Detailed Program

Workshop Time: Mon, Aug 26, 2024, 9:00 AM - 1:00 PM
Your Local Time:
Workshop Room: 131 - 132
Zoom Link: https://iu.zoom.us/j/3229975334

Opening, Keynote and Spotlight Talks (9:00 AM - 10:30 AM)

Session Chair: Lyuheng Yuan (Indiana University Bloomington)

9:00 AM - 9:10 AM Opening Remarks by Dr. Jake Chen / Dr. Da Yan

9:10 AM - 10:00 AM Keynote: Advantages of Quantum-Enhanced Generative AI For Biologics Design and Optimization
Christopher Savoie

10:00 AM - 10:05 AM 12. Effectiveness of Cross-linguistic Extraction of Genetic Information using Generative Large Language Models
Milindi Kodikara and Karin Verspoor

10:05 AM - 10:10 AM 22. Adapting Large Language Models to Predict Gene Interactions
Mark Heimann, Christine Klymko and Jayaraman J. Thiagarajan

10:10 AM - 10:15 AM 25. LayLLM: Adapting Large Language Models for Lay Summarization of Biomedical Literature and Clinical Reports
Jieli Zhou and Hongyi Xin

10:15 AM - 10:20 AM 11. HervEVO: Accurate Classification and Generation of Human Endogenous Retroviruses with DNA Foundation Model
Jieli Zhou, Duo Du, Hongyi Xin and Lei Liu

10:20 AM - 10:25 AM 17. scGHSOM: Hierarchical clustering and visualization of single-cell and CRISPR data using growing hierarchical SOM
Shang-Jung Wen, Jia-Ming Chang and Fang Yu

10:25 AM - 10:30 AM 21. A novel approach for predicting breast cancer metastasis through measurement of global transcriptional dysregulation
Tanzira Najnin, Sakhawat H. Saimon, Maryam Zand, Nahim Adnan, Zhijie Liu, Tim H. Huang and Jianhua Ruan

Coffee Break (10:30 AM - 11:00 AM)

Paper Session and Closing Remarks (10:30 AM - 1:05 PM)
Session Chair: Lyuheng Yuan (Indiana University Bloomington)
The session begins in parallel with the coffee break, since we have many papers to present.

10:30 AM - 10:45 AM Late-Breaking: 20. A comprehensive evaluation of large Language models on benchmark biomedical text processing tasks
Israt Jahan, Md Tahmid Rahman Laskar, Chun Peng and Jimmy Huang

10:45 AM - 11:00 AM Research: 3. Could Chemical LLMs benefit from Message Passing
Jiaqing Xie and Ziheng Chi

11:00 AM - 11:15 AM Research: 4. Temporal Subspace Clustering for Molecular Dynamics Data
Anna Beer, Martin Heinrigs, Claudia Plant and Ira Assent

11:15 AM - 11:30 AM Research: 7. Isometry-Preserving Generative Modeling for Spatial Transcriptomics
Wenbin Zhou and Jin-Hong Du

11:30 AM - 11:45 AM Research: 8. gFlora: a topology-aware method to discover functional co-response groups in soil microbial communities
Nan Chen, Merlijn Schram and Doina Bucur

11:45 AM - 12:00 PM Research: 9. Hybrid Deep Learning Framework for Enhanced Melanoma Detection
Peng Zhang and Divya Chaudhary

12:00 PM - 12:15 PM Research: 14. Context-Aware Hierarchical Fusion for Drug Relational Learning
Yijingxiu Lu, Yinhua Piao, Sangseon Lee and Sun Kim

12:15 PM - 12:30 PM Research: 15. Mixture-of-Experts Approach for Enhanced Drug-Target Interaction Prediction and Confidence Assessment
Yijingxiu Lu, Sangseon Lee, Soosung Kang and Sun Kim

12:30 PM - 12:45 PM Research: 23. ACR: A Benchmark for Automatic Cohort Retrieval
Dung Ngoc Thai, Victor Ardulov, Jose Ulises Mena, Simran Tiwari, Gleb Erofeev, Ramy Eskander, Karim Tarabishy, Ravi B Parikh and Wael Salloum

