Aviary: training language agents on challenging scientific tasks

Solving complex real-world tasks requires cycles of actions and observations. This is particularly true in science, where tasks require many cycles of analysis, tool use, and experimentation. Language agents are promising for automating intellectual tasks in science because they can interact with tools via natural language or code. Yet their flexibility creates conceptual and practical challenges for software implementations, since agents may comprise non-standard components such as internal reasoning, planning, tool usage, as well as the inherent stochasticity of temperature-sampled language models. Here, we introduce Aviary, an extensible gymnasium for language agents. We formalize agents as policies solving language-grounded partially observable Markov decision processes, which we term language decision processes. We then implement five environments, including three challenging scientific environments: (1) manipulating DNA constructs for molecular cloning, (2) answering research questions by accessing scientific literature, and (3) engineering protein stability. These environments were selected for their focus on multi-step reasoning and their relevance to contemporary biology research. Finally, with online training and scaling inference-time compute, we show that language agents backed by open-source, non-frontier LLMs can match and exceed both frontier LLM agents and human experts on multiple tasks at up to 100x lower inference cost.

Reinforcement learning on structure-conditioned categorical diffusion for protein inverse folding

Protein inverse folding-that is, predicting an amino acid sequence that will fold into the desired 3D structure-is an important problem for structure-based protein design. Machine learning based methods for inverse folding typically use recovery of the original sequence as the optimization objective. However, inverse folding is a one-to-many problem where several sequences can fold to the same structure. Moreover, for many practical applications, it is often desirable to have multiple, diverse sequences that fold into the target structure since it allows for more candidate sequences for downstream optimizations. Here, we demonstrate that although recent inverse folding methods show increased sequence recovery, their "foldable diversity"-i.e. their ability to generate multiple non-similar sequences that fold into the structures consistent with the target-does not increase. To address this, we present RL-DIF, a categorical diffusion model for inverse folding that is pre-trained on sequence recovery and tuned via reinforcement learning on structural consistency. We find that RL-DIF achieves comparable sequence recovery and structural consistency to benchmark models but shows greater foldable diversity: experiments show RL-DIF can achieve an foldable diversity of 29% on CATH 4.2, compared to 23% from models trained on the same dataset. The PyTorch model weights and sampling code are available on GitHub.

LAB-Bench: Measuring Capabilities of Language Models for Biology Research

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and reasoning on textbook-style science questions, but few if any benchmarks are designed to evaluate language model performance on practical tasks required for scientific research, such as literature search, protocol planning, and data analysis. As a step toward building such benchmarks, we introduce the Language Agent Biology Benchmark (LAB-Bench), a broad dataset of over 2,400 multiple choice questions for evaluating AI systems on a range of practical biology research capabilities, including recall and reasoning over literature, interpretation of figures, access and navigation of databases, and comprehension and manipulation of DNA and protein sequences. Importantly, in contrast to previous scientific benchmarks, we expect that an AI system that can achieve consistently high scores on the more difficult LAB-Bench tasks would serve as a useful assistant for researchers in areas such as literature search and molecular cloning. As an initial assessment of the emergent scientific task capabilities of frontier language models, we measure performance of several against our benchmark and report results compared to human expert biology researchers. We will continue to update and expand LAB-Bench over time, and expect it to serve as a useful tool in the development of automated research systems going forward. A public subset of LAB-Bench is available for use at the following URL: https://huggingface.co/datasets/futurehouse/lab-bench