Unlocking deep and interpretable biological reasoning from complex genomic data remains a major AI challenge limiting scientific progress. While current DNA foundation models excel at representing sequences, they struggle with multi-step reasoning and lack transparent, biologically meaningful explanations. BioReason addresses this by tightly integrating a DNA foundation model with a large language model (LLM), enabling the LLM to directly interpret and reason over genomic information. Through supervised fine-tuning and reinforcement learning, BioReason learns to produce logical, biologically coherent deductions. It achieves major performance gains, boosting KEGG-based disease pathway prediction accuracy from 86% to 98% and improving variant effect prediction by an average of 15% over strong baselines. BioReason can reason over unseen biological entities and explain its decisions step by step, offering a transformative framework for interpretable, mechanistic AI in biology. All data, code, and checkpoints are available at https://github.com/bowang-lab/BioReason

The success of the machine learning field has reliably depended on training on large datasets. While effective, this trend comes at an extraordinary cost. This is due to two deeply intertwined factors: the size of models and the size of datasets. While promising research efforts focus on reducing the size of models, the other half of the equation remains fairly mysterious. Indeed, it is surprising that the standard approach to training remains to iterate over and over, uniformly sampling the training dataset. In this paper we explore a series of alternative training paradigms that leverage insights from hard-data-mining and dropout, simple enough to implement and use that can become the new training standard. The proposed Progressive Data Dropout reduces the number of effective epochs to as little as 12.4% of the baseline. This savings actually do not come at any cost for accuracy. Surprisingly, the proposed method improves accuracy by up to 4.82%. Our approach requires no changes to model architecture or optimizer, and can be applied across standard training pipelines, thus posing an excellent opportunity for wide adoption. Code can be found here: https://github.com/bazyagami/LearningWithRevision

World models have recently attracted growing interest in Multi-Agent Reinforcement Learning (MARL) due to their ability to improve sample efficiency for policy learning. However, accurately modeling environments in MARL is challenging due to the exponentially large joint action space and highly uncertain dynamics inherent in multi-agent systems. To address this, we reduce modeling complexity by shifting from jointly modeling the entire state-action transition dynamics to focusing on the state space alone at each timestep through sequential agent modeling. Specifically, our approach enables the model to progressively resolve uncertainty while capturing the structured dependencies among agents, providing a more accurate representation of how agents influence the state. Interestingly, this sequential revelation of agents' actions in a multi-agent system aligns with the reverse process in diffusion models--a class of powerful generative models known for their expressiveness and training stability compared to autoregressive or latent variable models. Leveraging this insight, we develop a flexible and robust world model for MARL using diffusion models. Our method, Diffusion-Inspired Multi-Agent world model (DIMA), achieves state-of-the-art performance across multiple multi-agent control benchmarks, significantly outperforming prior world models in terms of final return and sample efficiency, including MAMuJoCo and Bi-DexHands. DIMA establishes a new paradigm for constructing multi-agent world models, advancing the frontier of MARL research. Codes are open-sourced at https://github.com/breez3young/DIMA.

This work introduces Structured Linear Controlled Differential Equations (SLiCEs), a unifying framework for sequence models with structured, input-dependent state-transition matrices that retain the maximal expressivity of dense matrices whilst being cheaper to compute. The framework encompasses existing architectures, such as input-dependent block-diagonal linear recurrent neural networks and DeltaNet's diagonal-plus-low-rank structure, as well as two novel variants based on sparsity and the Walsh-Hadamard transform. We prove that, unlike the diagonal state-transition matrices of S4D and Mamba, SLiCEs employing block-diagonal, sparse, or Walsh-Hadamard matrices match the maximal expressivity of dense matrices. Empirically, SLiCEs solve the $A_5$ state-tracking benchmark with a single layer, achieve best-in-class length generalisation on regular language tasks among parallel-in-time models, and match the performance of log neural controlled differential equations on six multivariate time-series classification datasets while cutting the average time per training step by a factor of twenty.

Sample-wise learning curves plot performance versus training set size. They are useful for studying scaling laws and speeding up hyperparameter tuning and model selection. Learning curves are often assumed to be well-behaved: monotone (i.e. improving with more data) and convex. By constructing the Learning Curves Database 1.1 (LCDB 1.1), a large-scale database with high-resolution learning curves including more modern learners (CatBoost, TabNet, RealMLP and TabPFN), we show that learning curves are less often well-behaved than previously thought. Using statistically rigorous methods, we observe significant ill-behavior in approximately 15% of the learning curves, almost twice as much as in previous estimates. We also identify which learners are to blame and show that specific learners are more ill-behaved than others. Additionally, we demonstrate that different feature scalings rarely resolve ill-behavior. We evaluate the impact of ill-behavior on downstream tasks, such as learning curve fitting and model selection, and find it poses significant challenges, underscoring the relevance and potential of LCDB 1.1 as a challenging benchmark for future research.

