LCD improves causal discovery in high-dimensional gene data.
problem Predicting causal effects in large-scale gene expression data.
method Local Causal Discovery (LCD) with practical estimators, ICP algorithm inspiration, preselection method, and statistical tests.
result LCD estimator closely matches ICP's accuracy but is simpler and faster.
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.
Background: Predictive, stable and interpretable gene signatures are generally seen as an important step towards a better personalized medicine. During the last decade various methods have been proposed for that purpose. However, one important obstacle for making gene signatures a standard tool in clinics is the typica…
Molecular profiling data (e.g., gene expression) has been used for clinical risk prediction and biomarker discovery. However, it is necessary to integrate other prior knowledge like biological pathways or gene interaction networks to improve the predictive ability and biological interpretability of biomarkers. Here, we…
New datasets support supervised learning for fungal BGC discovery.
problem Lack of labeled data for fungal BGCs.
method Developed new publicly available datasets for supervised learning.
result Supervised learning outperforms data-driven methods in fungal BGC prediction.
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.
Estimates target GGM using auxiliary studies with false discovery rate control.
problem Estimating high-dimensional GGMs from related studies.
method Transfer learning with Trans-CLIME and debiased Trans-CLIME estimators.
result Debiased Trans-CLIME estimator provides element-wise asymptotic normality and false discovery rate control.
ASCEND discovers causal relationships in multi-omics data by leveraging known hierarchical structure.
problem Causal inference in high-dimensional multi-omics data, especially when ignoring the hierarchical structure.
method Two-tiered divide-and-conquer strategy with ancestral conditioning sets.
result Achieves polynomial-time complexity and accurately recovers ancestral relationships.
Univariate and multivariate feature selection methods can be used for biomarker discovery in analysis of toxicant exposure. Among the univariate methods, differential expression analysis (DEA) is often applied for its simplicity and interpretability. A characteristic of methods for DEA is that they treat genes individu…
Paper introduces SUEL model for integrating predictors without labeled data.
problem Combining predictors with unknown accuracy and high correlation.
method Structured unsupervised ensemble learning (SUEL) with correlation-based decomposition algorithms.
result Efficient integration of dependent predictors without labeled data.
Unsupervised two-view learning, or detection of dependencies between two paired data sets, is typically done by some variant of canonical correlation analysis (CCA). CCA searches for a linear projection for each view, such that the correlations between the projections are maximized. The solution is invariant to any lin…
Motivation: Algorithms that discover variables which are causally related to a target may inform the design of experiments. With observational gene expression data, many methods discover causal variables by measuring each variable's degree of statistical dependence with the target using dependence measures (DMs). Howev…
Unsupervised method selects genes for tumor subtype discovery.
problem High-dimensional tumor gene expression data with noisy variables and heterogeneity.
method Autoencoders for latent space learning, Multiple Kernel Learning for feature selection, clustering.
result Lower redundancy and better clustering performance compared to benchmarks.
New method for causal discovery using peeling algorithms for various data types.
problem Challenges in causal discovery due to unmeasured confounders.
method Two peeling algorithms (bottom-up and top-down) for causal discovery with generalized structural equation models.
result Valid discovery of causal relationships and parent-child effects in diverse data types.
AcceleratedLiNGAM speeds up causal discovery methods for large datasets.
problem Slow causal discovery methods for large-scale datasets.
method Parallelized LiNGAM method with GPU acceleration.
result Up to 32-fold speed-up on benchmark datasets.
A very important topic in systems biology is developing statistical methods that automatically find causal relations in gene regulatory networks with no prior knowledge of causal connectivity. Many methods have been developed for time series data. However, discovery methods based on steady-state data are often necessar…
Method uses network biology to construct gene expression models for cancer.
problem Building models for cancer phenotypes using gene expression data.
method Unsupervised construction of computational graphs based on protein-protein networks.
result The method outperforms other models in cancer phenotype analysis.
