We introduce SIM-CE, an advanced, user-friendly modeling and simulation environment in Simulink for performing multi-scale behavioral analysis of the nervous system of Caenorhabditis elegans (C. elegans). SIM-CE contains an implementation of the mathematical models of C. elegans's neurons and synapses, in Simulink, whi…
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17 results for “C. elegans”
We develop a stochastic whole-brain and body simulator of the nematode roundworm Caenorhabditis elegans (C. elegans) and show that it is sufficiently regularizing to allow imputation of latent membrane potentials from partial calcium fluorescence imaging observations. This is the first attempt we know of to "complete t…
New algorithm for robust circular coordinates in recurrent time series data.
problem Inefficient and sensitive methods for finding circular coordinates on recurrent data.
method Subsampling, aligning, and averaging to correct uneven sampling density.
result More robust and efficient circular coordinates for neuronal recordings.
The roundworm C. elegans exhibits robust escape behavior in response to rapidly rising temperature. The behavior lasts for a few seconds, shows history dependence, involves both sensory and motor systems, and is too complicated to model mechanistically using currently available knowledge. Instead we model the process p…
Graph spectral analysis can yield meaningful embeddings of graphs by providing insight into distributed features not directly accessible in nodal domain. Recent efforts in graph signal processing have proposed new decompositions-e.g., based on wavelets and Slepians-that can be applied to filter signals defined on the g…
Decomposed Linear Dynamical Systems (dLDS) for learning the latent components of neural dynamicsstat.ML
dLDS models neural dynamics as sparse combinations of simpler components.
problem Understanding complex neural dynamics at a population level.
method Proposes a decomposed dynamical system model trained through dictionary learning.
result Model efficiently captures and demix diverse neural dynamics.
The interplay between inter-neuronal network topology and cognition has been studied deeply by connectomics researchers and network scientists, which is crucial towards understanding the remarkable efficacy of biological neural networks. Curiously, the deep learning revolution that revived neural networks has not paid …
Improves spline quality and accuracy in computational microscopy.
problem Detecting slender, overlapping structures in microscopy images.
method Differentiable rendering approach for spline refinement.
result Achieves high reliability and sub-pixel accuracy.
We propose a neural information processing system which is obtained by re-purposing the function of a biological neural circuit model, to govern simulated and real-world control tasks. Inspired by the structure of the nervous system of the soil-worm, C. elegans, we introduce Neuronal Circuit Policies (NCPs), defined as…
Neural connectomics has begun producing massive amounts of data, necessitating new analysis methods to discover the biological and computational structure. It has long been assumed that discovering neuron types and their relation to microcircuitry is crucial to understanding neural function. Here we developed a nonpara…
Graph neural networks detect structural perturbations from time series data.
problem Detecting structural causes of disturbances in complex systems.
method Graph neural network approach to infer structural perturbations from functional time series.
result Data-driven approach outperforms typical reconstruction methods and meets Bayesian inference accuracy.
sEM uses optimal transport to improve EM algorithm for better convergence and avoiding local optima.
problem Improving the EM algorithm for better convergence and avoiding local optima.
method sEM uses entropic optimal transport to compute responsibilities in the expectation step, leading to better global convergence guarantees and avoiding local optima.
result sEM learns cell labels significantly better than other approaches, improving convergence and avoiding local optima.
We propose methods for estimating correspondence between two point sets under the presence of outliers in both the source and target sets. The proposed algorithms expand upon the theory of the regression without correspondence problem to estimate transformation coefficients using unordered multisets of covariates and r…
New method optimizes clustering with better log-likelihood landscape.
problem Nonconvex log-likelihood optimization in model-based clustering.
method Entropic optimal transport loss for Sinkhorn-EM algorithm.
result New loss function avoids spurious local optima.
Co-clustering for directed graphs: the Stochastic co-Blockmodel and spectral algorithm Di-Simstat.ML
Directed graphs have asymmetric connections, yet the current graph clustering methodologies cannot identify the potentially global structure of these asymmetries. We give a spectral algorithm called di-sim that builds on a dual measure of similarity that correspond to how a node (i) sends and (ii) receives edges. Using…
Statistical inference on graphs is a burgeoning field in the applied and theoretical statistics communities, as well as throughout the wider world of science, engineering, business, etc. In many applications, we are faced with the reality of errorfully observed graphs. That is, the existence of an edge between two vert…
A new sampling scheme based on DOE improves Shapley value estimation accuracy and speed.
problem Heavy computational burden of calculating Shapley values in large coalition games.
method Design of Experiments (DOE) order-of-addition experimental designs for sampling.
result DOE-based sampling scheme yields more accurate and sometimes deterministic estimates of Shapley values.