Motivation: Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample. Despite computational advances, interpreting collected measurements and determining their biological role remains a challenge. Results: To interpret measurement…
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48 results for “Biological Pathways”
PKB framework boosts genomic data analysis by integrating pathway knowledge.
problem Boosting discovery power and connecting new findings with biological mechanisms in genomic data.
method Pathway-based Kernel Boosting (PKB) framework integrating clinical and pathway information for prediction of various outcomes.
result PKB substantially outperforms other methods in predicting drug response and cancer survival.
SENA-discrepancy-VAE interprets latent causal factors in biological pathways.
problem Interpreting latent causal factors in biological pathways.
method SENA-discrepancy-VAE, a model based on discrepancy-VAE, that produces interpretable latent causal factors.
result Sena-discrepancy-VAE achieves comparable predictive performance with non-interpretable counterparts while providing biologically meaningful causal factors.
Bayesian approach infers signaling pathways from data.
problem Accurately understand cellular regulation processes.
method Dynamic Bayesian Network structure estimation using Markov Chain Monte Carlo.
result Efficient sampling of sparse graphs improves inference.
Bayesian Semi-nonnegative Tri-matrix Factorization to Identify Pathways Associated with Cancer Typesstat.ML
Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop novel therapeutic agents as well as to understand the molecular mechanisms of variou…
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
problem Predicting biological effects of chemical structures for drug discovery.
method Siamese Graph Convolutional Neural Networks for structure-biological effect mapping.
result Highly accurate predictions of biological effects for structurally dissimilar compounds.
The analysis of cancer genomic data has long suffered "the curse of dimensionality". Sample sizes for most cancer genomic studies are a few hundreds at most while there are tens of thousands of genomic features studied. Various methods have been proposed to leverage prior biological knowledge, such as pathways, to more…
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.
Autonomous Discovery of Unknown Reaction Pathways from Data by Chemical Reaction Neural Networkq-bio.MN
CRNN discovers chemical reaction pathways from data.
problem Challenging to infer reaction pathways for complex systems.
method Neural network approach that satisfies fundamental physics laws.
result CRNN autonomously discovers reaction pathways from species concentration data.
New method detects and compares folding pathways of knotted proteins.
problem Understanding the function of knots in protein folding.
method Topological analysis of protein knotoid distributions and entanglement.
result Reveals unique folding pathway for shallow knotted Carbonic Anhydrases.
engGNN: A Dual-Graph Neural Network for Omics-Based Disease Classification and Feature Selectioncs.LG
engGNN combines external and generated graphs to improve disease classification and biomarker discovery.
problem Challenges in integrating omics data due to high dimensionality and small sample sizes.
method Dual-graph framework that integrates external biological networks with data-driven generated graphs.
result engGNN outperforms state-of-the-art methods in disease classification and biomarker discovery.
Group induced graphical lasso allows for discovery of molecular pathways-pathways interactionsq-bio.QM
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 …
Complex architectures of biological neural circuits, such as parallel processing pathways, has been behaviorally implicated in many cognitive studies. However, the theoretical consequences of circuit complexity on neural computation have only been explored in limited cases. Here, we introduce a mechanism by which direc…
Oja's rule improves neural network training without engineered tricks.
problem Training deep neural networks with biological constraints.
method Incorporating Oja's plasticity rule into error-driven training.
result Stable, efficient learning in feedforward and recurrent architectures.
Proposes a new neural network approach to credit assignment.
problem Credit assignment problem in deep neural networks.
method Contrastive similarity matching objective function.
result Deep networks learn to match similarity between layers.
New method analyzes complex multivariate pathways in high-dimensional data.
problem High-dimensional mediation analysis of multivariate exposures, mediators, and outcomes.
method Simultaneous variable selection, indirect effect matrix estimation, and prediction of multivariate outcomes.
result Identifies biologically interpretable genetic-neural-cognitive pathways.
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
problem Lack of methods to model pleiotropy in multi-phenotype GWAS.
method Bayesian inference model using summary statistics, fast computation, and biologically informed priors.
result Demonstrates utility in metabolite GWAS with interpretable pathway-level inference.
Exclusive Group Lasso improves feature selection in correlated biological data.
problem Correlated features hinder Lasso performance in biological classification problems.
method Proposes and solves the exclusive group Lasso, combining stability selection and random group allocation.
result Exclusive Group Lasso outperforms Lasso in comprehensive selection of informative features.
A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially va…
We analyze large, multi-dimensional, sparse counting data sets, finding unsupervised groups to provide unique insights into genetic data. We create gene and biological pathway groups based on patients' variants to find common risk factors for four common types of cancer (breast, lung, prostate, and colorectal) and auti…
The backpropagation (BP) algorithm is often thought to be biologically implausible in the brain. One of the main reasons is that BP requires symmetric weight matrices in the feedforward and feedback pathways. To address this "weight transport problem" (Grossberg, 1987), two more biologically plausible algorithms, propo…
MediEncoder: Nonlinear Representation Learning for High-Dimensional Causal Mediation Analysisstat.ME
MediEncoder learns nonlinear representations for causal mediation analysis.
problem High-dimensional noisy covariates and mediators in biomedical studies.
method Coupled encoder-decoder architecture with cross-factor network.
result Improves estimation accuracy in high-dimensional causal mediation analysis.
Identification of feasible pathway information for c-di-GMP binding proteins in cellulose productionq-bio.QM
Paper uses machine learning to identify key pathways for c-di-GMP in bacterial genomes.
problem Understanding pathways essential for c-di-GMP in bacterial cellulose production.
method Applied Lasso and Random Forests for feature selection and modeling gene count data.
result Bacterial chemotaxis is identified as the most essential pathway for c-di-GMP encoding domains.
