Sequence-based model predicts protein-protein interactions with high accuracy.
problem Predicting protein-protein interactions for alternative treatment options.
method Sequence clustering, discrete cosine transform, supervised machine learning, SVM with RBF.
result Mesh model achieved an average AUC of 0.84.
Two deep learning models predict protein-protein interactions with high accuracy.
problem Overfitting and information leak in deep learning models for PPI prediction.
method Carefully designed deep learning models, strict conditions for training and testing, and methodology to avoid information leak.
result Best model predicts more than 78% of human PPI with strong confidence.
Study improves LLMs for PPI analysis by addressing uncertainty.
problem Uncertainty in LLM predictions for PPIs.
method Fine-tuned LLaMA-3 and BioMedGPT models, LoRA ensembles, Bayesian LoRA for UQ.
result Competitive PPI identification performance across diverse disease contexts.
Study develops large margin machine learning models for predicting host-pathogen protein interactions.
problem Identifying host-pathogen interactions to develop new drugs for infectious diseases.
method Large margin machine learning models, specifically SVM with weighted negative sampling and distance-based weight assignment.
result Proposed and validated a new method for predicting host-pathogen protein interactions.
Protein-protein interaction (PPI) prediction is an important problem in machine learning and computational biology. However, there is no data set for training or evaluation purposes, where all the instances are accurately labeled. Instead, what is available are instances of positive class (with possibly noisy labels) a…
SL2MF predicts synthetic lethality using logistic matrix factorization.
problem Predicting synthetic lethality in human cancers from limited experimental data.
method Logistic matrix factorization incorporating biological knowledge.
result SL2MF effectively predicts known and unknown SL interactions.
A fast algorithm speeds up training of pairwise kernels.
problem Training pairwise kernels efficiently for large datasets.
method Generalized vec trick for Kronecker product kernels.
result Pairwise kernels can be expressed as sums of Kronecker products.
HopGAT improves node classification in sparsely labeled graphs by learning from distant neighbors.
problem Classifying nodes in sparsely labeled graphs with limited labeled data.
method Hop-aware supervision mechanism and simulated annealing learning strategy.
result The model achieves high accuracy even with 40% labeled data, reducing performance loss to 3.9%.
A framework for multilayer networks predicts links without shared structures.
problem Link prediction in multilayer networks without shared structures.
method Bi-level model averaging with K-fold cross-validation. result Framework outperforms existing methods in predictive accuracy and robustness.
The paper tests for association between latent community memberships in multi-view network data.
problem Evaluating the independence of latent community memberships in multi-view network data.
method Extended stochastic block model for two-view network data, developed a new hypothesis test.
result Evidence of weak association between latent community memberships in binary interaction and co-complex association data.
Protein Thoughts interprets protein interactions with clear reasoning, improving prediction accuracy.
problem Lack of mechanistic justification in protein-protein interaction predictions.
method Interpretable search problem reformulation, hypothesis-guided entropy-regularized Tree-of-Thoughts search, embedding-space flow matching.
result Improves mean best-binder rank from 47.7 to 11.2 on SHS148k benchmark.
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…
Novel model predicts anticancer compound sensitivity with high accuracy and interpretability.
problem Predicting anticancer compound sensitivity with high accuracy and interpretability.
method Multimodal attention-based convolutional encoder using SMILES, gene expression profiles, and protein-protein interaction networks.
result The model significantly outperforms baseline models and demonstrates high interpretability.
Bi-GNN models drug interactions using a bi-level graph approach.
problem Predicting drug-drug interactions using machine learning.
method Bi-level graph neural networks that consider both interaction graph and representation graphs of drugs.
result Bi-GNN model improves DDI prediction accuracy compared to existing methods.
Study identifies cancer genes through graph anomaly analysis of protein interactions.
problem Insufficient modeling of biological information in protein interaction networks for cancer gene identification.
method Proposes HIerarchical-Perspective Graph Neural Network (HIPGNN) to detect weight heterogeneity and spectral flattening in cancer gene nodes.
result HIPGNN detects weight heterogeneity and spectral flattening, leading to improved cancer gene identification.
