Daily Papers

Large language models (LLMs) are increasingly deployed on long-horizon tasks in partially observable environments, where they must act while inferring and tracking a complex environment state over many steps. This leads to two challenges: partial observability requires maintaining uncertainty over unobserved world attributes, and long interaction history causes context to grow without bound, diluting task-relevant information. A principled solution to both challenges is a belief state: a posterior distribution over environment states given past observations and actions, which compactly encodes history for decision making regardless of episode length. In LLM agents, however, the open-ended nature of text makes it unclear how to represent such a distribution. Therefore, we introduce Agent-BRACE: Agent Belief state Representation via Abstraction and Confidence Estimation, a method that decouples an LLM agent into a belief state model and a policy model, jointly optimized via reinforcement learning. The belief state model produces a structured approximation of the belief distribution: a set of atomic natural language claims about the environment, each annotated with an ordinal verbalized certainty label ranging from certain to unknown. The policy model conditions on this compact, structured approximate belief rather than the full history, learning to select actions under explicit uncertainty. Across long-horizon, partially observable embodied language environments, Agent-BRACE achieves an average absolute improvement of +14.5% (Qwen2.5-3B-Instruct) and +5.3% (Qwen3-4B-Instruct), outperforming strong RL baselines while maintaining a near-constant context window independent of episode length. Further analysis shows that the learned belief becomes increasingly calibrated over the course of an episode as evidence accumulates.

LLM agents increasingly act by writing code, yet a split persists between the runtime that drives the agent and the code the model writes. The runtime owns the loop, context, and control flow, and the model has little say over any of them. Letting model-written code shape the runtime itself would make agents more expressive, but it would also sharpen safety problems. A model can be diverted by a prompt injection, call the wrong tool, or fail partway and leave an inconsistent state, and each such failure reaches further when the code shapes the runtime than when it expresses a single action. We present LACUNA, a programming model for agents that closes this split while preserving safety. Each agent action is a typed call agent[T](task) that the LLM fills with code when execution reaches it, and the code is type-checked against the surrounding program before it runs. Because each action is accepted or rejected as a whole, a rejected one leaves the environment untouched, and its compiler diagnostics drive a retry. The same check also bounds which tools and data an action may use and how they flow. Our primitive expresses ReAct loops, sub-agents, skills, parallel decomposition, and multi-model planning as ordinary control flow. We evaluate LACUNA on a collection of test cases, BrowseComp-Plus, and τ^2-bench. On BrowseComp-Plus, 8.6% of generations are rejected before execution, with 0.7 retries per query on average, and the agent reaches 27.1% accuracy. On τ^2-bench, LACUNA solves 76.0% of 392 tasks across four domains with a capable model, on par with the baseline agent.

Large language model (LLM)-powered agents are increasingly used to plan and execute scientific workflows, yet most research cyberinfrastructure (CI) exposes heterogeneous APIs and implements security models that present barriers for use by agents. We report on our experience using the Model Context Protocol (MCP) as a unifying interface that makes research capabilities discoverable, invokable, and composable. Our approach is pragmatic: we implement thin MCP servers over mature services, including Globus Transfer, Compute, and Search; status APIs exposed by computing facilities; Octopus event fabric; and domain-specific tools such as Garden and Galaxy. We use case studies in computational chemistry, bioinformatics, quantum chemistry, and filesystem monitoring to illustrate how this MCP-oriented architecture can be used in practice. We distill lessons learned and outline open challenges in evaluation and trust for agent-led science.

Language models for scientific tasks are trained on text from scientific publications, most distributed as PDFs that require parsing. PDF parsing approaches range from inexpensive heuristics (for simple documents) to computationally intensive ML-driven systems (for complex or degraded ones). The choice of the "best" parser for a particular document depends on its computational cost and the accuracy of its output. To address these issues, we introduce an Adaptive Parallel PDF Parsing and Resource Scaling Engine (AdaParse), a data-driven strategy for assigning an appropriate parser to each document. We enlist scientists to select preferred parser outputs and incorporate this information through direct preference optimization (DPO) into AdaParse, thereby aligning its selection process with human judgment. AdaParse then incorporates hardware requirements and predicted accuracy of each parser to orchestrate computational resources efficiently for large-scale parsing campaigns. We demonstrate that AdaParse, when compared to state-of-the-art parsers, improves throughput by 17times while still achieving comparable accuracy (0.2 percent better) on a benchmark set of 1000 scientific documents. AdaParse's combination of high accuracy and parallel scalability makes it feasible to parse large-scale scientific document corpora to support the development of high-quality, trillion-token-scale text datasets. The implementation is available at https://github.com/7shoe/AdaParse/

