Improved analysis of calcium imaging data with higher SNR and compression.
problem Challenges in analyzing large-scale calcium imaging datasets.
method Spatially-localized penalized matrix decomposition (PMD) for denoising and compression.
result Significant improvement in SNR and compression rates with minimal signal loss.
Calcium imaging permits optical measurement of neural activity. Since intracellular calcium concentration is an indirect measurement of neural activity, computational tools are necessary to infer the true underlying spiking activity from fluorescence measurements. Bayesian model inversion can be used to solve this prob…
New unsupervised learning method for fast imaging metal dendrites.
problem Fast imaging of metal dendrites in materials science.
method Unsupervised learning using Hierarchical Gaussian Mixture Models (HGMM) for dynamic sampling.
result Dynamic sampling of metal dendrites can be achieved efficiently using HGMM.
A new model improves analysis of neural activity from calcium imaging.
problem Statistical modeling of deconvolved calcium signals for neural activity interpretation.
method Proposed a zero-inflated gamma (ZIG) model to characterize calcium responses as a mixture of a gamma distribution and a point mass.
result The ZIG model outperforms simpler models in neural encoding and decoding problems.
New methods estimate brain connectivity from calcium imaging data with missing data.
problem Estimating functional neuronal connectivity from calcium imaging data with missing data.
method Two approaches for nonparanormal Graph Quilting based on the Gaussian copula graphical model.
result Our methods yield more meaningful functional connectivity estimates than existing Gaussian graph quilting methods.
A fundamental challenge in calcium imaging has been to infer the timing of action potentials from the measured noisy calcium fluorescence traces. We systematically evaluate a range of spike inference algorithms on a large benchmark dataset recorded from varying neural tissue (V1 and retina) using different calcium indi…
Improved neural spike inference from calcium imaging data.
problem Neural spike inference from calcium imaging data.
method Importance weighted adversarial variational autoencoders (IWAE) with adversarial training.
result Adversarial IWAE methods outperform VAEs in inferring neural spikes.
Researchers create a simulator to infer worm brain states from calcium imaging data.
problem Impute C. elegans membrane potentials from calcium imaging data.
method Developed a stochastic whole-brain simulator and used SMC method for imputation.
result First to infer worm brain states from partial calcium imaging observations.
In this work, we propose a simple yet effective solution to the problem of connectome inference in calcium imaging data. The proposed algorithm consists of two steps. First, processing the raw signals to detect neural peak activities. Second, inferring the degree of association between neurons from partial correlation …
Combines spatial context priors with data term for better dendritic spine segmentation.
problem Poor segmentation results due to overlapping pixel intensity distributions.
method Combines nonparametric context priors with learned-intensity data term and nonparametric shape priors.
result Significant improvements in dendritic spine segmentation.
We show that a compact n-polyhedron PL embeds in a product of n trees if and only if it collapses onto an (n-1)-polyhedron. If the n-polyhedron is contractible and n\ne 3 (or n=3 and the Andrews-Curtis Conjecture holds), the product of trees may be assumed to collapse onto the image of the embedding. In contrast, there…
In this paper, we consider linear state-space models with compressible innovations and convergent transition matrices in order to model spatiotemporally sparse transient events. We perform parameter and state estimation using a dynamic compressed sensing framework and develop an efficient solution consisting of two nes…
Efficient method predicts coronary calcium scores in cardiac and chest CTs.
problem Quantifying coronary artery calcium for risk assessment.
method Two ConvNets for direct regression of calcium scores, with optional decision feedback.
result Predicted calcium scores are highly correlated with manual scores and provide insight into decision-making.
New method estimates neuronal connectivity from partially observed data.
problem Estimating neuronal connectivity from partially observed data.
method Two-step approach: low-rank covariance completion followed by graph structure estimation.
result Graph selection consistency demonstrated for one approach.
We give a short answer to the question in the title: {\em dendrits}. Precisely we show that the C∗-algebra C(X) of all complex-valued continuous functions on a compactum X is projective in the category C1 of all (not necessarily commutative) unital C∗-algebras if and only if X is a…
Single neuron with ADA learns XOR and outperforms other functions.
problem Classifying linearly non-separable data.
method Proposed a new artificial neuron with apical dendrite activation.
result ADA function achieves 100% accuracy on XOR and superior performance on benchmark datasets.
