Due to the dynamic nature of biological systems, biological networks underlying temporal process such as the development of {\it Drosophila melanogaster} can exhibit significant topological changes to facilitate dynamic regulatory functions. Thus it is essential to develop methodologies that capture the temporal evolut…
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24 results for “Drosophila melanogaster”
siRF identifies transcription factor binding near enhancers in flies.
problem Identifying functional transcription factor binding near enhancers.
method Signed iterative random forests (siRF) for machine learning.
result Infers regulatory interactions among transcription factors and enhancers.
Physically-Inspired Gaussian Process Models for Post-Transcriptional Regulation in Drosophilastat.ML
Physically-inspired Gaussian process models study post-transcriptional regulation in Drosophila.
problem Understanding spatiotemporal interactions between mRNAs and gap proteins in post-transcriptional regulation.
method Two physically-inspired Gaussian process models based on reaction-diffusion equations, tested with mRNA expression data.
result Novel GP model requires only kernel function differentiation, simplifying spatial discretisation.
New model predicts traits from gene expression, accounting for heterogeneity and gene networks.
problem Predicting phenotypes from gene expression data, considering heterogeneity and gene networks.
method Developed a novel model that considers heterogeneity and gene regulatory networks.
result Model performs well on prediction and provides clusters and gene regulatory networks.
Stochastic networks are a plausible representation of the relational information among entities in dynamic systems such as living cells or social communities. While there is a rich literature in estimating a static or temporally invariant network from observation data, little has been done toward estimating time-varyin…
Proposes CVKT to complete missing kernel matrices across multiple views.
problem Missing data in multiple views of kernel matrices.
method Cross-View Kernel Transfer (CVKT) with kernel alignment.
result Predicts missing values in kernel matrices using other views' data.
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.
Modeling the Drosophila connectome using semiparametric spectral methods.
problem Understanding the structure and function of the Drosophila mushroom body network.
method Semiparametric spectral modeling, latent structure model (LSM), Gaussian mixture modeling (GMM), adjacency spectral embedding (ASE).
result Captures latent connectome structure and elucidates neuronal properties.
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.
Controller-Augmented Hidden Markov Models (CHMMs) are a framework for constrained sequential inference.
problem Hidden Markov models fail under pathwise constraints like precedence, visitation, or monotonic state progression.
method CHMMs compile constraints into finite-state controllers, then use standard forward-backward and Viterbi recursions to compute exact constrained posteriors and paths.
result CHMMs provide exact constrained inference, monotone ascent in constrained EM, and linear complexity in controller cardinality.
New sparse CCA method finds interpretable associations in multi-view data.
problem Discovering interpretable associations in high-dimensional multi-view data.
method Inspired by sparse PCA, proposed a convex maximization program equivalent to non-convex sparse CCA formulation, using gradient method to reduce search space.
result Proposed two-step algorithm and new sparse CCA variants (Directed Sparse CCA, Multi-View sCCA) for multi-omic studies.
EigenNetworksstat.ML
EigenNetworks approximate time-varying graphs as linear combinations of fixed eigennetworks.
problem Challenges in tracking large, time-varying networks.
method Approximate time-varying networks as weighted linear combinations of eigennetworks, estimated through Principal Network Analysis.
result Smooth eigentrajectories reveal underlying patterns and potential structural shifts in networks.
Study proposes curvature flow model for Drosophila dorsal closure.
problem Modeling and understanding Drosophila dorsal closure during embryonic development.
method Curvature-based mathematical model, analysis of maximum-principle and integral-estimates, numerical approximation scheme.
result Established global existence and convergence for the model.
The paper predicts responses on out-of-sample nodes using latent positions on unknown curves.
problem Predicting responses on out-of-sample nodes with latent positions on unknown curves.
method Manifold learning and graph embedding technique using latent positions.
result Convergence guarantees for predicting responses on out-of-sample nodes.
Survey on statistical inference methods for random dot product graphs.
problem Statistical inference on random dot product graphs.
method Spectral embeddings of adjacency and Laplacian matrices.
result Consistency and asymptotic normality of spectral embeddings.
iRF detects stable high-order interactions in genomics data.
problem Understanding high-order interactions in genomics data.
method Iterative Random Forest algorithm (iRF) for stable high-order interaction detection.
result iRF identifies stable high-order interactions with computational cost similar to Random Forest.
New method uses manifold learning to infer latent positions of 1D submanifolds in random dot product graphs.
problem Inference on latent positions of unknown 1D submanifolds in RDPGs.
method Apply Isomap for manifold learning to estimate arc lengths on the unknown submanifold.
result Test statistics based on Isomap converge to known submanifold power as auxiliary vertices increase.
We propose a robust, scalable, integrated methodology for community detection and community comparison in graphs. In our procedure, we first embed a graph into an appropriate Euclidean space to obtain a low-dimensional representation, and then cluster the vertices into communities. We next employ nonparametric graph in…
Estimates effect sizes and power from a pilot experiment.
problem Estimating the distribution of effect sizes in multiple testing settings.
method Uses an inexpensive pilot experiment to estimate effect sizes and power.
result Simple and computationally efficient estimator guarantees the number of discoveries.
Random forest improves nearest neighbor estimation of information-theoretic quantities.
problem Estimating information-theoretic quantities in high-dimensional and scale-different settings.
method Decision forest-based adaptive nearest neighbor estimators.
result Forest-based estimators effectively estimate posterior probabilities and mutual information.
Graph matching method for noisy induced subgraph detection.
problem Finding vertex correspondence between noisy graphs of different sizes.
method Graph matching using matched filters with centering and padding.
result Optimization problem can recover true vertex correspondence under statistical model.
BioHash improves similarity search performance using sparse high-dimensional hash codes.
problem Improving similarity search performance in high-dimensional data.
method BioHash produces sparse high-dimensional hash codes through a data-driven approach based on synaptic plasticity.
result BioHash outperforms previous hashing methods in various similarity search tasks.
Deep learning tracks body parts without markers, improving efficiency in neuroscience.
problem Efficiently tracking specific behaviors in animals without intrusive markers.
method Transfer learning with deep neural networks for markerless tracking.
result Deep learning achieves excellent tracking performance with minimal labeled data.
A novel algorithm optimizes sparsity in reservoir computing inspired by insect brain.
problem Optimizing sparsity in reservoir computing networks.
method Inspired by insect brain, the algorithm optimizes sparsity levels by adjusting node firing thresholds.
result The algorithm outperforms standard gradient descent on tasks involving better classification, memorization, and convergence.