Search Results for author: Mark Gerstein

Found 17 papers, 9 papers with code

MIMIR: A Streamlined Platform for Personalized Agent Tuning in Domain Expertise

no code implementations3 Apr 2024 Chunyuan Deng, Xiangru Tang, Yilun Zhao, Hanming Wang, Haoran Wang, Wangchunshu Zhou, Arman Cohan, Mark Gerstein

Recently, large language models (LLMs) have evolved into interactive agents, proficient in planning, tool use, and task execution across a wide variety of tasks.

A Survey of Generative AI for De Novo Drug Design: New Frontiers in Molecule and Protein Generation

1 code implementation13 Feb 2024 Xiangru Tang, Howard Dai, Elizabeth Knight, Fang Wu, Yunyang Li, Tianxiao Li, Mark Gerstein

Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models.

ChatCell: Facilitating Single-Cell Analysis with Natural Language

1 code implementation13 Feb 2024 Yin Fang, Kangwei Liu, Ningyu Zhang, Xinle Deng, Penghui Yang, Zhuo Chen, Xiangru Tang, Mark Gerstein, Xiaohui Fan, Huajun Chen

As Large Language Models (LLMs) rapidly evolve, their influence in science is becoming increasingly prominent.

Prioritizing Safeguarding Over Autonomy: Risks of LLM Agents for Science

no code implementations6 Feb 2024 Xiangru Tang, Qiao Jin, Kunlun Zhu, Tongxin Yuan, Yichi Zhang, Wangchunshu Zhou, Meng Qu, Yilun Zhao, Jian Tang, Zhuosheng Zhang, Arman Cohan, Zhiyong Lu, Mark Gerstein

Intelligent agents powered by large language models (LLMs) have demonstrated substantial promise in autonomously conducting experiments and facilitating scientific discoveries across various disciplines.

Igniting Language Intelligence: The Hitchhiker's Guide From Chain-of-Thought Reasoning to Language Agents

1 code implementation20 Nov 2023 Zhuosheng Zhang, Yao Yao, Aston Zhang, Xiangru Tang, Xinbei Ma, Zhiwei He, Yiming Wang, Mark Gerstein, Rui Wang, Gongshen Liu, Hai Zhao

Large language models (LLMs) have dramatically enhanced the field of language intelligence, as demonstrably evidenced by their formidable empirical performance across a spectrum of complex reasoning tasks.

MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning

1 code implementation16 Nov 2023 Xiangru Tang, Anni Zou, Zhuosheng Zhang, Ziming Li, Yilun Zhao, Xingyao Zhang, Arman Cohan, Mark Gerstein

Large language models (LLMs), despite their remarkable progress across various general domains, encounter significant barriers in medicine and healthcare.

Investigating Data Contamination in Modern Benchmarks for Large Language Models

no code implementations16 Nov 2023 Chunyuan Deng, Yilun Zhao, Xiangru Tang, Mark Gerstein, Arman Cohan

Recent observations have underscored a disparity between the inflated benchmark scores and the actual performance of LLMs, raising concerns about potential contamination of evaluation benchmarks.

Common Sense Reasoning Multiple-choice +1

ML-Bench: Evaluating Large Language Models for Code Generation in Repository-Level Machine Learning Tasks

1 code implementation16 Nov 2023 Yuliang Liu, Xiangru Tang, Zefan Cai, Junjie Lu, Yichi Zhang, Yanjun Shao, Zexuan Deng, Helan Hu, Kaikai An, Ruijun Huang, Shuzheng Si, Sheng Chen, Haozhe Zhao, Liang Chen, Yan Wang, Tianyu Liu, Zhiwei Jiang, Baobao Chang, Yujia Qin, Wangchunshu Zhou, Yilun Zhao, Arman Cohan, Mark Gerstein

While Large Language Models (LLMs) have demonstrated proficiency in code generation benchmarks, translating these results into practical development scenarios - where leveraging existing repository-level libraries is the norm - remains challenging.

Code Generation Navigate

Struc-Bench: Are Large Language Models Really Good at Generating Complex Structured Data?

1 code implementation16 Sep 2023 Xiangru Tang, Yiming Zong, Jason Phang, Yilun Zhao, Wangchunshu Zhou, Arman Cohan, Mark Gerstein

Despite the remarkable capabilities of Large Language Models (LLMs) like GPT-4, producing complex, structured tabular data remains challenging.

Hallucination

BioCoder: A Benchmark for Bioinformatics Code Generation with Contextual Pragmatic Knowledge

1 code implementation31 Aug 2023 Xiangru Tang, Bill Qian, Rick Gao, Jiakang Chen, Xinyun Chen, Mark Gerstein

This is evident from the performance gain of GPT-3. 5/4 compared to the smaller models on the benchmark (50% vs up to ~25%).

Code Generation

Scalable privacy-preserving cancer type prediction with homomorphic encryption

no code implementations12 Apr 2022 Esha Sarkar, Eduardo Chielle, Gamze Gursoy, Leo Chen, Mark Gerstein, Michail Maniatakos

Privacy concerns in outsourced ML, especially in the field of genetics, motivate the use of encrypted computation, like Homomorphic Encryption (HE).

Decision Making feature selection +3

Higher-Order Generalization Bounds: Learning Deep Probabilistic Programs via PAC-Bayes Objectives

no code implementations30 Mar 2022 Jonathan Warrell, Mark Gerstein

Here, we offer a framework for representing and learning flexible PAC-Bayes bounds as stochastic programs using DPP-based methods.

Generalization Bounds Meta-Learning +1

Hybrid Quantum-Classical Stochastic Networks with Boltzmann Layers

no code implementations1 Jan 2021 Jonathan H Warrell, Prashant Emani, Mark Gerstein

Quantum Machine Learning (QML) has the potential to significantly advance the state-of-the-art in artificial intelligence, due to recent developments in quantum computing hardware and algorithm design.

Quantum Machine Learning

Rank Projection Trees for Multilevel Neural Network Interpretation

no code implementations1 Dec 2018 Jonathan Warrell, Hussein Mohsen, Mark Gerstein

A variety of methods have been proposed for interpreting nodes in deep neural networks, which typically involve scoring nodes at lower layers with respect to their effects on the output of higher-layer nodes (where lower and higher layers are closer to the input and output layers, respectively).

Network Interpretation

Cannot find the paper you are looking for? You can Submit a new open access paper.