We introduce a comprehensive framework for modeling single cell transcriptomic responses to perturbations, aimed at standardizing benchmarking in this rapidly evolving field. Our approach includes a modular and user-friendly model development and evaluation platform, a collection of diverse perturbational datasets, and a set of metrics designed to fairly compare models and dissect their performance. Through extensive evaluation of both published and baseline models across diverse datasets, we highlight the limitations of widely used models, such as mode collapse. We also demonstrate the importance of rank metrics which complement traditional model fit measures, such as RMSE, for validating model effectiveness. Notably, our results show that while no single model architecture clearly outperforms others, simpler architectures are generally competitive and scale well with larger datasets. Overall, this benchmarking exercise sets new standards for model evaluation, supports robust model development, and furthers the use of these models to simulate genetic and chemical screens for therapeutic discovery.

Large reasoning models (LRMs) excel at complex reasoning tasks but typically generate lengthy sequential chains-of-thought, resulting in long inference times before arriving at the final answer. To address this challenge, we introduce SPRINT, a novel post-training and inference-time framework designed to enable LRMs to dynamically identify and exploit opportunities for parallelization during their reasoning process. SPRINT incorporates an innovative data curation pipeline that reorganizes natural language reasoning trajectories into structured rounds of longhorizon planning and parallel execution. By fine-tuning LRMs on a small amount of such curated data, the models learn to dynamically identify independent subtasks within extended reasoning processes and effectively execute them in parallel. Through extensive evaluations, we demonstrate that models fine-tuned with the SPRINT framework match the performance of reasoning models on complex domains such as mathematics while generating up to 39% fewer sequential tokens on problems requiring more than 8,000 output tokens. Finally, we observe consistent results transferred to two out-of-distribution tasks, namely GPQA and Countdown, with up to 45% and 65% reduction in average sequential tokens respectively for longer reasoning trajectories, while matching the performance of the fine-tuned reasoning model.

Recurrent neural networks (RNNs) trained on neuroscience-inspired tasks offer powerful models of brain computation. However, typical training paradigms rely on open-loop, supervised settings, whereas real-world learning unfolds in closed-loop environments. Here, we develop a mathematical theory describing the learning dynamics of linear RNNs trained in closed-loop contexts. We first demonstrate that two otherwise identical RNNs, trained in either closed-or open-loop modes, follow markedly different learning trajectories. To probe this divergence, we analytically characterize the closed-loop case, revealing distinct stages aligned with the evolution of the training loss. Specifically, we show that the learning dynamics of closed-loop RNNs, in contrast to open-loop ones, are governed by an interplay between two competing objectives: short-term policy improvement and long-term stability of the agent-environment interaction. Finally, we apply our framework to a realistic motor control task, highlighting its broader applicability. Taken together, our results underscore the importance of modeling closed-loop dynamics in a biologically plausible setting.

Direct Preference Optimization (DPO) is a key framework for aligning text-to-image models with human preferences, extended by Stepwise Preference Optimization (SPO) to leverage intermediate steps for preference learning, generating more aesthetically pleasing images with significantly less computational cost.

Uncovering cause-effect relationships from observational time series is fundamental to understanding complex systems. While many methods infer static causal graphs, real-world systems often exhibit dynamic causality--where relationships evolve over time. Accurately capturing these temporal dynamics requires time-resolved causal graphs. We propose UnCLe, a novel deep learning method for scalable dynamic causal discovery. UnCLe employs a pair of Uncoupler and Recoupler networks to disentangle input time series into semantic representations and learns inter-variable dependencies via auto-regressive Dependency Matrices. It estimates dynamic causal influences by analyzing datapoint-wise prediction errors induced by temporal perturbations. Extensive experiments demonstrate that UnCLe not only outperforms state-of-the-art baselines on static causal discovery benchmarks but, more importantly, exhibits a unique capability to accurately capture and represent evolving temporal causality in both synthetic and real-world dynamic systems (e.g., human motion). UnCLe offers a promising approach for revealing the underlying, time-varying mechanisms of complex phenomena.

When do diffusion models reproduce their training data, and when are they able to generate samples beyond it?

Encoding models using word embeddings or artificial neural network (ANN) features reliably predict brain responses to naturalistic stimuli, yet interpreting these models remains challenging. A central limitation is superposition: distinct semantic features become entangled along correlated directions in dense embeddings when latent features outnumber embedding dimensions. This entanglement renders regression weights non-identifiable--different combinations of semantic directions can produce identical predictions, precluding principled interpretation of voxel selectivity. To address this, we introduce the Sparse Concept Encoding Model, which transforms dense embeddings into a higher-dimensional, sparse, non-negative space of learned concept atoms.

As language models scale, their performance improves dramatically across a wide range of tasks, but so does their tendency to memorize and regurgitate parts of their training data verbatim. This tradeoff poses serious legal, ethical, and safety concerns, especially in real-world deployments. Existing mitigation techniques, such as differential privacy or model unlearning, often require retraining or access to internal weights making them impractical for most users. In this work, we introduce TOKENSWAP, a lightweight, post-hoc defense designed for realistic settings where the user can only access token-level outputs. Our key insight is that while large models are necessary for high task performance, small models (e.g., DistilGPT-2) are often sufficient to assign fluent, grammatically plausible probabilities to common function words - and crucially, they memorize far less. By selectively swapping token probabilities between models, TOKENSWAP preserves the capabilities of large models while reducing their propensity for verbatim reproduction.

Recent Graphical User Interface (GUI) agents replicate the R1-Zero paradigm, coupling online Reinforcement Learning (RL) with explicit chain-of-thought reasoning prior to object grounding and thereby achieving substantial performance gains.

Retrieval-Augmented Generation (RAG) based on knowledge graphs (KGs) enhances large language models (LLMs) with structural and textual external knowledge. Yet, existing KG-based RAG methods struggle to retrieve accurate and diverse information when handling complex queries. By modeling KG-based retrieval as a multi-step decision process, Process Reward Models (PRMs) offer a promising solution to align the retrieval behavior with the query-specific knowledge requirements. However, PRMs heavily rely on process-level supervision signals that are expensive and hard to obtain on KGs. To address this challenge, we propose GraphFlow, a framework that efficiently retrieves accurate and diverse knowledge required for complex queries from text-rich KGs. GraphFlow employs a detailed balance objective with local exploration to jointly optimize a retrieval policy and a flow estimator.