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.
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
problem Efficient design of genomic perturbation experiments in drug discovery.
method Integrates Bayesian optimization with multimodal gene embeddings and enrichment analysis.
result Improves labeling efficiency by 25-40% and identifies top-performing perturbations more effectively.
Motivation : Molecular signatures for diagnosis or prognosis estimated from large-scale gene expression data often lack robustness and stability, rendering their biological interpretation challenging. Increasing the signature's interpretability and stability across perturbations of a given dataset and, if possible, acr…
BaCaDI discovers causal structures from unknown interventions.
problem Inferring causal structures from unknown interventions with limited data.
method Bayesian framework with gradient-based variational inference.
result BaCaDI outperforms related methods in identifying causal structures and intervention targets.
JojoSCL improves scRNA-seq clustering by reducing intra-cluster dispersion.
problem High dimensionality and sparsity of scRNA-seq data challenge clustering models.
method Integrates shrinkage estimator and contrastive learning for improved clustering.
result JojoSCL outperforms existing methods on ten scRNA-seq datasets.
DCCD-CONF discovers causal graphs with unmeasured confounders.
problem Discovering causal relationships in systems with unmeasured confounders.
method Differentiable learning of nonlinear cyclic causal graphs using interventional data.
result DCCD-CONF outperforms state-of-the-art methods in causal graph recovery and confounder identification.
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…
MetaCaDI learns causal graphs and unknown interventions from few data instances.
problem Discovering causal mechanisms in systems with high data costs and unknown interventions.
method MetaCaDI is a Bayesian meta-learning framework that optimizes for rapid adaptation to new intervention targets.
result MetaCaDI significantly outperforms state-of-the-art methods in causal graph recovery and intervention target prediction.
DASH simplifies neural networks for gene regulatory dynamics using domain knowledge.
problem Pruning neural networks for gene regulatory dynamics lacks biologically meaningful structure learning.
method DASH uses domain-specific structural information to guide network pruning, leading to sparser, better interpretable models.
result DASH outperforms general pruning methods in gene regulatory network inference, yielding deeper insights.
Synthetic lethality (SL) is a promising concept for novel discovery of anti-cancer drug targets. However, wet-lab experiments for detecting SLs are faced with various challenges, such as high cost, low consistency across platforms or cell lines. Therefore, computational prediction methods are needed to address these is…
Study improves cancer classification using gene selection and projection methods.
problem Overfitting in high-dimensional microarray datasets for cancer classification.
method FSWOR technique, random projection, Kendall test, ensemble classifiers, LDA projection, Naïve Bayes.
result Achieved a test score of 96%, significantly outperforming existing methods.
A method clusters genes in large gene regulatory networks using semi-supervised hierarchical clustering.
problem Challenging task of identifying interaction clusters in large gene regulatory networks due to data noise and inconsistency.
method SHC-DC: a semi-supervised hierarchical clustering method using deconvolved correlation matrix.
result SHC-DC discovers interaction modules enriched in various signal pathways, validating sleep's impact on interleukin levels and related pathways.
Expands experimental design for causal discovery from limited data.
problem Challenges in causal discovery from observational and interventional data.
method Bayesian optimal experimental design incorporating recent advances in causal discovery.
result Active causal discovery of large, nonlinear SCMs with both intervention target and value selection.
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms…
This work tackles causal graph discovery with stochastic interventions to minimize the number of interventions.
problem Discovering the true causal graph from observational data with limited interventions.
method Proposes a stochastic intervention model and studies verification and search problems with approximation algorithms.
result Provides approximation algorithms with competitive ratios for verification and search problems.
Develops a new method to discover causal relationships from nonstationary time series data.
problem Challenges in inferring causal relationships from observational data, especially for nonstationary time series.
method State-Dependent Causal Inference (SDCI) for conditionally stationary time series.
result SDCI can recover underlying causal dependencies with provable identifiability for state-dependent causal structures.