NetBiTE predicts drug sensitivity and identifies biomarkers in cancer.
problem Predicting drug sensitivity and identifying biomarkers in cancer.
method NetBiTE combines prior knowledge and gene expression data using a biased tree ensemble approach.
result NetBiTE outperforms RF in predicting IC50 drug sensitivity for drugs targeting membrane receptor pathways.
Link prediction is one of the fundamental problems in network analysis. In many applications, notably in genetics, a partially observed network may not contain any negative examples of absent edges, which creates a difficulty for many existing supervised learning approaches. We develop a new method which treats the obs…
A new method predicts higher-order interactions in evolving graphs using simplicial complexes.
problem Predicting higher-order interactions in dynamic graphs with theoretical guarantees.
method Capturing higher-order interactions as simplices, modeling neighborhoods with face-vectors, and developing a nonparametric kernel estimator.
result Our method outperforms existing higher-order prediction methods and is theoretically consistent.
Graphs improve deep learning for gene expression data.
problem Challenges in applying deep learning to gene expression data due to non-linear signal and low sample sizes.
method Graph Convolutional Neural Networks (GCNN) with dropout and gene embeddings.
result GCNN with graph information provides an advantage in a low data regime.
SGAS improves neural architecture search by choosing and pruning operations greedily.
problem NAS often fails to generalize in final evaluation.
method Divides search into sub-problems and chooses/prunes candidate operations greedily.
result SGAS finds state-of-the-art architectures with minimal computational cost.
TIP model improves POSE prediction with less resources.
problem Predicting polypharmacy side effects from drug-protein interactions.
method TIP model operates on three subgraphs for progressive representation learning.
result Improves accuracy by 7%+, time efficiency by 83imes, and space efficiency by 3imes. 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…
Protein function prediction is the important problem in modern biology. In this paper, the un-normalized, symmetric normalized, and random walk graph Laplacian based semi-supervised learning methods will be applied to the integrated network combined from multiple networks to predict the functions of all yeast proteins …
Decagon models polypharmacy side effects using graph convolutional networks.
problem Discovering polypharmacy side effects due to complex drug interactions.
method Developed a graph convolutional neural network for multirelational link prediction in multimodal networks.
result Accurately predicts polypharmacy side effects, outperforming baselines by up to 69%.
Biological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins, drugs) and edges represent relational ties among these objects (binds-to, interacts-with, regulates). This approach has been highly successful owing to the theory, methodology and software that …
Low-dimensional embeddings of nodes in large graphs have proved extremely useful in a variety of prediction tasks, from content recommendation to identifying protein functions. However, most existing approaches require that all nodes in the graph are present during training of the embeddings; these previous approaches …
Graph embedding method captures both local and global network structure.
problem Representing and analyzing complex graph networks.
method Spectral embedding based on a generalized graph Laplacian.
result Significant improvement in data analysis tasks.
LMI approximates mutual information in high dimensions using learned low-dimensional representations.
problem Estimating mutual information between high-dimensional variables is challenging due to sample size limitations.
method Developed a method called latent MI (LMI) approximation that applies a nonparametric MI estimator to low-dimensional representations learned by a simple model architecture.
result LMI can approximate MI well for variables with >10^3 dimensions if their dependence structure has low intrinsic dimensionality.
New approach learns latent motifs in networks for mesoscale structure analysis.
problem Understanding large-scale behavior in complex systems through mesoscale structures.
method Network dictionary learning (NDL) combining network sampling and nonnegative matrix factorization.
result Networks can be approximated using a small set of latent motifs.
Graph Attention Networks use masked self-attention to improve graph neural networks.
problem Improving graph neural networks to better handle graph data.
method Stacked masked self-attention layers that allow nodes to attend to their neighborhoods with different weights.
result GAT models achieve state-of-the-art results across various graph benchmarks.
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.
Graph auto-encoder predicts unobserved node features from biological networks and omics data.
problem Integrating biological networks and continuous node features for better prediction.
method Graph neural networks and feature auto-encoders trained on feature reconstruction.
result Graph feature auto-encoder outperforms auto-encoders trained on graph reconstruction for predicting unobserved node features.
