EpiRL learns to detect gene-gene interactions.
problem Computational challenges in epistasis detection.
method Modeling epistasis as a Markov Decision Process and using reinforcement learning.
result EpiRL discovers highly interacted genes.
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169,051 papers · 148 categories
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48 results for “gene-gene interaction”
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.
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…
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.
Gene-Gene association for Imaging Genetics Data using Robust Kernel Canonical Correlation Analysisstat.ML
In genome-wide interaction studies, to detect gene-gene interactions, most methods are divided into two folds: single nucleotide polymorphisms (SNP) based and gene-based methods. Basically, the methods based on the gene are more effective than the methods based on a single SNP. Recent years, while the kernel canonical …
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.
Discovering causal genetic variants from large genetic association studies poses many difficult challenges. Assessing which genetic markers are involved in determining trait status is a computationally demanding task, especially in the presence of gene-gene interactions. A non-parametric Bayesian approach in the form o…
Group induced graphical lasso allows for discovery of molecular pathways-pathways interactionsq-bio.QM
Method infers multi-layer networks from gene expression data.
problem Inference of multi-level networks from gene expression data.
method Extension of latent graphical lasso method leveraging group structure.
result Efficacy in retrieving multi-layer network structure from synthetic data.
Transposable data represents interactions among two sets of entities, and are typically represented as a matrix containing the known interaction values. Additional side information may consist of feature vectors specific to entities corresponding to the rows and/or columns of such a matrix. Further information may also…
We propose a novel diverse feature selection method based on determinantal point processes (DPPs). Our model enables one to flexibly define diversity based on the covariance of features (similar to orthogonal matching pursuit) or alternatively based on side information. We introduce our approach in the context of Bayes…
We propose a novel hierarchical model for multitask bipartite ranking. The proposed approach combines a matrix-variate Gaussian process with a generative model for task-wise bipartite ranking. In addition, we employ a novel trace constrained variational inference approach to impose low rank structure on the posterior m…
A new method for identifying significant gene subsets improves disease prediction.
problem Identifying significant subsets of genes for disease prediction.
method Kernel gene shaving using influence function of kernel CCA.
result The proposed method outperformed three popular gene selection methods.
Generative model designs drug combinations for improved efficacy and reduced side effects.
problem Designing effective drug combinations to overcome resistance and reduce side effects.
method Developed a deep generative model using HVGAE and a novel reward system.
result Network-principled drug combinations show reduced toxicity and potential for new strategies.
We consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct from each other and from the underlying species tree, possibly confounding phyloge…
GLasso: Regularized Multi-task Graphical Lasso for Joint Estimation of eQTL Mapping and Gene Networkstat.ML
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.
IFM improves recommender systems by learning flexible feature interactions.
problem Dealing with feature interactions in recommender systems can degrade performance.
method Introduces Interaction-Aware Mechanism (IAM) to learn feature and field interactions.
result Improves performance on two well-known datasets compared to state-of-the-art methods.
Surrogate-based analysis of interactions via local effect smooths
problem Detecting and characterizing feature interactions in machine learning models
method Surrogate-based analysis using generalized additive models
result Empirical validation of effectiveness for pairwise interactions
A new method detects interactions in neural networks using topological analysis.
problem Detecting interactions between input features in neural networks.
method Topological analysis of neural network connectivity to quantify interaction strength.
result The PID algorithm outperforms state-of-the-art baselines in interaction detection tasks.
Interactive learning framework for various settings.
problem Various interactive learning settings.
method Adapted active learning algorithm for interactive structure discovery.
result Noise-tolerant algorithm with favorable query complexity.
InteractE: Improving Convolution-based Knowledge Graph Embeddings by Increasing Feature Interactionscs.LG
InteractE improves link prediction in KGs by increasing feature interactions.
problem Improving link prediction in knowledge graphs by inferring missing links.
method Feature permutation, novel feature reshaping, circular convolution.
result InteractE outperforms ConvE on multiple KG datasets.
