ACCEPTED PAPERS

• Understanding the Natural Language of DNA using Encoder-Decoder Foundation Models with Byte-level Precision

  Aditya Malusare, Harish Kothandaraman, Dipesh Tamboli, Nadia A. Lanman, Vaneet Aggarwal

• DrugAgent: Automating AI-aided Drug Discovery Programming through LLM Multi-Agent Collaboration

  Sizhe Liu, Yizhou Lu, Siyu Chen, Xiyang Hu, Jieyu Zhao, Tianfan Fu, Yue Zhao

• AbAffinity: A Large Language Model for Predicting Antibody Binding Affinity against SARS-CoV-2

  Faisal Bin Ashraf, Animesh Ray, Stefano Lonardi

• Foundation Models for AI-enabled Biological Design

  Asher Moldwin, Amarda Shehu

• Scalable DNA Feature Generation and Transcription Factor Binding Prediction via Deep Surrogate Models

  Anowarul Kabir, Toki Tahmid Inan, Kim Rasmussen, Amarda Shehu, Anny Usheva, Alan Bishop, Boian Alexandrov, Manish Bhattarai

• Efficient High-Throughput DNA Breathing Features Generation Using Jax-EPBD

  Toki Tahmid Inan, Anowarul Kabir, Kim Rasmussen, Amarda Shehu, Anny Usheva, Alan Bishop, Boian Alexandrov, Manish Bhattarai

• Position Paper Towards Automated Biological Discovery: LLM-based Multi-Agent AI System for Single-Cell Disease Marker Identification and Discovery

  Jieli Zhou, Luting Zhou, Hongyi Xin

• DeepAge: Harnessing Deep Neural Network for Epigenetic Age Estimation From DNA Methylation Data of Human Blood Samples

  Sajib Acharjee Dip, Da Ma, Liqing Zhang

• PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation Model

  Sajib Acharjee Dip, Uddip Acharjee Shuvo, Tran Chau, Haoqiu Song, Petra Choi, Xuan Wang, Liqing Zhang

• Energy Efficient Protein Language Models: Leveraging Small Language Models with LoRA for Controllable Protein Generation

  Aayush Shah, Shankar Jayaratnam

• Multi-Omic Integration for Breast Cancer Subtype Classification Using Advanced AI Techniques

  Sajib Acharjee Dip, Liqing Zhang

• Transformer-Based Approach for Automated Functional Group Replacement in Chemical Compounds

  Bo Pan, Zhiping Zhang, Kevin Spiekermann, Tianchi Chen, Xiang Yu, Liying Zhang, Liang Zhao

• Leveraging Multi-modal Representations to Predict Protein Melting Temperatures

  Daiheng Zhang, Yan Zeng, Xinyu Hong, Jinbo Xu