Complex, temporally evolving phenomena, from climate to brain activity, are governed by dynamical systems (DS). DS reconstruction (DSR) seeks to infer generative surrogate models of these from observed data, reproducing their long-term behavior. Existing DSR approaches require purpose-training for any new system observed, lacking the zero-shot and in-context inference capabilities known from LLMs. Here we introduce DynaMix, a novel multivariate ALRNN-based mixture-of-experts architecture pre-trained for DSR, the first DSR model able to generalize zero-shot to out-of-domain DS. Just from a provided context signal, without any re-training, DynaMix faithfully forecasts the long-term evolution of novel DS where existing time series (TS) foundation models, like Chronos, fail -- at a fraction of the number of parameters (0.1%) and orders of magnitude faster inference times. DynaMix outperforms TS foundation models in terms of long-term statistics, and often also short-term forecasts, even on real-world time series, like traffic or weather data, typically used for training and evaluating TS models, but not at all part of DynaMix' training corpus. We illustrate some of the failure modes of TS models for DSR problems, and conclude that models built on DS principles may bear a huge potential also for advancing the TS prediction field.

Imagine hearing a dog bark and turning toward the sound only to see a parked car, while the real, silent dog sits elsewhere. Such sensory conflicts test perception, yet humans reliably resolve them by prioritizing sound over misleading visuals. Despite advances in multimodal AI integrating vision and audio, little is known about how these systems handle cross-modal conflicts or whether they favor one modality. In this study, we systematically examine modality bias and conflict resolution in AI sound localization. We assess leading multimodal models and benchmark them against human performance in psychophysics experiments across six audiovisual conditions, including congruent, conflicting, and absent cues. Humans consistently outperform AI, demonstrating superior resilience to conflicting or missing visuals by relying on auditory information. In contrast, AI models often default to visual input, degrading performance to near chance levels. To address this, we propose a neuroscience-inspired model, EchoPin, which uses a stereo audio-image dataset generated via 3D simulations. Even with limited training data, EchoPin surpasses existing benchmarks. Notably, it also mirrors human-like horizontal localization bias favoring left-right precision-likely due to the stereo audio structure reflecting human ear placement. These findings underscore how sensory input quality and system architecture shape multimodal representation accuracy.

This paper introduces an automated framework WSW2.0 for analyzing vocal interactions in preschool classrooms, enhancing both accuracy and scalability through the integration of wav2vec2-based speaker classification and Whisper (large-v2 and large-v3) speech transcription. A total of 235 minutes of audio recordings (160 minutes from 12 children and 75 minutes from 5 teachers), were used to compare system outputs to expert human annotations. WSW2.0 achieves a weighted F1 score of .845, accuracy of .846, and an error-corrected kappa of .672 for speaker classification (child vs. teacher). Transcription quality is moderate to high with word error rates of .119 for teachers and .238 for children. WSW2.0 exhibits relatively high absolute agreement intraclass correlations (ICC) with expert transcriptions for a range of classroom language features. These include teacher and child mean utterance length, lexical diversity, question asking, and responses to questions and other utterances, which show absolute agreement intraclass correlations between .64 and .98. To establish scalability, we apply the framework to an extensive dataset spanning two years and over 1,592 hours of classroom audio recordings, demonstrating the framework's robustness for broad real-world applications. These findings highlight the potential of deep learning and natural language processing techniques to revolutionize educational research by providing accurate measures of key features of preschool classroom speech, ultimately guiding more effective intervention strategies and supporting early childhood language development.

AI promises personalized learning and scalable education. As AI agents increasingly permeate education in support of teaching and learning, there is a critical and urgent need for data architectures for collecting and analyzing data on learning, and feeding the results back to teachers, learners, and the AI agents for personalization of learning at scale. At the National AI Institute for Adult Learning and Online Education, we are developing an Architecture for AI-Augmented Learning (A4L) for supporting adult learning through online education. We present the motivations, goals, requirements of the A4L architecture. We describe preliminary applications of A4L and discuss how it advances the goals of making learning more personalized and scalable.

We introduce MLRC-Bench, a benchmark designed to quantify how effectively language agents can tackle challenging Machine Learning (ML) Research Competitions, with a focus on open research problems that demand novel methodologies. Unlike prior work, e.g., AI Scientist, which evaluates the end-to-end agentic pipeline by using LLM-as-a-judge, MLRC-Bench measures the key steps of proposing and implementing novel research methods and evaluates them with rigorous protocol and objective metrics. Our curated suite of 7 competition tasks reveals significant challenges for LLM agents. Even the best-performing tested agent (gemini-exp-1206 under MLAB) closes only 9.3% of the gap between baseline and top human participant scores. Furthermore, our analysis reveals a misalignment between the LLM-judged innovation and actual performance on cutting-edge ML research problems. MLRC-Bench is a dynamic benchmark, designed to grow with new ML competitions and encourage rigorous, objective evaluations of AI research capabilities. Our leaderboard and code are available at: https://huggingface.co/spaces/launch/MLRC_Bench