introduce an end-to-end differentiable tokenizer that adapts to image content with pixel-level granularity while remaining backward-compatible with existing architectures for retrofitting pretrained models. Our method uses hierarchical model selection with information criteria to provide competitive performance in both image-level classification and dense-prediction tasks, and even supports out-of-the-box raster-to-vector conversion.

We study the problem of likelihood maximization when the likelihood function is intractable but model simulations are readily available. We propose a sequential, gradient-based optimization method that directly models the Fisher score based on a local score matching technique which uses simulations from a localized region around each parameter iterate. By employing a linear parameterization for the surrogate score model, our technique admits a closed-form, least-squares solution. This approach yields a fast, flexible, and efficient approximation to the Fisher score, effectively smoothing the likelihood objective and mitigating the challenges posed by complex likelihood landscapes. We provide theoretical guarantees for our score estimator, including bounds on the bias introduced by the smoothing. Empirical results on a range of synthetic and real-world problems demonstrate the superior performance of our method compared to existing benchmarks.

Recent progress in Large Vision-Language Models (LVLMs) has enabled promising applications in medical tasks, such as report generation and visual question answering. However, existing benchmarks focus mainly on the final diagnostic answer, offering limited insight into whether models engage in clinically meaningful reasoning. To address this, we present CheXStruct and CXReasonBench, a structured pipeline and benchmark built on the publicly available MIMIC-CXR-JPG dataset. CheXStruct automatically derives a sequence of intermediate reasoning steps directly from chest X-rays, such as segmenting anatomical regions, deriving anatomical landmarks and diagnostic measurements, computing diagnostic indices, and applying clinical thresholds. CXReasonBench leverages this pipeline to evaluate whether models can perform clinically valid reasoning steps and to what extent they can learn from structured guidance, enabling fine-grained and transparent assessment of diagnostic reasoning.The benchmark comprises 18,988 QA pairs across 12 diagnostic tasks and 1,200 cases, each paired with up to 4 visual inputs, and supports multi-path, multi-stage evaluation including visual grounding via anatomical region selection and diagnostic measurements.Even the strongest of 12 evaluated LVLMs struggle with structured reasoning and generalization, often failing to link abstract knowledge with anatomically grounded visual interpretation.

We introduce TRiCo, a novel triadic game-theoretic co-training framework that rethinks the structure of semi-supervised learning by incorporating a teacher, two students, and an adversarial generator into a unified training paradigm. Unlike existing co-training or teacher-student approaches, TRiCo formulates SSL as a structured interaction among three roles: (i) two student classifiers trained on frozen, complementary representations, (ii) a meta-learned teacher that adaptively regulates pseudo-label selection and loss balancing via validation-based feedback, and (iii) a non-parametric generator that perturbs embeddings to uncover decision boundary weaknesses. Pseudo-labels are selected based on mutual information rather than confidence, providing a more robust measure of epistemic uncertainty. This triadic interaction is formalized as a Stackelberg game, where the teacher leads strategy optimization and students follow under adversarial perturbations. By addressing key limitations in existing SSL frameworks--such as static view interactions, unreliable pseudo-labels, and lack of hard sample modeling--TRiCo provides a principled and generalizable solution. Extensive experiments on CIFAR-10, SVHN, STL-10, and ImageNet demonstrate that TRiCo consistently achieves state-of-the-art performance in low-label regimes, while remaining architecture-agnostic and compatible with frozen vision backbones.

Large-scale neural language models exhibit remarkable performance in in-context learning: the ability to learn and reason about the input context on the fly. This work studies in-context counterfactual reasoning in language models, that is, the ability to predict consequences of a hypothetical scenario. We focus on a well-defined, synthetic linear regression task that requires noise abduction. Accurate prediction is based on (1) inferring an unobserved latent concept and (2) copying contextual noise from factual observations. We show that language models are capable of counterfactual reasoning. Further, we enhance existing identifiability results and reduce counterfactual reasoning for a broad class of functions to a transformation on in-context observations.

Counterfactual inference is a powerful tool for analysing and evaluating autonomous agents, but its application to language model (LM) agents remains challenging. Existing work on counterfactuals in LMs has primarily focused on token-level counterfactuals, which are often inadequate for LM agents due to their open-ended action spaces. Unlike traditional agents with fixed, clearly defined action spaces, the actions of LM agents are often implicit in the strings they output, making their action spaces difficult to define and interpret. Furthermore, the meanings of individual tokens can shift depending on the context, adding complexity to token-level reasoning and sometimes leading to biased or meaningless counterfactuals. We introduce \emph{Abstract Counterfactuals}, a framework that emphasises high-level characteristics of actions and interactions within an environment, enabling counterfactual reasoning tailored to user-relevant features. Our experiments demonstrate that the approach produces consistent and meaningful counterfactuals while minimising the undesired side effects of token-level methods. We conduct experiments on text-based games and counterfactual text generation, while considering both token-level and latent-space interventions.

Diffusion models have achieved impressive success in high-fidelity image generation but suffer from slow sampling due to their inherently iterative denoising process. While recent one-step methods accelerate inference by learning direct noise-to-image mappings, they sacrifice the interpretability and fine-grained control intrinsic to diffusion dynamics, key advantages that enable applications like editable generation.