NeurIPS 2023 Workshop AI4D3 Submissions

Identifying regularization schemes that make feature attributions faithful
Julius Adebayo, Samuel Don Stanton, Simon Kelow, Michael Maser, Richard Bonneau, Vladimir Gligorijevic, Kyunghyun Cho, Stephen Ra, Nathan C. Frey
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Inpainting Protein Sequence and Structure with ProtFill
Elizaveta Kozlova, Arthur Valentin, Daniel Nakhaee-Zadeh Gutierrez
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
DrugImprover: Utilizing Reinforcement Learning for Multi-Objective Alignment in Drug Optimization
Xuefeng Liu, Songhao Jiang, Archit Vasan, Alexander Brace, Ozan Gokdemir, Thomas Brettin, Fangfang Xia, Ian Foster, Rick Stevens
- Published: 25 Oct 2023, Last Modified: 12 Dec 2023
- AI4D3 2023 Oral
- Readers: Everyone
A framework for conditional diffusion modelling with applications in motif scaffolding for protein design
Kieran Didi, Francisco Vargas, Simon Mathis, Vincent Dutordoir, Emile Mathieu, Urszula Julia Komorowska, Pietro Lio
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Oral
- Readers: Everyone
SALSA: Semantically-Aware Latent Space Autoencoder
Kathryn E Kirchoff, Travis Maxfield, Alexander Tropsha, Shawn M Gomez
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
ExPT: Synthetic Pretraining for Few-Shot Experimental Design
Tung Nguyen, Sudhanshu Agrawal, Aditya Grover
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
All You Need is LOVE: Large Optimized Vector Embeddings Network for Drug Repurposing
Sina Akbarian, Sepehr Asgarian, Jouhyun Jeon
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Online Learning of Optimal Prescriptions under Bandit Feedback with Unknown Contexts
Hongju Park, Mohamad Kazem Shirani Faradonbeh
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
GraphPrint: Extracting Features from 3D Protein Structure for Drug Target Affinity Prediction
Amritpal
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Evaluating Zero-Shot Scoring for In Vitro Antibody Binding Prediction with Experimental Validation
Divya Nori, Simon V Mathis, Amir Pouya Shanehsazzadeh
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
$\textit{In vitro}$ validated antibody design against multiple therapeutic antigens using generative inverse folding
Amir Pouya Shanehsazzadeh
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Oral
- Readers: Everyone
On Modelability and Generalizability: Are Machine Learning Models for Drug Synergy Exploiting Artefacts and Biases in Available Data?
Arushi GK Majha, Ian Stott, Andreas Bender
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
MolSiam: Simple Siamese Self-supervised Representation Learning for Small Molecules
Joshua Yao-Yu Lin
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Hit Expansion Driven By Machine Learning
Jin Xu, Steven Kearnes, JW Feng
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Ab-DeepGA: A generative modeling framework leveraging deep learning for antibody affinity tuning
BoRam Lee, Yara Seif, Kevin Teng, Xiao Xiao, Isha Verma, Ming-Tang Chen, Alan C Cheng
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
AbLEF: Antibody Language Ensemble Fusion for thermodynamically empowered property predictions
Zachary A Rollins, Talal Widatalla, Andrew Waight, Alan C Cheng, Essam Metwally
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Leveraging expert feedback to align proxy and ground truth rewards in goal-oriented molecular generation
Julien Martinelli, Yasmine Nahal, Duong Lê, Ola Engkvist, Samuel Kaski
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
PoseCheck: Generative Models for 3D Structure-based Drug Design Produce Unrealistic Poses
Charles Harris, Kieran Didi, Arian Jamasb, Chaitanya Joshi, Simon Mathis, Pietro Lio, Tom Blundell
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Tree Search-Based Evolutionary Bandits for Protein Sequence Optimization
Jiahao Qiu, Hui Yuan, Jinghong Zhang, Wentao Chen, Huazheng Wang, Mengdi Wang
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
DGFN: Double Generative Flow Networks
Elaine Lau, Nikhil Murali Vemgal, Doina Precup, Emmanuel Bengio
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Neurosymbolic AI Reveals Biases and Limitations in ML-Driven Drug Discovery
Lauren DeLong, Yojana Gadiya, Jacques D. Fleuriot, Daniel Domingo-Fernández
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
VN-EGNN: Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification
Florian Sestak, Lisa Schneckenreiter, Sepp Hochreiter, Andreas Mayr, Günter Klambauer
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Protein Language Models Enable Accurate Cryptic Ligand Binding Pocket Prediction
David A Bloore, Joseph Chahn Kim, Karan Kapoor, Eric Chen, Kaifu Gao, Mengdi Wang, Ming-Hong Hao
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Removing Biases from Molecular Representations via Information Maximization
Chenyu Wang, Sharut Gupta, Caroline Uhler, Tommi Jaakkola
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone
Scalable Normalizing Flows Enable Boltzmann Generators for Macromolecules
Joseph Chahn Kim, David A Bloore, Karan Kapoor, Jun Feng, Ming-Hong Hao, Mengdi Wang
- Published: 25 Oct 2023, Last Modified: 10 Dec 2023
- AI4D3 2023 Poster
- Readers: Everyone