Gene Regulatory Neural Network

Gene regulatory neural networks (GRNNs) leverage the inherent computational properties of gene regulatory networks (GRNs) to model and predict cellular behavior. Current research focuses on improving GRN inference from single-cell data, employing techniques like graph neural networks and transformer models to account for data noise (e.g., dropouts) and incorporate prior biological knowledge. These advancements aim to create more accurate models of GRNs, enabling better understanding of cellular processes and potentially leading to improved drug discovery and the development of novel bio-hybrid computing systems. The field is also exploring the use of causal inference methods to better understand the dynamic and often cyclic interactions within GRNs.

Papers

July 25, 2024

Gene Regulatory Network Inference from Pre-trained Single-Cell Transcriptomics Transformer with Joint Graph Learning
Sindhura Kommu, Yizhi Wang, Yue Wang, Xuan Wang
Transformer Language Model Pre Trained BERT Regulatory Network scRNA Seq Gene Regulatory Neural Network

March 21, 2024

Gene Regulatory Network Inference in the Presence of Dropouts: a Causal View
Haoyue Dai, Ignavier Ng, Gongxu Luo, Peter Spirtes, Petar Stojanov, Kun Zhang
Speech Presence Structured Dropout Gene Expression Data Causal View Causal Graphical Model Transcriptomic Data Gene Regulatory Neural Network

March 13, 2024

Wet TinyML: Chemical Neural Network Using Gene Regulation and Cell Plasticity
Samitha Somathilaka, Adrian Ratwatte, Sasitharan Balasubramaniam, Mehmet Can Vuran, Witawas Srisa-an, Pietro Liò
TinyML Model Tiny Machine Learning Neuromorphic Processor Gene Regulation Gene Regulatory Neural Network Cellular Plasticity

September 14, 2023

Stability Analysis of Non-Linear Classifiers using Gene Regulatory Neural Network for Biological AI
Adrian Ratwatte, Samitha Somathilaka, Sasitharan Balasubramaniam, Assaf A. Gilad
Stability Analysis Non Linear Regulatory Network Reaction Network Elementary Perceptron Biological Intelligence Gene Regulatory Neural Network

August 29, 2023

The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data
Mathieu Chevalley, Jacob Sackett-Sanders, Yusuf Roohani, Pascal Notin, Artemy Bakulin, Dariusz Brzezinski, Kaiwen Deng, Yuanfang Guan, Justin Hong, Michael Ibrahim, Wojciech Kotlowski, Marcin Kowiel, Panagiotis Misiakos, Achille Nazaret, Markus Püschel, Chris Wendler, Arash Mehrjou, Patrick Schwab
Gene Regulatory Neural Network CausalBench Challenge

June 13, 2023

Inferring dynamic regulatory interaction graphs from time series data with perturbations
Dhananjay Bhaskar, Sumner Magruder, Edward De Brouwer, Aarthi Venkat, Frederik Wenkel, Guy Wolf, Smita Krishnaswamy
Time Series Data Additive Perturbation Regulatory Network Interaction Graph Time Varying Graph Gene Regulatory Neural Network

January 10, 2023

Inferring Gene Regulatory Neural Networks for Bacterial Decision Making in Biofilms
Samitha Somathilaka, Daniel P. Martins, Xu Li, Yusong Li, Sasitharan Balasubramaniam
Human Decision Regulatory Network Gene Regulatory Neural Network

November 11, 2022

Reconstruction of gene regulatory network via sparse optimization
Jiashu Lou, Leyi Cui, Wenxuan Qiu
Many Sparse Full State Reconstruction Sparse Optimization Regulatory Network Genome Understanding Inference Algorithm Gene Regulatory Neural Network

Gene Regulatory Neural Network

Papers

Gene Regulatory Network Inference from Pre-trained Single-Cell Transcriptomics Transformer with Joint Graph Learning

Gene Regulatory Network Inference in the Presence of Dropouts: a Causal View

Wet TinyML: Chemical Neural Network Using Gene Regulation and Cell Plasticity

Stability Analysis of Non-Linear Classifiers using Gene Regulatory Neural Network for Biological AI

The CausalBench challenge: A machine learning contest for gene network inference from single-cell perturbation data

Inferring dynamic regulatory interaction graphs from time series data with perturbations

Inferring Gene Regulatory Neural Networks for Bacterial Decision Making in Biofilms

Reconstruction of gene regulatory network via sparse optimization