ICML 2024 Workshop AccMLBio Submissions

Rethinking Molecular Design: Integrating Latent Variable and Auto-Regressive Models for Enhanced Goal Directed Generation
Arthur-Louis Heath, Amina Mollaysa, Michael Krauthammer
- Published: 17 Jun 2024, Last Modified: 24 Jul 2024
- AccMLBio Poster
- Readers: Everyone
2Bits of Protein: Efficient Protein Language Models at the Scale of 2-bits
Oliver M. Turnbull, Mohamed Baioumy, Charlotte Deane
- Published: 17 Jun 2024, Last Modified: 26 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Graph2Token: Make LLMs Understand Molecule Graphs
Runze Wang, Mingqi Yang, Yanming Shen
- Published: 17 Jun 2024, Last Modified: 16 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Multi-Task Training Increases Native Sequence Recovery of Antigen-Specific T-cell Receptor Sequences
Dhuvarakesh Karthikeyan, Alex Rubinsteyn
- Published: 17 Jun 2024, Last Modified: 27 Jul 2024
- AccMLBio Poster
- Readers: Everyone
scTree: Discovering Cellular Hierarchies in the Presence of Batch Effects in scRNA-seq Data
Moritz Vandenhirtz, Florian Barkmann, Laura Manduchi, Julia E Vogt, Valentina Boeva
- Published: 17 Jun 2024, Last Modified: 09 Jul 2024
- AccMLBio Spotlight
- Readers: Everyone
Are Protein Language Models Compute Optimal?
Yaiza Serrano, Alvaro Ciudad Serrano, Alexis Molina
- Published: 17 Jun 2024, Last Modified: 22 Jul 2024
- AccMLBio Poster
- Readers: Everyone
ProtMamba: a homology-aware but alignment-free protein state space model
Damiano Sgarbossa, Cyril Malbranke, Anne-Florence Bitbol
- Published: 17 Jun 2024, Last Modified: 11 Jul 2024
- AccMLBio Spotlight
- Readers: Everyone
SWUS: Active Learning with Structure Weighted Uncertainty Score
Andrea Karlova, Brooks Paige
- Published: 17 Jun 2024, Last Modified: 23 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Likelihood-based fine-tuning of protein language models for few-shot fitness prediction and design
Alex Hawkins-Hooker, Jakub Kmec, Oliver Bent, Paul Duckworth
- Published: 17 Jun 2024, Last Modified: 24 Jul 2024
- AccMLBio Spotlight
- Readers: Everyone
Geometric Algebra based encoding for graph prompting
Sotirios Panagiotis Chytas, Rudrasis Chakraborty, Vikas Singh
- Published: 17 Jun 2024, Last Modified: 24 Jul 2024
- AccMLBio Poster
- Readers: Everyone
MSA Pairing Transfomer: protein interaction partner prediction with few-shot contrastive learning
Alex Hawkins-Hooker, Daniel Burkhardt Cerigo, Umberto Lupo, David Jones, Brooks Paige
- Published: 17 Jun 2024, Last Modified: 24 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling
Yair Schiff, Chia Hsiang Kao, Aaron Gokaslan, Tri Dao, Albert Gu, Volodymyr Kuleshov
- Published: 17 Jun 2024, Last Modified: 05 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Interactome-scale comparison of co-immunoprecipitation and yeast two-hybrid assays for protein interaction prediction
Kapil Devkota, Lenore Cowen, Rohit Singh
- Published: 17 Jun 2024, Last Modified: 27 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Learning Generative Population Models From Multiple Clinical Datasets Via Probabilistic Programming
João Loula, Katherine M. Collins, Ulrich Schaechtle, Joshua B. Tenenbaum, Adrian Weller, Feras Saad, Timothy J. O'Donnell, Vikash Mansinghka
- Published: 17 Jun 2024, Last Modified: 26 Jul 2024
- AccMLBio Poster
- Readers: Everyone
PLUTO: Pathology-Universal Transformer
Dinkar Juyal, Harshith Padigela, Chintan Shah, Daniel Shenker, Natalia Harguindeguy, Yi Liu, Blake Martin, Yibo Zhang, Michael Nercessian, Miles Markey, Isaac Finberg, Kelsey Luu, Daniel Borders, Syed Ashar Javed, Emma L Krause, Raymond Biju, Aashish Sood, Allen Ma, Jackson Nyman, John Shamshoian et al. (13 additional authors not shown)
- Published: 17 Jun 2024, Last Modified: 12 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Identifying Biological Priors and Structure in Single-Cell Foundation Models
Flavia Pedrocchi, Stefan Stark, Gunnar Ratsch, Amir Joudaki
- Published: 17 Jun 2024, Last Modified: 26 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Compressing the Latent Space of Single-Sequence Protein Predictors for Multimodal Generation
Amy X. Lu, Wilson Yan, Vladimir Gligorijevic, Pieter Abbeel, Kevin K Yang, Nathan C. Frey
- Published: 17 Jun 2024, Last Modified: 17 Jun 2024
- AccMLBio Poster
- Readers: Everyone
Prot2Token: A multi-task framework for protein language processing using autoregressive language modeling
Mahdi Pourmirzaei, Farzaneh Esmaili, Mohammadreza Pourmirzaei, Duolin Wang, Dong Xu
- Published: 17 Jun 2024, Last Modified: 11 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Generative Model for Small Molecules with Latent Space RL Fine-Tuning to Protein Targets
Ulrich Armel Mbou Sob, Qiulin Li, Miguel Arbesú, Oliver Bent, Andries Petrus Smit, Arnu Pretorius
- Published: 17 Jun 2024, Last Modified: 03 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Simple and Effective Masked Diffusion Language Models
Subham Sekhar Sahoo, Marianne Arriola, Aaron Gokaslan, Edgar Mariano Marroquin, Alexander M Rush, Yair Schiff, Justin T Chiu, Volodymyr Kuleshov
- Published: 17 Jun 2024, Last Modified: 19 Jul 2024
- AccMLBio Spotlight
- Readers: Everyone
FusOn-pLM: A Fusion Oncoprotein-Specific Language Model via Focused Probabilistic Masking
Sophia Vincoff, Shrey Goel, Kseniia Kholina, Pranam Chatterjee
- Published: 17 Jun 2024, Last Modified: 17 Jun 2024
- AccMLBio Poster
- Readers: Everyone
xMINT: A Multimodal Integration Transformer for Xenium Gene Imputation
Xiaohui Jiang, Yuxia Xie, Jichun Xie
- Published: 17 Jun 2024, Last Modified: 23 Jul 2024
- AccMLBio Poster
- Readers: Everyone
Injecting Hierarchical Biological Priors into Graph Neural Networks for Flow Cytometry Prediction
Fatemeh Nassajian Mojarrad, Lorenzo Bini, Thomas Matthes, Stephane Marchand-Maillet
- Published: 17 Jun 2024, Last Modified: 16 Jul 2024
- AccMLBio Poster
- Readers: Everyone
RFamLlama: an efficient conditional language model for RNA sequence generation across diverse structural families
Jinyuan Sun, Han Li, Yifan Deng
- Published: 17 Jun 2024, Last Modified: 26 Jul 2024
- AccMLBio Poster
- Readers: Everyone
MolEval: An Evaluation Toolkit for Molecular Embeddings via LLMs
Shaghayegh Sadeghi, Ali Forooghi, Jianguo Lu, Alioune Ngom
- Published: 17 Jun 2024, Last Modified: 24 Jul 2024
- AccMLBio Poster
- Readers: Everyone