ERICA assesses replicability of cluster analysis results.
problem Lack of quantitative scrutiny for clustering results.
method ERICA: a framework to assess replicability of cluster analysis.
result Clusters are found to be replicable in synthetic data but not in real-world datasets.
ERICA assesses reproducibility in cluster analysis.
problem Lack of a unified framework for evaluating cluster analysis replicability.
method ERICA (iterative clustering assignments) method to quantify replicability.
result Demonstrates ERICA's ability to identify reproducible cluster structure.
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads", which constitute a fundamentally discrete measure of the level of gene expression. A…
Boosting strategies for merging vs. ensembling studies analyzed.
problem Deciding between merging and ensembling studies for boosting.
method Analytical transition point and bias-variance decomposition for boosting with linear learners.
result Theoretical guidelines for merging vs. ensembling studies.
Decomposes information into copying and transformation modes.
problem Lack of distinction between copying and transformation in information measures.
method Derives a decomposition of mutual information into copying and transformation components.
result Copy information can be interpreted as minimal physical copying work.
Understanding cell identity is an important task in many biomedical areas. Expression patterns of specific marker genes have been used to characterize some limited cell types, but exclusive markers are not available for many cell types. A second approach is to use machine learning to discriminate cell types based on th…
A new method uses gene interaction networks to predict gene functions.
problem Predicting gene functions from gene interactions.
method Context graph kernel approach in a machine learning framework.
result The proposed method outperforms linkage-assumption-based methods.
VEGN uses graph neural networks to predict disease-causing mutations from genetic variants.
problem Identifying disease-causing mutations from millions of genetic variants.
method VEGN employs a graph neural network on a heterogeneous graph of genes and variants, learning gene-gene interactions.
result VEGN outperforms existing state-of-the-art models in variant effect prediction.
Bioinformatics tools have been developed to interpret gene expression data at the gene set level, and these gene set based analyses improve the biologists' capability to discover functional relevance of their experiment design. While elucidating gene set individually, inter gene sets association is rarely taken into co…
Bayesian model learns cell types and gene networks from two data views.
problem Estimating cell types and their regulatory networks from single-cell gene expression and epigenetic data.
method Symphony Bayesian hierarchical multi-view mixture model with Variational EM inference.
result Symphony outperforms other methods in learning cell types and regulatory networks.
Identifying significant subsets of the genes, gene shaving is an essential and challenging issue for biomedical research for a huge number of genes and the complex nature of biological networks,. Since positive definite kernel based methods on genomic information can improve the prediction of diseases, in this paper we…
New method expands seed genes to functionally related clusters.
problem Discovering functionally related genes lacking GO terms.
method Semi-supervised learning with positive and unlabeled examples.
result LPU approaches significantly outperform existing methods.
A new method for joint eQTL mapping and gene network estimation.
problem Discovering SNP-gene relationships and gene-gene relationships in gene expression regulation.
method L1-2 regularized multi-task graphical lasso (L1-2 GLasso).
result Competitive performance on capturing true sparse structures of eQTL mapping and gene network.
New method handles correlated genes for better genomic prediction.
problem Technical issues with highly correlated genes in prediction models.
method Grouping algorithm that treats correlated genes as a group and uses their common patterns.
result Significantly outperforms standard models in prediction and feature selection.
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never before been considered as a resource for integrative analysis. By harnessing gene s…
VGAE learns gene-disease associations from networks, predicting disease-genes.
problem Predicting gene-disease associations from disease-gene networks.
method Introducing VGAE, a variational graph auto-encoder for disease-gene prediction.
result VGAE and C-VGAE outperform baseline methods in disease-gene prediction.
Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes among the candidates remains time-con…
We present the extention and application of a new unsupervised statistical learning technique--the Partition Decoupling Method--to gene expression data. Because it has the ability to reveal non-linear and non-convex geometries present in the data, the PDM is an improvement over typical gene expression analysis algorith…
A novel method selects genes for high-dimensional gene expression data with class imbalance.
problem Class imbalance in gene expression datasets.
method Synthetic data balancing, greedy search, weighted robust score.
result The proposed method outperforms existing feature selection procedures.
The problem of multilabel classification when the labels are related through a hierarchical categorization scheme occurs in many application domains such as computational biology. For example, this problem arises naturally when trying to automatically assign gene function using a controlled vocabularies like Gene Ontol…
New algorithm ensures consistent results in constrained MAB problems.
problem Achieving consistent results in constrained MAB problems.
method Developed replicable algorithms for constrained MAB problems using the optimism principle.
result Regret and constraint violation of replicable algorithms match those of non-replicable ones.
Identifying latent structure in large data matrices is essential for exploring biological processes. Here, we consider recovering gene co-expression networks from gene expression data, where each network encodes relationships between genes that are locally co-regulated by shared biological mechanisms. To do this, we de…
The method integrates survival constraints into NMF for identifying survival-associated gene clusters.
problem Understanding and interpreting high-dimensional biological data for disease markers.
method Cox proportional hazards regression integrated with NMF via proportional hazards non-negative matrix factorization.
result The method can uncover survival-associated gene clusters in cancer gene expression data.
Unified framework for fixed-income pricing and liability replication.
problem Static arbitrage and discount curve construction.
method Model-free framework for static fixed-income pricing and liability replication.
result Existence of strictly positive discount curves reproducing market prices and least-cost super-replicating portfolios.
When searching for gene pathways leading to specific disease outcomes, additional information on gene characteristics is often available that may facilitate to differentiate genes related to the disease from irrelevant background when connections involving both types of genes are observed and their relationships to the…
New methods detect continuous variation in single-cell data.
problem Continuous variation within and between cell types not detected by discrete analyses.
method Three topologically motivated mathematical methods for unsupervised feature selection.
result Detect additional biologically meaningful genes with coherent expression patterns.
