NeurIPS 2025 Workshop AI4D3 Submissions

MoAgent: A Hypothesis-Driven Multi-Agent Framework for Drug Mechanism of Action Discovery
Jun Hyeong Kim, Seokhyun Moon, Seonghwan Kim, Junhyeok Jeon, Taein Kim, Jisu Seo, Songmi Kim, Woo Youn Kim
- Published: 23 Sept 2025, Last Modified: 17 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
Cross-Species Graph Neural Network for Translating Animal Disease Resistance to Human Drug Targets
Deek Guruge, Michelle M Li, Natalie DeForest, Phil McNamara, Manashvi Borad, Linda B. Goodman
- Published: 23 Sept 2025, Last Modified: 26 Sept 2025
- AI4D3 2025 Poster
- Readers: Everyone
Constrained Molecular Generation with Discrete Diffusion for Drug Discovery
Michael Cardei, Jacob K Christopher, Bhavya Kailkhura, Thomas Hartvigsen, Ferdinando Fioretto
- Published: 23 Sept 2025, Last Modified: 13 Oct 2025
- AI4D3 2025 Oral
- Readers: Everyone
Patient-level prediction from single-cell data using attention-based multiple instance learning with regulatory priors
Kristin C. Y. Tsui, Kameron B. Rodrigues, Xianghao Zhan, Yiyun Chen, Kelvin C. Mo, Crystal L. Mackall, David B Miklos, Olivier Gevaert, Zinaida Good
- Published: 23 Sept 2025, Last Modified: 18 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
Early Prediction of Overall Survival in Oncology Trials Using Tumor Dynamic Neural-ODE
Gengbo Liu, Victor Poon, Omid Bazgir, Phyllis Chan, Kenta Yoshida, Chanu Pascal
- Published: 23 Sept 2025, Last Modified: 15 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
Label-free biochemical imaging of neural organoids via deep learning-enhanced Raman microspectroscopy
Dimitar Georgiev, Ruoxiao Xie, Daniel Reumann, Xiaoyu Zhao, Álvaro Fernández-Galiana, Mauricio Barahona, Molly M. Stevens
- Published: 23 Sept 2025, Last Modified: 17 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
High-Throughput Protein Perturbation Screens with AI-Designed Degraders
Lin Zhao, Aastha Pal, Tong Chen, Pranam Chatterjee
- Published: 23 Sept 2025, Last Modified: 17 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
Improving Classification of Cell Types in Acute Myeloid Leukemia with Self-guided Masking Technique
Amirreza Naziri, Arash Asgari, Eleftherios Sachlos, Aijun An, Laleh Seyyed-Kalantari
- Published: 23 Sept 2025, Last Modified: 30 Sept 2025
- AI4D3 2025 Poster
- Readers: Everyone
Beyond Atoms: Evaluating Electron Density Representation for 3D Molecular Learning
Patricia Adriana Suriana, Joshua A Rackers, Ewa Nowara, Pedro O. Pinheiro, Vishnu Sresht, John M Nicoludis
- Published: 23 Sept 2025, Last Modified: 16 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
D-Flow: Multi-modality Flow Matching for D-peptide Design
Fang Wu, Shuting Jin, Xiangru Tang, Junlin Xu, James Zou, Mark Gerstein
- Published: 23 Sept 2025, Last Modified: 29 Sept 2025
- AI4D3 2025 Poster
- Readers: Everyone
PatchDNA: A Flexible and Biologically-Informed Alternative to Tokenization for DNA
Alice Del Vecchio, Chantriolnt-Andreas Kapourani, Abdullah M Athar, Agnieszka Dobrowolska, Andrew Anighoro, Benjamin Tenmann, Lindsay Edwards, Cristian Regep
- Published: 23 Sept 2025, Last Modified: 26 Sept 2025
- AI4D3 2025 Oral
- Readers: Everyone
Refine Drugs, Don’t Complete Them: Uniform-Source Discrete Flows for Fragment-Based Drug Discovery
Benno Kaech, Luis Wyss, Karsten Borgwardt, Gianvito Grasso
- Published: 23 Sept 2025, Last Modified: 01 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
OligoGym: Curated Datasets and Benchmarks for Oligonucleotide Drug Discovery
Rachapun Rotrattanadumrong, Carlo De Donno
- Published: 23 Sept 2025, Last Modified: 26 Sept 2025
- AI4D3 2025 Spotlight
- Readers: Everyone
LLM-Integrated Representative Path Selection for Context-Aware Drug Repurposing on Biomedical Knowledge Graphs
Haerin Song, Dongmin Bang, Bonil Koo, Sun Kim, Sangseon Lee
- Published: 23 Sept 2025, Last Modified: 14 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
Smiles2Dock: a large-scale dataset for ML-based docking score prediction using AlphaFold structures
Thomas Le Menestrel, Manuel Rivas Cruz
- Published: 23 Sept 2025, Last Modified: 16 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone
Context-aware geometric deep learning for RNA sequence design
Parth Bibekar, Lucien F. Krapp, Matteo Dal Peraro
- Published: 23 Sept 2025, Last Modified: 01 Oct 2025
- AI4D3 2025 Poster
- Readers: Everyone