Semi-supervised methods improve GRN prediction from gene expression data.
problem Challenging task of predicting gene regulatory networks from gene expression data.
method Semi-supervised machine learning methods using SVM and RF.
result Transductive learning approach outperformed inductive learning for both organisms.
Study predicts coastal water quality using machine learning, identifying salinity as key factor.
problem Predicting and managing coastal water quality for public health and tourism.
method Machine learning models (Catboost, Xgboost, Random Forests, Support Vector Regression, Artificial Neural Networks) trained on environmental data.
result Catboost algorithm performed best, with R² values of 0.71 and 0.68 for E. Coli and enterococci predictions.
Proposes a method to estimate sparse low-rank matrices from noisy data.
problem Estimating sparse low-rank matrices from noisy observations.
method Objective function with non-convex penalties, ADMM algorithm.
result Proposed method outperforms convex methods in estimating sparse low-rank matrices.
Machine learning identifies key metabolic control circuits in bacterial pathways.
problem Identifying regulated metabolic pathways in bacteria.
method Machine learning approach analyzing multi-omics data.
result Identification of E. coli Glycolysis regulatory circuits.
A nonparametric Bayesian extension of Factor Analysis (FA) is proposed where observed data Y is modeled as a linear superposition, G, of a potentially infinite number of hidden factors, X. The Indian Buffet Process (IBP) is used as a prior on G to incorporate sparsity and to …
We present a procedure for effective estimation of entropy and mutual information from small-sample data, and apply it to the problem of inferring high-dimensional gene association networks. Specifically, we develop a James-Stein-type shrinkage estimator, resulting in a procedure that is highly efficient statistically …
Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of nega…
New method infers causal factors from large-scale data without full graph reconstruction.
problem Inferring causal variables from large-scale systems without full causal graph reconstruction.
method Supervised learning on simulated data using a neural network and subsampled-ensemble inference.
result Efficiently identifies causal relationships in large-scale gene regulatory networks.
A new model infers transcription factor activities from gene expression data.
problem Challenges in measuring and capturing quick-time dynamics of transcription factors.
method Switched dynamical latent force model based on differential equations.
result The model accurately infers continuous-time transcription factor profiles from gene expression data.
New method detects RNA modifications without prior training, revealing novel sites.
problem Detecting RNA modifications with high accuracy and sensitivity.
method Anomaly detection using nanopore raw ionic current signals and nearest neighbor comparison.
result Detects diverse RNA modifications without prior training, including a novel 2'-O-methylated site in DENV.
Graph auto-encoder predicts unobserved node features from biological networks and omics data.
problem Integrating biological networks and continuous node features for better prediction.
method Graph neural networks and feature auto-encoders trained on feature reconstruction.
result Graph feature auto-encoder outperforms auto-encoders trained on graph reconstruction for predicting unobserved node features.