Thought Graph: Generating Thought Process for Biological Reasoning

no code implementations • 11 Mar 2024 • Chi-Yang Hsu, Kyle Cox, Jiawei Xu, Zhen Tan, Tianhua Zhai, Mengzhou Hu, Dexter Pratt, Tianlong Chen, Ziniu Hu, Ying Ding

We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes.

Evaluation of large language models for discovery of gene set function

1 code implementation • 7 Sep 2023 • Mengzhou Hu, Sahar Alkhairy, Ingoo Lee, Rudolf T. Pillich, Dylan Fong, Kevin Smith, Robin Bachelder, Trey Ideker, Dexter Pratt

Gene set analysis is a mainstay of functional genomics, but it relies on curated databases of gene functions that are incomplete.

Benchmarking Language Modelling +1

Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing

no code implementations • 24 May 2023 • Andreas Maier, Michael Hartung, Mark Abovsky, Klaudia Adamowicz, Gary D. Bader, Sylvie Baier, David B. Blumenthal, Jing Chen, Maria L. Elkjaer, Carlos Garcia-Hernandez, Mohamed Helmy, Markus Hoffmann, Igor Jurisica, Max Kotlyar, Olga Lazareva, Hagai Levi, Markus List, Sebastian Lobentanzer, Joseph Loscalzo, Noel Malod-Dognin, Quirin Manz, Julian Matschinske, Miles Mee, Mhaned Oubounyt, Alexander R. Pico, Rudolf T. Pillich, Julian M. Poschenrieder, Dexter Pratt, Nataša Pržulj, Sepideh Sadegh, Julio Saez-Rodriguez, Suryadipto Sarkar, Gideon Shaked, Ron Shamir, Nico Trummer, Ugur Turhan, Ruisheng Wang, Olga Zolotareva, Jan Baumbach

In recent decades, the development of new drugs has become increasingly expensive and inefficient, and the molecular mechanisms of most pharmaceuticals remain poorly understood.

Drug Discovery