Microarray cancer gene expression data comprise of very high dimensions. Reducing the dimensions helps in improving the overall analysis and classification performance. We propose two hybrid techniques, Biogeography - based Optimization - Random Forests (BBO - RF) and BBO - SVM (Support Vector Machines) with gene ranki…
Characterizes super-replication prices in a financial market model.
problem Characterizing prices in a financial market model.
method Characterizes prices as the supremum of mono-prior super-replication prices through extreme priors and martingale measures.
result Super-replication prices are the supremum of mono-prior super-replication prices.
New study on replicability and stability in machine learning algorithms.
problem Ensuring consistent results in machine learning models without fixing randomness.
method Introduced global stability and list replicability concepts, proving their equivalence and boosting list replicability.
result Global stability can only be achieved weakly, while list replicability can be boosted to achieve high probability of consistent results.
New gene selection method improves tumor classification accuracy.
problem Efficiently selecting relevant genes from high-dimensional tumor gene expression data.
method Fuzzy-Rough Set Theory for feature dependency analysis.
result The proposed method outperforms state-of-the-art techniques in tumor classification.
Various approaches to gene selection for cancer classification based on microarray data can be found in the literature and they may be grouped into two categories: univariate methods and multivariate methods. Univariate methods look at each gene in the data in isolation from others. They measure the contribution of a p…
Study on computational aspects of replicable learning, bridging statistical and algorithmic perspectives.
problem Understanding the computational connections between replicability and various learning paradigms.
method Design of replicable learners, lifting framework, and transformation techniques.
result Efficient replicable learners for specific learning problems under various distributions.
The paper classifies self-replicating 3D shapes using algebraic models.
problem Understanding self-replicating 3D shapes.
method Using idempotents in the (2+1)-cobordism category to classify 3-manifolds.
result A classification theorem for self-replicating 3-manifolds.
New model generates realistic single-cell gene expression data.
problem Generating realistic single-cell gene expression profiles is challenging.
method scLDM, a latent diffusion model using Diffusion Transformers and linear interpolants.
result Superior performance in generating realistic single-cell gene expression data.
A model to fill in missing gene data from spatial studies and scRNA-seq.
problem Imputing missing gene expression measurements from spatial transcriptomics.
method A deep generative model (gimVI) for integrating spatial transcriptomic and scRNA-seq data.
result gimVI outperforms existing methods in imputing missing genes.
We address the problem of synthetic gene design using Bayesian optimization. The main issue when designing a gene is that the design space is defined in terms of long strings of characters of different lengths, which renders the optimization intractable. We propose a three-step approach to deal with this issue. First, …
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of sa…
NO-BEARS algorithm speeds up gene network inference from transcriptomic data.
problem Constructing accurate gene regulatory networks from transcriptomic data.
method NO-BEARS algorithm, based on NOTEARS, with new constraint and polynomial regression loss.
result Significantly reduced computational time and improved accuracy in inferring gene regulatory networks.
InfoSEM infers gene regulatory networks without GT labels, improving performance.
problem Inferring GRNs from gene expression data with high accuracy and avoiding biases.
method InfoSEM uses deep generative models with informative priors (textual gene embeddings).
result InfoSEM outperforms existing models by 38.5% across four datasets.
Stem uses diffusion models to infer gene expression from H&E images.
problem Inference of gene expression from H&E stained images is time-consuming and expensive.
method Conditional diffusion generative model to infer gene expression.
result Stem achieves state-of-the-art performance in spatial gene expression prediction.
New method infers centromere locations in yeast using Hi-C data.
problem Difficulty in inferring centromere locations in yeast.
method Simulation-based inference using Hi-C data and simulated contact maps.
result Infers stochastic locations of all centromeres in budding yeast.
In most gene expression data, the number of training samples is very small compared to the large number of genes involved in the experiments. However, among the large amount of genes, only a small fraction is effective for performing a certain task. Furthermore, a small subset of genes is desirable in developing gene e…
Unified framework improves gene prioritization in disease studies.
problem Identifying genes involved in diseases using heterogeneous biological data.
method Network propagation-based gene prioritization with integrated biological information.
result Significant improvements in prioritizing genes not identified by traditional methods.
Bayesian method discovers local causal relationships among genes from gene expression data.
problem Discovering gene regulatory relationships from gene expression data.
method Bayesian approach scoring covariance structures for triplets of normally distributed variables, incorporating background knowledge as priors.
result Stable and conservative posterior probability estimates of local causal structures.
New algorithm prevents strategic replication in multi-armed bandit problems.
problem Strategic replication by agents can exploit bandit algorithms' balance.
method Designs Hierarchical UCB (H-UCB) and Robust Hierarchical UCB (RH-UCB) algorithms.
result Achieves O(lnT)-regret and sublinear regret in realistic scenarios. Extends super-replication theorem with dynamic strategies and transaction costs.
problem Dynamic super-replication under proportional transaction costs.
method Generalizes admissible strategies and defines a well-defined super-replication price process.
result Well-defined super-replication price process in dynamic setting.
Study reveals statistical bias in dataset replication, reducing accuracy drop from 11-14% to 3.6%.
problem Statistical bias in dataset replication affects model generalization accuracy.
method Analyzed ImageNet-v2, identified and corrected for bias, and compared results.
result Correcting bias reduces accuracy drop from 11-14% to 3.6%.
Most network-based protein (or gene) function prediction methods are based on the assumption that the labels of two adjacent proteins in the network are likely to be the same. However, assuming the pairwise relationship between proteins or genes is not complete, the information a group of genes that show very similar p…