12:45 PM - 1:00 PM Research: 26. Pre-Trained Foundation Model Representations to Uncover Breathing Patterns in Speech
Vikramjit Mitra, Anirban Chatterjee, Ke Zhai, Helen Weng, Ayuko Hill, Nicole Hay, Christopher Webb, Jamie Cheng and Erdrin Azemi

1:00 PM - 1:05 PM Closing Remarks by Dr. Ahmed Abdeen Hamed / Dr. Da Yan

9:00 AM - 9:10 AM	Opening Remarks by Dr. Jake Chen / Dr. Da Yan
9:10 AM - 10:00 AM	Keynote: Advantages of Quantum-Enhanced Generative AI For Biologics Design and Optimization Christopher Savoie
10:00 AM - 10:05 AM	12. Effectiveness of Cross-linguistic Extraction of Genetic Information using Generative Large Language Models Milindi Kodikara and Karin Verspoor
10:05 AM - 10:10 AM	22. Adapting Large Language Models to Predict Gene Interactions Mark Heimann, Christine Klymko and Jayaraman J. Thiagarajan
10:10 AM - 10:15 AM	25. LayLLM: Adapting Large Language Models for Lay Summarization of Biomedical Literature and Clinical Reports Jieli Zhou and Hongyi Xin
10:15 AM - 10:20 AM	11. HervEVO: Accurate Classification and Generation of Human Endogenous Retroviruses with DNA Foundation Model Jieli Zhou, Duo Du, Hongyi Xin and Lei Liu
10:20 AM - 10:25 AM	17. scGHSOM: Hierarchical clustering and visualization of single-cell and CRISPR data using growing hierarchical SOM Shang-Jung Wen, Jia-Ming Chang and Fang Yu
10:25 AM - 10:30 AM	21. A novel approach for predicting breast cancer metastasis through measurement of global transcriptional dysregulation Tanzira Najnin, Sakhawat H. Saimon, Maryam Zand, Nahim Adnan, Zhijie Liu, Tim H. Huang and Jianhua Ruan

10:30 AM - 10:45 AM	Late-Breaking: 20. A comprehensive evaluation of large Language models on benchmark biomedical text processing tasks Israt Jahan, Md Tahmid Rahman Laskar, Chun Peng and Jimmy Huang
10:45 AM - 11:00 AM	Research: 3. Could Chemical LLMs benefit from Message Passing Jiaqing Xie and Ziheng Chi
11:00 AM - 11:15 AM	Research: 4. Temporal Subspace Clustering for Molecular Dynamics Data Anna Beer, Martin Heinrigs, Claudia Plant and Ira Assent
11:15 AM - 11:30 AM	Research: 7. Isometry-Preserving Generative Modeling for Spatial Transcriptomics Wenbin Zhou and Jin-Hong Du
11:30 AM - 11:45 AM	Research: 8. gFlora: a topology-aware method to discover functional co-response groups in soil microbial communities Nan Chen, Merlijn Schram and Doina Bucur
11:45 AM - 12:00 PM	Research: 9. Hybrid Deep Learning Framework for Enhanced Melanoma Detection Peng Zhang and Divya Chaudhary
12:00 PM - 12:15 PM	Research: 14. Context-Aware Hierarchical Fusion for Drug Relational Learning Yijingxiu Lu, Yinhua Piao, Sangseon Lee and Sun Kim
12:15 PM - 12:30 PM	Research: 15. Mixture-of-Experts Approach for Enhanced Drug-Target Interaction Prediction and Confidence Assessment Yijingxiu Lu, Sangseon Lee, Soosung Kang and Sun Kim
12:30 PM - 12:45 PM	Research: 23. ACR: A Benchmark for Automatic Cohort Retrieval Dung Ngoc Thai, Victor Ardulov, Jose Ulises Mena, Simran Tiwari, Gleb Erofeev, Ramy Eskander, Karim Tarabishy, Ravi B Parikh and Wael Salloum
12:45 PM - 1:00 PM	Research: 26. Pre-Trained Foundation Model Representations to Uncover Breathing Patterns in Speech Vikramjit Mitra, Anirban Chatterjee, Ke Zhai, Helen Weng, Ayuko Hill, Nicole Hay, Christopher Webb, Jamie Cheng and Erdrin Azemi
1:00 PM - 1:05 PM	Closing Remarks by Dr. Ahmed Abdeen Hamed / Dr. Da Yan