Computational systems biology

H Kitano - Nature, 2002 - nature.com
To understand complex biological systems requires the integration of experimental and
computational research—in other words a systems biology approach. Computational …

OpenWorm: overview and recent advances in integrative biological simulation of Caenorhabditis elegans

GP Sarma, CW Lee, T Portegys… - … of the Royal …, 2018 - royalsocietypublishing.org
The adoption of powerful software tools and computational methods from the software
industry by the scientific research community has resulted in a renewed interest in …

Neural circuit policies enabling auditable autonomy

M Lechner, R Hasani, A Amini, TA Henzinger… - Nature Machine …, 2020 - nature.com
A central goal of artificial intelligence in high-stakes decision-making applications is to
design a single algorithm that simultaneously expresses generalizability by learning …

Liquid time-constant networks

R Hasani, M Lechner, A Amini, D Rus… - Proceedings of the AAAI …, 2021 - ojs.aaai.org
We introduce a new class of time-continuous recurrent neural network models. Instead of
declaring a learning system's dynamics by implicit nonlinearities, we construct networks of …

Closed-form continuous-time neural networks

R Hasani, M Lechner, A Amini, L Liebenwein… - Nature Machine …, 2022 - nature.com
Continuous-time neural networks are a class of machine learning systems that can tackle
representation learning on spatiotemporal decision-making tasks. These models are …

A complete biomechanical model of Hydra contractile behaviors, from neural drive to muscle to movement

H Wang, J Swore, S Sharma… - Proceedings of the …, 2023 - National Acad Sciences
How does neural activity drive muscles to produce behavior? The recent development of
genetic lines in Hydra that allow complete calcium imaging of both neuronal and muscle …

A natural lottery ticket winner: Reinforcement learning with ordinary neural circuits

R Hasani, M Lechner, A Amini… - … on machine learning, 2020 - proceedings.mlr.press
We propose a neural information processing system obtained by re-purposing the function
of a biological neural circuit model to govern simulated and real-world control tasks. Inspired …

Designing worm-inspired neural networks for interpretable robotic control

M Lechner, R Hasani, M Zimmer… - … on Robotics and …, 2019 - ieeexplore.ieee.org
In this paper, we design novel liquid time-constant recurrent neural networks for robotic
control, inspired by the brain of the nematode, C. elegans. In the worm's nervous system …

Learning the dynamics of realistic models of C. elegans nervous system with recurrent neural networks

R Barbulescu, G Mestre, AL Oliveira, LM Silveira - Scientific reports, 2023 - nature.com
Given the inherent complexity of the human nervous system, insight into the dynamics of
brain activity can be gained from studying smaller and simpler organisms. While some of the …

Generalizable machine learning in neuroscience using graph neural networks

PY Wang, S Sapra, VK George… - Frontiers in artificial …, 2021 - frontiersin.org
Although a number of studies have explored deep learning in neuroscience, the application
of these algorithms to neural systems on a microscopic scale, ie parameters relevant to …