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…
We present a general framework for classifying partially observed dynamical systems based on the idea of learning in the model space. In contrast to the existing approaches using model point estimates to represent individual data items, we employ posterior distributions over models, thus taking into account in a princi…
As an increasing number of genome-wide association studies reveal the limitations of attempting to explain phenotypic heritability by single genetic loci, there is growing interest for associating complex phenotypes with sets of genetic loci. While several methods for multi-locus mapping have been proposed, it is often…
We categorise coherent band (aka nullification) pathways between knots and 2-component links. Additionally, we characterise the minimal coherent band pathways (with intermediates) between any two knots or 2-component links with small crossing number. We demonstrate these band surgeries for knots and links with small cr…
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…
Motivation: The rapid growth of diverse biological data allows us to consider interactions between a variety of objects, such as genes, chemicals, molecular signatures, diseases, pathways and environmental exposures. Often, any pair of objects--such as a gene and a disease--can be related in different ways, for example…
Bayesian hypergraph inference models disease pathways from EHR data.
problem Modeling rare diseases influenced by shared risk factors.
method Bayesian hypergraph inference framework reframing multi-disease modeling.
result Interpretable disease pathways and well-calibrated uncertainty quantification.
In many scientific studies, it becomes increasingly important to delineate the causal pathways through a large number of mediators, such as genetic and brain mediators. Structural equation modeling (SEM) is a popular technique to estimate the pathway effects, commonly expressed as products of coefficients. However, it …
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…
Motivated by an important insight from neural science, we propose a new framework for understanding the success of the recently proposed "maxout" networks. The framework is based on encoding information on sparse pathways and recognizing the correct pathway at inference time. Elaborating further on this insight, we pro…
Clustering with variable selection is a challenging yet critical task for modern small-n-large-p data. Existing methods based on sparse Gaussian mixture models or sparse K-means provide solutions to continuous data. With the prevalence of RNA-seq technology and lack of count data modeling for clustering, the current pr…
Method learns shared and specific factors in multi-study gene expression data.
problem Understanding shared and specific factors in high-dimensional multi-study data.
method Nonlinear multi-study factor model with sparse variational autoencoder.
result Method recovers meaningful shared and specific factors in platelet gene expression data.
Joint replacement is the most common inpatient surgical treatment in the US. We investigate the clinical pathway optimization for knee replacement, which is a sequential decision process from onset to recovery. Based on episodic claims from previous cases, we view the pathway optimization as an intelligence crowdsourci…
This research improves multitask learning by creating task-specific pathways.
problem Creating task-specific representations for efficient learning.
method Developed generalization bounds for learning multiple tasks over multiple pathways.
result Proves the superiority of multipath representation over traditional shallow supernets.
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than others in term of their multi-omics follows from the analysis of these circuits . T…
We introduce tools to capture the dynamics of three different pathways, in which the synchronization of human decision-making could lead to turbulent periods and contagion phenomena in financial markets. The first pathway is caused when stock market indices, seen as a set of coupled integrate-and-fire oscillators, sync…
Computing Transition Pathways for the Study of Rare Events Using Deep Reinforcement Learningphysics.comp-ph
Deep reinforcement learning method finds rare events in complex systems.
problem Computing transition pathways in high-dimensional systems.
method Formulated as a cost minimization problem, solved using DDPG with physical properties.
result Efficiently samples and computes globally optimal transition pathways.
New method makes neural networks transparent, revealing learning modes.
problem Lack of interpretability in neural networks.
method Weight pathway analysis (WPA) to decompose neural networks into subnetworks.
result Neural networks store and utilize information holographically, with linear and nonlinear learning modes.
Simulates patient pathways to detect delayed rare disease diagnoses.
problem Delayed rare disease diagnoses in France, causing health system and patient harm.
method Probabilistic modelling of patient pathways to create an alert system.
result Alert system detects and refers wandering patients to CRMRs.
In this work, we developed a network inference method from incomplete data ("PathInf") , as massive and non-uniformly distributed missing values is a common challenge in practical problems. PathInf is a two-stages inference model. In the first stage, it applies a data summarization model based on maximum likelihood to …
Bayesian method detects mesoscale structures in pathway data networks.
problem Mesoscale structures in pathway data networks are hard to detect due to dependencies between interactions.
method Bayesian approach modeling optimal partitioning and higher-order dynamics.
result Method can recover both proximity-based and role-based groupings of nodes.
Expanding neural networks improves their learning from noisy data.
problem Improving neural network performance in noisy conditions.
method Sparse expansion of neural network inputs, followed by pruning, enhances generalization.
result Sparse expansion of neural networks improves generalization performance, even after pruning.
ESN model helps understand climate event impacts.
problem Understanding complex climate event impacts.
method Feature importance methods for ESNs on spatio-temporal climate data.
result Characterized relationships between Mount Pinatubo eruption variables.
Modern medicine requires generalised approaches to the synthesis and integration of multimodal data, often at different biological scales, that can be applied to a variety of evidence structures, such as complex disease analyses and epidemiological models. However, current methods are either slow and expensive, or inef…
The paper proposes a method to predict the performance of data-driven algorithms using surrogate models.
problem Improving the performance prediction of data-driven knowledge discovery algorithms.
method Surrogate-assisted performance prediction using evolutionary modeling of clinical pathways.
result The proposed approach provides interpretable prediction of algorithm performance and quality.