MicroRNAs (miRNAs) are small RNA molecules composed of 19-22 nt, which play important regulatory roles in post-transcriptional gene regulation by inhibiting the translation of the mRNA into proteins or otherwise cleaving the target mRNA. Inferring miRNA targets provides useful information for understanding the roles of…
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We derive generalized estimators for a number of spatial statistics that have been used in the analysis of spatially resolved omics data, such as Ripley's K, H and L functions, clustering index, and degree of clustering, which allow these statistics to be calculated on data modelled by arbitrary random measures (RMs). …
Quantitative modeling of post-transcriptional regulation process is a challenging problem in systems biology. A mechanical model of the regulatory process needs to be able to describe the available spatio-temporal protein concentration and mRNA expression data and recover the continuous spatio-temporal fields. Rigorous…
Deep learning predicts RNA degradation from crowdsourced data.
problem Predicting RNA degradation to improve thermostability.
method Crowdsourced machine learning competition on Kaggle.
result 41% of predictions matched experimental data, and models generalized to longer RNA molecules.
Physically-Inspired Gaussian Process Models for Post-Transcriptional Regulation in Drosophilastat.ML
The regulatory process of Drosophila is thoroughly studied for understanding a great variety of biological principles. While pattern-forming gene networks are analysed in the transcription step, post-transcriptional events (e.g. translation, protein processing) play an important role in establishing protein expression …
DeePathology: Deep Multi-Task Learning for Inferring Molecular Pathology from Cancer Transcriptomestat.ML
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Networks (DNNs) that is capable of simultaneous inference of various properti…
Proposes PSCCA for estimating correlations and canonical correlations in sparse count data.
problem Estimating correlations and canonical correlations in sparse count data from next-generation sequencing.
method Probabilistic approach for sparse count data sets (PSCCA).
result PSCCA outperforms other methods in estimating true correlations and canonical correlations at the natural parameter level.
Deep learning models improve cancer detection and typing classification from gene expression data.
problem Challenges in establishing specificity for cancer diagnosis using gene expression data.
method Developed deep learning models using mRNA datasets for cancer detection and typing classification.
result Achieved 98% accuracy in cancer detection and 18 out of 32 cancer-typing classifications over 90% accuracy.
Omics-GAN uses GANs to generate synthetic multi-omics data for improved disease prediction.
problem Limited sample sizes, noise, and heterogeneity in multi-omics data reduce predictive power.
method Omics-GAN is a GAN-based framework that generates high-quality synthetic multi-omics profiles.
result Synthetic datasets consistently improved prediction accuracy compared to original omics profiles.
SnapMMD forecasts cell differentiation outcomes from snapshot data.
problem Forecasting cell differentiation outcomes from limited snapshot data.
method SnapMMD learns dynamics by directly fitting the joint distribution of state measurements and observation time with MMD loss, allowing for unknown and state-dependent volatilities.
result SnapMMD delivers accurate forecasts and an R2-style statistic for diagnosing fit.
Optimizing over the set of orthogonal matrices is a central component in problems like sparse-PCA or tensor decomposition. Unfortunately, such optimization is hard since simple operations on orthogonal matrices easily break orthogonality, and correcting orthogonality usually costs a large amount of computation. Here we…
With the wealth of high-throughput sequencing data generated by recent large-scale consortia, predictive gene expression modelling has become an important tool for integrative analysis of transcriptomic and epigenetic data. However, sequencing data-sets are characteristically large, and previously modelling frameworks …
Biconvex Biclusteringstat.ML
Improves convex biclustering for high-dimensional data.
problem Discovering meaningful biclusters in high-dimensional data.
method Biconvex modification with adaptive feature weighting.
result Consistently recovers biclusters and selects features appropriately.
Improved SBI with neural networks for complex models.
problem Accurate inference for complex models with intractable likelihood.
method Structured mixtures of probability distributions for likelihood and posterior approximation.
result Accurate posterior inference with smaller computational footprint.
Predictive Correlation Screening: Application to Two-stage Predictor Design in High Dimensionstat.ML
We introduce a new approach to variable selection, called Predictive Correlation Screening, for predictor design. Predictive Correlation Screening (PCS) implements false positive control on the selected variables, is well suited to small sample sizes, and is scalable to high dimensions. We establish asymptotic bounds f…
The medical research facilitates to acquire a diverse type of data from the same individual for particular cancer. Recent studies show that utilizing such diverse data results in more accurate predictions. The major challenge faced is how to utilize such diverse data sets in an effective way. In this paper, we introduc…
Switched latent force models for reverse-engineering transcriptional regulation in gene expression dataphysics.bio-ph
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the activation of special proteins called transcription factors (TFs). Due to the difficult …
MOTGNN integrates multi-omics data for disease classification with improved accuracy and interpretability.
problem Challenges in integrating multi-omics data due to high dimensionality, heterogeneity, and lack of reliable interaction networks.
method MOTGNN uses XGBoost for graph construction, modality-specific GNNs for representation learning, and a deep feedforward network for cross-omics integration.
result MOTGNN outperforms state-of-the-art baselines by 5-10% in accuracy, ROC-AUC, and F1-score across three real-world disease datasets.
A scalable Bayesian inference method for mixed-effects models in systems biology.
problem Scalable Bayesian inference for complex hierarchical mixed-effects models in systems biology.
method Constructing amortized approximations of likelihood and posterior distributions, refined for each individual dataset.
result Our method is both fast and competitive in statistical accuracy compared to exact pseudomarginal Bayesian inference.
BIDIFAC integrates multi-platform, multi-cohort data for shared and unique patterns.
problem Integration of multi-platform, multi-cohort data for shared and unique patterns.
method BIDIFAC integrates bidimensionally linked matrices into four components: globally shared, row-shared, column-shared, and single-matrix structural components.
result BIDIFAC reveals shared and unique patterns of variability in multi-platform, multi-cohort data.
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms fo…
Sparse multi-view matrix factorisation: a multivariate approach to multiple tissue comparisonsstat.ML
Gene expression levels in a population vary extensively across tissues. Such heterogeneity is caused by genetic variability and environmental factors, and is expected to be linked to disease development. The abundance of experimental data now enables the identification of features of gene expression profiles that are s…
Proposes a novel classification criterion for high-dimensional data with few samples.
problem Challenges in classifying high-dimensional data with limited samples.
method Tolerance similarity criterion and No-separated Data Maximum Dispersion classifier (NPDMD).
result NPDMD outperforms state-of-the-art methods in various real-world applications.
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.
We solve the vector embedding problem by minimizing total distortion under constraints.
problem Assigning representative vectors to items with similarity and dissimilarity constraints.
method Projected quasi-Newton method for MDE problems, scalable to large data sets.
result Our method provides principled ways to validate embeddings and scales to millions of items.