GraphNAS uses reinforcement learning to automatically design graph neural network architectures.
problem Designing effective graph neural network architectures requires manual work and domain knowledge.
method GraphNAS generates variable-length strings to describe architectures and trains a recurrent network with reinforcement learning to maximize validation accuracy.
result GraphNAS achieves consistently better performance on various citation and protein networks.
Paper proposes MLPCD for protein community detection in large PPI networks.
problem Identifying reliable protein communities from large-scale PPI networks.
method Integrates Gene Expression Data and uses Multi-source Learning with cloud computing.
result Demonstrates superior performance compared to existing methods.
We improve MoE models for classification with rigorous guarantees and practical methods.
problem Limited guarantees for stable maximum-likelihood training and model selection in softmax-gated MoE models.
method Derived a batch MM algorithm with closed-form updates, proved finite-sample rates, and developed a dendrogram selector.
result Achieved near-parametric optimal rates for parameter recovery and improved accuracy over baselines.
Proposes a method to identify relevant genes in autism-related diseases using auxiliary information.
problem Identifying relevant genes in autism-related diseases from diverse data sources.
method Uses logistic regression to filter irrelevant genes and clusters relevant genes into cohesive groups using adjacency matrix.
result Superior performance and robustness in finite samples observed in simulation studies.
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.
New algorithm recovers graph structure from noisy data.
problem Noise corrupts structure in Gaussian graphical models, making identification impossible.
method Developed an algorithm to recover graph structure up to an unavoidable ambiguity.
result Algorithm recovers graph structure up to an identified ambiguity, revealing local clustering and connectivity.
A new method infers causal gene regulatory networks from parallel CRISPR interventions and transcriptomic data.
problem Learning causal gene regulatory networks from observational data is complicated by lack of identifiability and a combinatorial solution space.
method A continuous optimization framework that leverages observational and interventional data to infer a single causal structure, assuming a linear Structural Equation Model (SEM).
result A provably consistent estimator of the true DAG under mild assumptions.
LGCL uses learnable filters to apply CNNs on graphs.
problem Applying CNNs to generic graphs like networks.
method Learnable graph convolutional layer (LGCL) and sub-graph training.
result LGCL achieves better performance on various graph datasets.
Numbers and numerical vectors account for a large portion of data. However, recently the amount of string data generated has increased dramatically. Consequently, classifying string data is a common problem in many fields. The most widely used approach to this problem is to convert strings into numerical vectors using …
The motivation for this paper is to apply Bayesian structure learning using Model Averaging in large-scale networks. Currently, Bayesian model averaging algorithm is applicable to networks with only tens of variables, restrained by its super-exponential complexity. We present a novel framework, called LSBN(Large-Scale …
A new model identifies genetic risk factors using gene-level priors.
problem Identifying genetic risk factors from nucleotide-level genetic variants.
method Sparse Group Lasso with Group-level Graph structure (SGLGG) model.
result SGLGG effectively identifies phenotype-associated risk SNPs.
Bayesian model identifies cancer pathways using genomic data.
problem Identifying altered pathways associated with specific cancer types.
method Bayesian semi-nonnegative tri-matrix factorization incorporating biological prior knowledge.
result Pathways identified can be used as prognostic biomarkers.
Develops a fast BMF approach for binary matrices.
problem Finding patterns in binary matrices for various applications.
method MEBF (Median Expansion for Boolean Factorization) using geometric segmentation and heuristic submatrix identification.
result Superior performance in reconstruction error and computational efficiency compared to existing methods.
DSL learns discriminative subgraphs from graphs for robust prediction.
problem Learning discriminative subgraphs from graph data for robust prediction.
method Discriminative Subgraph Learning (DSL) framework that enforces sparsity, connectivity, and high discriminative power.
result DSL improves prediction accuracy by up to 16% compared to baselines.
LEAP predicts graph edges and weights from path aggregations.
problem Predicting edges and weights in graphs.
method Trainable framework based on path aggregations.
result LEAP outperforms state-of-the-art methods in link and rating prediction.
Problems in machine learning (ML) can involve noisy input data, and ML classification methods have reached limiting accuracies when based on standard ML data sets consisting of feature vectors and their classes. Greater accuracy will require incorporation of prior structural information on data into learning. We study …