Enhances MTGP for better hierarchical latent interactions.
problem Current MTGPs struggle with hierarchical latent interactions.
method Proposes a novel kernel representation for hierarchical interactions in LMC of MTGP.
result Promotes knowledge transferring in MTGP through hierarchical interactions.
iKF method uncovers complex variable interactions for scientific discovery.
problem Limited interpretability of existing models in decision-making applications.
method Iterative Kings' Forests (iKF) method to uncover multi-order interactions.
result iKF provides strong interpretive power for explainable modeling.
Joint Interaction and Trajectory Prediction for Autonomous Driving using Graph Neural Networksstat.ML
Graph neural network predicts vehicle interactions and trajectories for autonomous driving.
problem Predicting future motion of vehicles in traffic scenes.
method Graph neural network that jointly predicts interaction modes and 5-second future trajectories.
result Jointly predicting trajectories and interaction modes leads to lower trajectory error.
A graph neural network detects beneficial feature interactions for recommender systems.
problem Feature interactions are crucial but not all are beneficial for recommendation accuracy.
method Graph neural network with L0 activation regularization for edge prediction.
result The model outperforms baselines and automatically identifies beneficial feature interactions.
Inference of time-ordered multibody interactionsphysics.soc-ph
We describe and extract time-ordered multibody interactions from complex systems.
problem Complex systems with temporal and multibody dependencies.
method Decompose multivariate Markov chains into time-ordered multibody interactions. Algorithm to extract interactions from data. Measure complexity of interaction ensembles.
result Robust and efficient algorithm to infer time-ordered multibody interactions from data.
Dropout regularizes against high-order interactions by canceling interaction rates.
problem Overfitting to high-order interactions in neural networks.
method Analyzes Dropout through the lens of interaction effects, showing how it effectively cancels out the probability of surviving interactions of different orders.
result Dropout regularizes against high-order interactions by effectively canceling out the probability of surviving interactions of different orders.
Understanding how features interact with each other is of paramount importance in many scientific discoveries and contemporary applications. Yet interaction identification becomes challenging even for a moderate number of covariates. In this paper, we suggest an efficient and flexible procedure, called the interaction …
SocialInteractionGAN generates realistic human interactions from low-dimensional data.
problem Generating realistic human interactions from limited data.
method Adversarial architecture with a recurrent encoder-decoder generator and dual-stream discriminator.
result SocialInteractionGAN produces high-quality action sequences of interacting people.
A new method detects interactions in machine learning models.
problem Interpreting non-linear and interaction effects in machine learning models.
method Regional effect plots with implicit interaction detection.
result The method quantifies and interprets feature effects reliably, less confounded by interactions.
Robot learns to imitate human interactions through deep learning.
problem Teaching robots to coordinate actions with human partners.
method Deep learning framework for motion embedding, prediction, and trajectory generation.
result Importance of predictive and adaptive components for successful imitation.
xDeepInt learns both vector-wise and bit-wise feature interactions.
problem Learning feature interactions for CTR prediction and recommendation.
method Polynomial Interaction Network (PIN) architecture with subspace-crossing mechanism.
result xDeepInt outperforms state-of-the-art models in CTR prediction and recommendation.
Bayesian neural networks detect complex interactions with uncertainty.
problem Estimating global pairwise interaction effects with uncertainty.
method Bayesian neural network for modeling interactions, GEH for estimating interaction effects.
result The method empirically outperforms alternatives and detects interpretable interactions.
This paper explores how interactive protocols enhance local differential privacy.
problem The power of interactive protocols in local differential privacy.
method Classification of locally private protocols by compositionality and transformation of fully interactive protocols into sequentially interactive ones.
result Fully interactive protocols can solve problems that sequentially interactive protocols cannot without a significant increase in sample complexity.
Mahé provides hierarchical explanations for complex interactions in machine learning models.
problem Capturing and explaining complex interactions in machine learning models.
method Model-agnostic hierarchical explanations through local interpretation and context-free generalization.
result Improved local interaction interpretations and successful explanation of context-free interactions.