Natural gradient learning improves synaptic plasticity in spiking neurons.
problem Parametrization dependence leads to inconsistencies in classical synaptic plasticity theories.
method Proposes natural gradient descent in Riemannian geometry for spiking neurons.
result Derives a synaptic learning rule that explains biological phenomena.
Trees emerge from group boundaries in hyperbolic geometry.
problem Understanding boundaries of hyperbolic groups and their maps.
method Analyzing short exact sequences of hyperbolic groups and their boundaries.
result The quotient of H boundary by ending laminations is a dendrite.
BNNs enhance reservoir computing by acting as generalization filters.
problem Understanding how BNNs integrate with reservoir computing.
method Optogenetics and calcium imaging to record BNNs, reservoir computing framework.
result BNNs improve reservoir computing performance through generalization.
Study of projective Fraïssé limits of trees with confluent epimorphisms.
problem Finite trees with monotone epimorphisms do not amalgamate.
method Developed new mappings and properties of continua to apply to topological graphs.
result Topological realization of the Fraïssé limit of finite trees with ramification vertices of order at most 3 is the Wa\. zewski dendrite D3. Hippocampal dentate granule cells are among the few neuronal cell types generated throughout adult life in mammals. In the normal brain, new granule cells are generated from progenitors in the subgranular zone and integrate in a typical fashion. During the development of epilepsy, granule cell integration is profoundly…
Bayesian model predicts drip-line locations in heavy calcium isotopes.
problem Determining the neutron drip line in the Ca region of heavy nuclei.
method Bayesian model averaging with Gaussian-process-based extrapolations.
result Predicted posterior probabilities for drip-line locations in heavy calcium isotopes.
Study shows how activation functions impact the storage capacity of treelike neural networks.
problem Understanding the role of activation functions in neural network expressive power.
method Analysis of treelike two-layer networks with various activation functions in the infinite-width limit.
result Activation functions affect storage capacity and robustness, with nonlinearity increasing capacity and decreasing robustness.
Mixed labyrinth fractals can have finite or infinite arc lengths.
problem Characterizing the length of arcs in mixed labyrinth fractals.
method Analyzing sequences of labyrinth patterns to determine arc lengths.
result Arc lengths can be finite or infinite depending on pattern choice.
A simple thresholding technique improves graph selection in neural connectivity studies.
problem Graphical model selection for functional neural connectivity in the presence of latent variables.
method Apply a hard thresholding operator to graphical Lasso, neighborhood selection, or CLIME estimators.
result Thresholded estimators outperform existing methods in graph selection consistency and empirical results.
VIND infers smooth nonlinear dynamics from electrophysiology data.
problem Analyzing smooth, nonlinear time series data from neuroscience experiments.
method Variational Inference for Nonlinear Dynamics (VIND) with structured approximate posterior and fixed-point iteration.
result VIND reconstructs 5D latent space variables similar to Hodgkin-Huxley models, and excels in predicting future neural activity.
Estimates neural representation dimensionality from small sample sizes.
problem Estimating neural representation dimensionality from limited data.
method Proposed a bias-corrected estimator for participation ratio of eigenvalues.
result The estimator is more accurate with finite samples and noise.
Study properties of self-similar continua with finite intersection property.
problem Characterize self-similar continua with finite intersection property.
method Prove intersection graph criterion, finite order theorem, and parameter matching theorem.
result All Jordan arcs starting from a intersection point in such continuum on a plane should have the same slope parameter at that point.
Developed Taylor series for muscle-finger system analysis.
problem Understanding the complex relationship between muscle activity and finger movement.
method Used Dendrite Net to develop Taylor series and construct relation spectrum.
result Found muscle synergy and coupling in hand movement.
Paper accelerates nonlinear mapping in online systems with lower time complexity.
problem Speeding up nonlinear mapping in online systems.
method Integrates an acceleration module into Dendrite Net (DD) to reduce time complexity.
result DD with AC has lower time complexity while maintaining nonlinear mapping and system identification properties.
New method speeds up sparse Bayesian learning without covariance matrix.
problem Sparse coding problem with uncertainty quantification.
method Covariance-free expectation maximization (CoFEM) that avoids explicit covariance matrix computation.
result Up to thousands of times faster than existing methods without sacrificing accuracy.
