NeurIPS 2022 Workshop LMRL Submissions

Personalised drug recommendation from augmented gene expression data - the right drug(s) for the right patient
Manuela Salvucci, Davy Suvee, Deniz Pirincci, Dimitrius Raphael, Eryk Kropiwnicki, Giovanni Dall’olio, James O’Reilly, Katie Sanford, Marika Catapano, Marta Sarrico, Xenia Galkina, Francesca Mulas
- Published: 28 Nov 2022, Last Modified: 05 May 2023
- LMRL 2022 Poster
- Readers: Everyone
Simultaneous alignment of cells and features of unpaired single-cell multi-omics datasets with co-optimal transport
Pinar Demetci, Quang Huy TRAN, Ievgen Redko, Ritambhara Singh
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Designing Proteins using Sparse Data
Ada Shaw, Jung-Eun Shin, Nicole Nisha Thadani, Alan Nawzad Amin, Debora Susan Marks
- Published: 28 Nov 2022, Last Modified: 05 May 2023
- LMRL 2022 Poster
- Readers: Everyone
Using co-localization priors and microenvironment statistics to reconstruct tissue organization from single-cell data
Yitzchak Vaknin, Noa Moriel, Mor Nitzan
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
A generative recommender system with GMM prior for cancer drug generation and sensitivity prediction
Krzysztof Koras, Marcin Możejko, Paulina Szymczak, Adam Izdebski, Eike Staub, Ewa Maria Szczurek
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Energy-based Modelling for Single-cell Data Annotation
Tianyi Liu, Philip Fradkin, Lazar Atanackovic, Leo J Lee
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Modeling Single-Cell Dynamics Using Unbalanced Parameterized Monge Maps
Luca Eyring, Dominik Klein, Giovanni Palla, Sören Becker, Philipp Weiler, Niki Kilbertus, Fabian J Theis
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Biological Cartography: Building and Benchmarking Representations of Life
Safiye Celik, Jan-Christian Huetter, Sandra Melo, Nathan Lazar, Rahul Mohan, Conor Tillinghast, Tommaso Biancalani, Marta Fay, Berton Earnshaw, Imran S Haque
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Protein language model rescue mutations highlight variant effects and structure in clinically relevant genes
Onuralp Soylemez, Pablo Cordero
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Regression-Based Elastic Metric Learning on Shape Spaces of Cell Curves
Adele Myers, Nina Miolane
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
SPOT: Spatial Optimal Transport for Analyzing Cellular Microenvironments
Shouvik Mani, Doron Haviv, Russell Kunes, Dana Pe'er
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Designing active and thermostable enzymes with sequence-only predictive models
Clara Fannjiang, Micah Olivas, Eric R. Greene, Craig J. Markin, Bram Wallace, Ben Krause, Margaux M. Pinney, James Fraser, Polly M Fordyce, Ali Madani, Nikhil Naik
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Joint Protein Sequence-Structure Co-Design via Equivariant Diffusion
Ria Vinod, Kevin K Yang, Lorin Crawford
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Interpretable visualization of single cell data using Janus autoencoders
Gokul Gowri, Philippa Anne Richter, Xiaokang Lun, Peng Yin
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Machine Learning enabled Pooled Optical Screening in Human Lung Cancer Cells
Srinivasan Sivanandan, Max Salick, Bobby Leitmann, Kara Marie Liu, Mohammad Sultan, Navpreet Ranu, Cynthia Vivian Hao, Owen Chen, John Bisognano, Eric Lubeck, Ajamete Kaykas, Eilon Sharon, Ci Chu
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
An Empirical Study of ML-based Phenotyping and Denoising for Improved Genomic Discovery
Bo Yuan, Cory Y McLean, Farhad I Hormozdiari, Justin Cosentino
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
EpiAttend: A transformer model of gene regulation combining single cell epigenomes with DNA sequence
Russell Li, Heng Xu, Eran A Mukamel
- Published: 28 Nov 2022, Last Modified: 05 May 2023
- LMRL 2022 Poster
- Readers: Everyone
Multimodal Cell-Free DNA Embeddings are Informative for Early Cancer Detection
Felix Jackson
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Continuous cell-state density inference and applications for single-cell data
Dominik Jenz Otto, Manu Setty, Brennan Dury
- Published: 28 Nov 2022, Last Modified: 05 May 2023
- LMRL 2022 Poster
- Readers: Everyone
Find your microenvironments faster with Neural Spatial LDA
Sivaramakrishnan Sankarapandian, Jun Xu, Zhenghao Chen
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
TranceptEVE: Combining Family-specific and Family-agnostic Models of Protein Sequences for Improved Fitness Prediction
Pascal Notin, Lood Van Niekerk, Aaron W Kollasch, Daniel Ritter, Yarin Gal, Debora Susan Marks
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Neural Unbalanced Optimal Transport via Cycle-Consistent Semi-Couplings
Frederike Lübeck, Charlotte Bunne, Gabriele Gut, Jacobo Sarabia del Castillo, Lucas Pelkmans, David Alvarez-Melis
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
ChromFormer: A transformer-based model for 3D genome structure prediction
Henry Valeyre, Pushpak Pati, Federico Gossi, Vignesh Ram Somnath, Adriano Martinelli, Marianna Rapsomaniki
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
Improving Protein Subcellular Localization Prediction with Structural Prediction & Graph Neural Networks
Geoffroy Dubourg-Felonneau, Arash Abbasi, Eyal Akiva, Lawrence Lee
- 09 Oct 2022 (modified: 05 May 2023)
- LMRL 2022 Paper
- Readers: Everyone
A single-cell gene expression language model
William Connell, Umair Khan, Michael Keiser
- 09 Oct 2022 (modified: 26 Mar 2024)
- LMRL 2022 Paper
- Readers: Everyone