New algorithm reduces conditional independence tests needed for causal discovery.
problem Efficiently infer causal relations from observational data.
method Established an algorithm with complexity pO(s) tests. result Achieves exponent-optimality up to a logarithmic factor in terms of conditional independence tests.
RobKMR improves robustness in multi-omics data analysis for osteoporosis biomarker discovery.
problem Sensitivity to adversarial outliers and lack of comprehensive multi-omics data integration.
method RobKMR, a non-linear M-estimator-based approach using robust kernel centered Gram matrix and robust score test.
result Selected biomarkers (DKK1, MTND5, FASTKD2) significantly bond with four drugs for osteoporosis.
Genome-wide association studies (GWA studies or GWAS) investigate the relationships between genetic variants such as single-nucleotide polymorphisms (SNPs) and individual traits. Recently, incorporating biological priors together with machine learning methods in GWA studies has attracted increasing attention. However, …
Gaussian Graphical Models (GGMs) are popular tools for studying network structures. However, many modern applications such as gene network discovery and social interactions analysis often involve high-dimensional noisy data with outliers or heavier tails than the Gaussian distribution. In this paper, we propose the Tri…
Nonparametric IPSS selects features with false discovery control.
problem Feature selection in high-dimensional data with theoretical false discovery control.
method Integrated Path Stability Selection (IPSS) applied to nonparametric feature importance scores.
result IPSS accurately controls false discovery rate and detects more true positives than existing methods.
Novel framework predicts cell responses to perturbations using GRNs.
problem Predicting cellular responses to perturbations for drug discovery and personalized therapeutics.
method Graph variational Bayesian causal inference framework with refined GRNs and robust estimator.
result Enhanced model performance and robust estimation of perturbation effects.
Model predicts anti-cancer drug responses using gene and molecular data.
problem Expensive and time-consuming cancer drug discovery and tailoring.
method Uses variational autoencoders and multi-layer perceptrons to encode gene expression and drug data.
result High average R2 of 0.83 and 0.845 in predicting drug responses for breast and pan-cancer cell lines, respectively. Clustering analysis is one of the most widely used statistical tools in many emerging areas such as microarray data analysis. For microarray and other high-dimensional data, the presence of many noise variables may mask underlying clustering structures. Hence removing noise variables via variable selection is necessary…
Complex systems may contain heterogeneous types of variables that interact in a multi-level and multi-scale manner. In this context, high-level layers may considered as groups of variables interacting in lower-level layers. This is particularly true in biology, where, for example, genes are grouped in pathways and two …
ENN method uses expectile regression for genetic data analysis of complex diseases.
problem Discover additional genetic variants contributing to complex diseases.
method Developed an expectile neural network (ENN) method integrating expectile regression and neural networks.
result ENN method outperforms existing expectile regression in discovering genetic variants predisposing to sub-populations.
New method controls false discoveries in structured hypothesis spaces.
problem Controlling false discoveries in large-scale, interconnected hypothesis spaces.
method Reproducing Kernel Hilbert Space (RKHS) optimization for structured FDR control.
result Unified framework for continuous domains, graphs, and hierarchies.
A model learns causal graphs from summary statistics of synthetic data.
problem Causal discovery algorithms are brittle with large sets of variables and limited data.
method A supervised model trained on synthetic data predicts causal graphs from summary statistics.
result The model generalizes well beyond its training set and runs on large graphs.
Deep neural networks (DNNs) are famous for their high prediction accuracy, but they are also known for their black-box nature and poor interpretability. We consider the problem of variable selection, that is, selecting the input variables that have significant predictive power on the output, in DNNs. We propose a backw…
A fundamental question in data analysis, machine learning and signal processing is how to compare between data points. The choice of the distance metric is specifically challenging for high-dimensional data sets, where the problem of meaningfulness is more prominent (e.g. the Euclidean distance between images). In this…
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.