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Yanjun Shao

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

3 papers
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3

ICLR Conference 2025 Conference Paper

ChemAgent: Self-updating Memories in Large Language Models Improves Chemical Reasoning

  • Xiangru Tang
  • Tianyu Hu
  • Muyang Ye
  • Yanjun Shao
  • Xunjian Yin
  • Siru Ouyang
  • Wangchunshu Zhou
  • Pan Lu

Chemical reasoning usually involves complex, multi-step processes that demand precise calculations, where even minor errors can lead to cascading failures. Furthermore, large language models (LLMs) encounter difficulties handling domain-specific formulas, executing reasoning steps accurately, and integrating code ef- effectively when tackling chemical reasoning tasks. To address these challenges, we present ChemAgent, a novel framework designed to improve the performance of LLMs through a dynamic, self-updating library. This library is developed by decomposing chemical tasks into sub-tasks and compiling these sub-tasks into a structured collection that can be referenced for future queries. Then, when presented with a new problem, ChemAgent retrieves and refines pertinent information from the library, which we call memory, facilitating effective task decomposition and the generation of solutions. Our method designs three types of memory and a library-enhanced reasoning component, enabling LLMs to improve over time through experience. Experimental results on four chemical reasoning datasets from SciBench demonstrate that ChemAgent achieves performance gains of up to 46% (GPT-4), significantly outperforming existing methods. Our findings suggest substantial potential for future applications, including tasks such as drug discovery and materials science. Our code can be found at https://github.com/gersteinlab/ChemAgent.

ICLR Conference 2025 Conference Paper

OpenHands: An Open Platform for AI Software Developers as Generalist Agents

  • Xingyao Wang 0002
  • Boxuan Li
  • Yufan Song
  • Frank F. Xu
  • Xiangru Tang
  • Mingchen Zhuge
  • Jiayi Pan
  • Yueqi Song

Software is one of the most powerful tools that we humans have at our disposal; it allows a skilled programmer to interact with the world in complex and profound ways. At the same time, thanks to improvements in large language models (LLMs), there has also been a rapid development in AI agents that interact with and effect change in their surrounding environments. In this paper, we introduce OpenHands, a platform for the development of powerful and flexible AI agents that interact with the world in similar ways to a human developer: by writing code, interacting with a command line, and browsing the web. We describe how the platform allows for the implementation of new agents, utilization of various LLMs, safe interaction with sandboxed environments for code execution, and incorporation of evaluation benchmarks. Based on our currently incorporated benchmarks, we perform an evaluation of agents over 13 challenging tasks, including software engineering (e.g., SWE-Bench) and web browsing (e.g., WebArena), amongst others. Released under the permissive MIT license, OpenHands is a community project spanning academia and industry with more than 2K contributions from over 186 contributors in less than six months of development, and will improve going forward.

ICLR Conference 2025 Conference Paper

Revisiting Convolution Architecture in the Realm of DNA Foundation Models

  • Yu Bo
  • Weian Mao
  • Yanjun Shao
  • Weiqiang Bai
  • Peng Ye 0006
  • Xinzhu Ma
  • Junbo Zhao
  • Hao Chen 0041

In recent years, A variety of methods based on Transformer and state space model (SSM) architectures have been proposed, advancing foundational DNA language models. However, there is a lack of comparison between these recent approaches and the classical architecture—convolutional networks (CNNs)—on foundation model benchmarks. This raises the question: are CNNs truly being surpassed by these recent approaches based on transformer and SSM architectures? In this paper, we develop a simple but well-designed CNN-based method, termed ConvNova. ConvNova identifies and proposes three effective designs: 1) dilated convolutions, 2) gated convolutions, and 3) a dual-branch framework for gating mechanisms. Through extensive empirical experiments, we demonstrate that ConvNova significantly outperforms recent methods on more than half of the tasks across several foundation model benchmarks. For example, in histone-related tasks, ConvNova exceeds the second-best method by an average of 5.8\%, while generally utilizing fewer parameters and enabling faster computation. In addition, the experiments observed findings that may be related to biological characteristics. This indicates that CNNs are still a strong competitor compared to Transformers and SSMs. We anticipate that this work will spark renewed interest in CNN-based methods for DNA foundation models.

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