Agent learns object segmentation through self-supervised interactions.
problem Object segmentation in visual observations.
method Self-supervised learning through interaction, robust set loss.
result Model generalizes to novel objects and backgrounds.
This study explores how feature graphs enhance GNNs' performance in modeling interactions.
problem Improving GNNs' ability to model feature interactions effectively.
method Investigates feature graphs and their importance in GNNs, using experiments and theoretical support.
result Edges between interacting features are crucial for GNNs, while non-interaction edges can degrade performance.
Interpreting neural networks is a crucial and challenging task in machine learning. In this paper, we develop a novel framework for detecting statistical interactions captured by a feedforward multilayer neural network by directly interpreting its learned weights. Depending on the desired interactions, our method can a…
Paper introduces IC-index to evaluate interaction prediction methods.
problem Evaluate interaction prediction methods using IC-index.
method IC-index measures interaction direction prediction performance.
result IC-index complements existing prediction performance estimators.
This paper uses Gaussian mixtures to mimic interactions in large language models.
problem Simulating interactions in large language models (LLMs) is computationally expensive.
method Developed an interacting Gaussian mixture model (GMM) system to mimic LLM interactions.
result The interacting Gaussian mixture model system can generate, exchange, and update data and parameters efficiently.
Study reveals self-attention's role in learning and generalizing interactions.
problem Understanding self-attention's theoretical role in neural architectures.
method Interacting entities analysis, including multi-agent RL and genetic sequences.
result Self-attention efficiently represents, learns, and generalizes pairwise interactions.
Automated tests detect interactions in unstructured data.
problem Detecting interactions between latent variables in low-dimensional systems.
method Derive two interaction tests based on pairwise interventions and integrate them into an active learning pipeline.
result Tests can identify more known biological interactions than random search and standard active learning baselines.
Archipelago provides interpretable explanations of feature interactions in machine learning models.
problem Interpreting the impact of feature interactions on predictions in machine learning models.
method Archipelago is a novel framework for extracting and attributing feature interactions in a scalable and interpretable manner.
result Archipelago provides significantly more interpretable explanations of feature interactions than comparable methods.
Graphs model traffic interactions, reducing prediction error by 30%.
problem Traffic prediction accuracy with complex interactions.
method Graph Neural Networks (GNN) for modeling vehicle interactions.
result Prediction error decreases by 30% with GNNs compared to non-interaction models.
PIN models feature interactions using a neural network that mimics decision trees.
problem Modeling feature interactions in tabular data for predictive modeling.
method Tree-like Pairwise Interaction Network (PIN) architecture that captures pairwise feature interactions through a shared feed-forward neural network.
result PIN outperforms traditional and modern neural networks benchmarks in predictive accuracy.
The paper explains DNNs by quantifying interactions among input variables.
problem Understanding and explaining the complex behavior of deep neural networks.
method The paper defines and quantifies the significance of interactions among multiple input variables using the Shapley value.
result The proposed method effectively explains the behavior of DNNs by assigning attribution values to input variables.
Modeling continuous movement of entities in latent space for interaction timing.
problem Analyzing timing and frequency of instantaneous interactions.
method Latent position model with continuous trajectories.
result Individual trajectories estimated from interaction data.
The study analyzes neural interactions using an Ising model to reveal contributions of pairwise interactions to sparseness and fluctuation.
problem Understanding the contributions of pairwise interactions to sparseness and fluctuation in neural activity.
method Inference methods for a time-dependent Ising model to analyze neural interactions and estimate time-dependent neural interactions with credible intervals.
result Pairwise interactions contribute to increasing sparseness and fluctuation in neural activity.
Interactions in information spread: quantification and interpretation using stochastic block modelscs.LG
New model quantifies interactions' role in real-world phenomena.
problem Understanding the role of interactions in real-world phenomena.
method Interactive Mixed Membership Stochastic Block Model (IMMSBM).
result Interactions significantly improve model predictive power.