Networks capture our intuition about relationships in the world. They describe the friendships between Facebook users, interactions in financial markets, and synapses connecting neurons in the brain. These networks are richly structured with cliques of friends, sectors of stocks, and a smorgasbord of cell types that go…
This paper presents a novel method for the reconstruction of a neural network connectivity using calcium fluorescence data. We introduce a fast unsupervised method to integrate different networks that reconstructs structural connectivity from neuron activity. Our method improves the state-of-the-art reconstruction meth…
Active learning method for neural population dynamics using optogenetics.
problem Efficiently selecting neurons to stimulate for identifying neural population dynamics.
method Developed active learning procedure for low-rank regression to determine informative photostimulation patterns.
result Demonstrated a two-fold reduction in data required for predictive power using low-rank linear dynamical systems model.
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…
Many real-world data sets, especially in biology, are produced by complex nonlinear dynamical systems. In this paper, we focus on brain calcium imaging (CaI) of different organisms (zebrafish and rat), aiming to build a model of joint activation dynamics in large neuronal populations, including the whole brain of zebra…
Labyrinth fractals are dendrites in the unit square. They were introduced and studied in the last decade first in the self-similar case [Cristea & Steinsky (2009,2011)], then in the mixed case [Cristea & Steinsky (2017), Cristea & Leobacher (2017)]. Supermixed fractals constitute a significant generalisation of mixed l…
Inspired by biophysical principles underlying nonlinear dendritic computation in neural circuits, we develop a scheme to train deep neural networks to make them robust to adversarial attacks. Our scheme generates highly nonlinear, saturated neural networks that achieve state of the art performance on gradient based adv…
Neural networks learn to mimic brain neurons with two-input activation functions, improving performance and robustness.
problem Training neural networks to mimic the complex interactions of brain neurons.
method Developed a network-in-network architecture with two-input activation functions, optimized hyperparameters, and compared to conventional ReLU networks.
result Two-input activation functions can learn soft XOR functions, improving network performance and robustness.
Study of SK-N-AS cells' response to methamidophos using transcriptomics.
problem Understanding the transcriptional response of SK-N-AS cells to methamidophos exposure.
method Combination of statistical and machine learning methods for anomaly detection and causal network inference.
result Identification of key processes and transcripts involved in the response to methamidophos.
T2FSNN improves deep SNNs by reducing spikes and latency.
problem Inefficiency in spiking neural networks due to lack of scalable training algorithms.
method Introduces time-to-first-spike coding with kernel-based dynamic threshold and dendrite, combined with gradient-based optimization and early firing methods.
result Reduces inference latency and spike count by 22% and less than 1% compared to burst coding.
Biological neural network mimics CCA for multi-channel data.
problem Implementing CCA in a biologically plausible neural network.
method Derive an online CCA algorithm with local synaptic updates for multi-compartmental neurons.
result The derived neural network architecture and synaptic updates resemble cortical pyramidal neuron behavior.
New model uncovers non-Euclidean neural representations.
problem Discovering latent neural states in complex, non-Euclidean spaces.
method Manifold GPLVM for identifying latent variables and neural contributions.
result mGPLVM correctly recovers non-Euclidean latent structures in neural data.
T-SVM improves learning in spiking neurons by maximizing dynamical margin.
problem Finding robust solutions in spiking neuronal networks with temporal correlations.
method Introduces Temporal Support Vector Machine (T-SVM) to maximize dynamical margin.
result T-SVM enables learning of tasks requiring nonlinear spatial integration.
Deep learning extracts terrain texture covariates for geostatistical modeling.
problem Improving prediction accuracy in geostatistical modeling using terrain texture data.
method Deep learning approach to automatically derive optimal terrain texture covariates from SRTM 90m DEM.
result Deep learning-derived covariates have strong explanatory power (R-squared around 0.6) for geochemical data.
CatSIM measures image similarity robustly to small changes.
problem Measuring similarity between images, especially with small perturbations.
method Uses structural similarity image quality paradigm, robust to small location changes.
result Structural similarity between images rated higher when not entirely overlapping.
Develops statistical guarantees for image-to-image regression models.
problem Current image-to-image regression models lack statistical guarantees for model mistakes and hallucinations.
method Uncertainty quantification techniques with rigorous statistical guarantees for image-to-image regression problems.
result Derives uncertainty intervals around each pixel with formal mathematical guarantees.
AugurOne trains single image generators without GANs using image warps.
problem Training end-to-end single image generators without GANs.
method Non-affine augmentations of single input images for training an upscaling neural network.
result End-to-end training yields state-of-the-art performance on conditional generation tasks.