Deduplication is a major focus for assembling and curating training datasets for large language models (LLM) -- detecting and eliminating additional instances of the same content -- in large collections of technical documents. Unrestrained, duplicates in the training dataset increase training costs and lead to undesirable properties such as memorization in trained models or cheating on evaluation. Contemporary approaches to document-level deduplication are often extremely expensive in both runtime and memory. We propose LSHBloom, an extension to MinhashLSH, which replaces the expensive LSHIndex with lightweight Bloom filters. LSHBloom demonstrates the same deduplication performance as MinhashLSH with only a marginal increase in false positives (as low as 1e-5 in our experiments); demonstrates competitive runtime (270\% faster than MinhashLSH on peS2o); and, crucially, uses just 0.6\% of the disk space required by MinhashLSH to deduplicate peS2o. We demonstrate that this space advantage scales with increased dataset size -- at the extreme scale of several billion documents, LSHBloom promises a 250\% speedup and a 54times space advantage over traditional MinHashLSH scaling deduplication of text datasets to many billions of documents.

AI agents that interact with the real world through tool calls pose fundamental safety challenges: agents might leak private information, cause unintended side effects, or be manipulated through prompt injection. To address these challenges, we propose to put the agent in a programming-language-based "safety harness": instead of calling tools directly, agents express their intentions as code in a capability-safe language: Scala 3 with capture checking. Capabilities are program variables that regulate access to effects and resources of interest. Scala's type system tracks capabilities statically, providing fine-grained control over what an agent can do. In particular, it enables local purity, the ability to enforce that sub-computations are side-effect-free, preventing information leakage when agents process classified data. We demonstrate that extensible agent safety harnesses can be built by leveraging a strong type system with tracked capabilities. Our experiments show that agents can generate capability-safe code with no significant loss in task performance, while the type system reliably prevents unsafe behaviors such as information leakage and malicious side effects.

Accurate prediction of atomistic, thermodynamic, and kinetic properties from molecular structures underpins materials innovation. Existing computational and experimental approaches lack the scalability required to efficiently navigate chemical space. Scientific foundation models trained on large unlabeled datasets offer a path toward exploring chemical space across diverse application domains. Here we develop MIST, a family of molecular foundation models with up to an order of magnitude more parameters and data than prior works. Trained using a novel tokenization scheme that comprehensively captures nuclear, electronic, and geometric information, MIST learns from a diverse range of molecules. MIST models have been fine-tuned to predict more than 400 structure -- property relationships and match or exceed state-of-the-art performance across benchmarks spanning physiology, electrochemistry, and quantum chemistry. We demonstrate the ability of these models to solve real-world problems across chemical space, including multiobjective electrolyte solvent screening, olfactory perception mapping, isotope half-life prediction, stereochemical reasoning for chiral organometallic compounds, and binary and multi-component mixture property prediction. Probing MIST models using mechanistic interpretability methods reveals identifiable patterns and trends not explicitly present in the training data, suggesting that the models learn generalizable scientific concepts. We formulate hyperparameter-penalized Bayesian neural scaling laws and use them to reduce the computational cost of model development by an order of magnitude. The methods and findings presented here represent a significant step toward accelerating materials discovery, design, and optimization using foundation models and provide valuable guidance for training compute-optimal scientific foundation models.

Artificial Intelligence models encoding biology and chemistry are opening new routes to high-throughput and high-quality in-silico drug development. However, their training increasingly relies on computational scale, with recent protein language models (pLM) training on hundreds of graphical processing units (GPUs). We introduce the BioNeMo Framework to facilitate the training of computational biology and chemistry AI models across hundreds of GPUs. Its modular design allows the integration of individual components, such as data loaders, into existing workflows and is open to community contributions. We detail technical features of the BioNeMo Framework through use cases such as pLM pre-training and fine-tuning. On 256 NVIDIA A100s, BioNeMo Framework trains a three billion parameter BERT-based pLM on over one trillion tokens in 4.2 days. The BioNeMo Framework is open-source and free for everyone to use.

In the upcoming decade, deep learning may revolutionize the natural sciences, enhancing our capacity to model and predict natural occurrences. This could herald a new era of scientific exploration, bringing significant advancements across sectors from drug development to renewable energy. To answer this call, we present DeepSpeed4Science initiative (deepspeed4science.ai) which aims to build unique capabilities through AI system technology innovations to help domain experts to unlock today's biggest science mysteries. By leveraging DeepSpeed's current technology pillars (training, inference and compression) as base technology enablers, DeepSpeed4Science will create a new set of AI system technologies tailored for accelerating scientific discoveries by addressing their unique complexity beyond the common technical approaches used for accelerating generic large language models (LLMs). In this paper, we showcase the early progress we made with DeepSpeed4Science in addressing two of the critical system challenges in structural biology research.