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.
FAB-PPI uses prior knowledge to improve prediction-powered inference.
problem Improving statistical inference with machine learning predictions.
method Informing PPI with prior knowledge on prediction quality.
result FAB-PPI improves inference accuracy and confidence intervals.
PPI++ outperforms gold-standard labels only if pseudo-labels are highly correlated.
problem Optimizing statistical estimation using noisy pseudo-labels.
method Exact finite-sample analysis of PPI++ on mean estimation problem.
result PPI++ has provably worse estimation error than gold-standard labels alone in some settings.
PPI++ uses machine learning predictions to improve inference from small datasets.
problem Efficient inference from small labeled datasets with high-quality predictions.
method Adapts prediction-powered inference (PPI) to compute confidence sets for any parameter dimensionality.
result Improves classical intervals using only labeled data, always yielding better results.
PPI uses survey sampling methods for inference, bridging ML and statistics.
problem Combining machine learning predictions with small labeled data for valid inference.
method Equivalence of PPI estimators to survey sampling methods.
result PPI estimators are algebraically equivalent to survey sampling methods.
New methods improve inference with scarce labels using regression.
problem Efficient inference with limited labeled data.
method Relates PPI++ to ordinary least squares regression and uses robust regressors.
result Improved variance in estimators for few-label scenarios.
PPI uses predictions and weighting to infer from partially labeled data.
problem Valid inference with partially labeled data.
method Combines model-based predictions with bias correction from labeled data, using Horvitz-Thompson and Hájek corrections.
result IPW-adjusted PPI with estimated propensities performs similarly to known-probability case.
Unified approach combines prediction-powered inference and variance reduction for semi-supervised optimization.
problem Scarcity of labeled data in semi-supervised optimization.
method PPI-SVRG, combining PPI and SVRG methods.
result Unified convergence bound with improved performance under label scarcity.
Generalizes prediction-powered inference for binary classifier evaluation.
problem Evaluation of binary classifiers with partially observed outcomes.
method Generalizes PPI to any regular asymptotically linear estimator and proposes modified estimators for covariate shift.
result PPI can be a computationally-simple alternative to existing methods, achieving no greater than the semi-parametric efficiency lower bound in certain scenarios.
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.
PPI uses predictions to improve inference from incomplete data.
problem Incomplete or costly-to-measure outcomes in research fields.
method Leverages large unlabeled datasets for improved statistical efficiency with bias correction.
result PPI variants produce tighter confidence intervals than complete-case analysis.
Calibrated Prediction-Powered Inference improves semisupervised mean estimation by calibrating prediction scores.
problem Semisupervised mean estimation with a small labeled sample and a large unlabeled sample, and miscalibrated prediction models.
method Calibrated Prediction-Powered Inference (Calibeating) post-hoc calibrates the prediction score on the labeled sample before using it for semisupervised estimation.
result Calibrated Prediction-Powered Inference can improve the original score both as a predictor of the outcome and as a regression adjustment for semisupervised inference.
MEC improves efficiency and robustness in semi-supervised inference.
problem Efficient inference with limited labeled data and robust uncertainty quantification.
method Machine-Learning-Assisted Generalized Entropy Calibration (MEC) using cross-fitted, calibration-weighted PPI.
result MEC achieves semiparametric efficiency bounds under weaker assumptions and provides near-nominal coverage.
Investigates optimal PPI strategies to reduce carbon emissions while managing financial risk.
problem Optimizing portfolio insurance strategies to mitigate carbon emissions.
method Modelled risky assets using stochastic factor model with partial information, solved optimization problem using CRRA utility function.
result Optimal carbon penalized PPI strategies reduce carbon emissions without sacrificing financial performance.
AM-PPI uses multiple predictors to reduce label cost in healthcare AI.
problem Reduces label cost in post-deployment monitoring of healthcare AI.
method Combines model predictions with a small labeled sample, routing each instance to a cost-appropriate subset of predictors.
result Produces narrower confidence intervals than single-predictor methods.
The study analyzes macroeconomic factors affecting copper futures volatility and long-term correlation with S&P 500.
problem Understanding the impact of macroeconomic variables on copper futures volatility and long-term correlation.
method Employed GARCH-MIDAS and DCC-MIDAS modeling frameworks to examine the influence of low-frequency macroeconomic variables on copper futures returns and long-term correlation with S&P 500.
result PPI is the most efficient macroeconomic variable impacting copper futures returns, and MIDAS filter improves model fitness and long-run relationship.
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.
Investigates optimal PPI strategies in jump-diffusion models to mitigate downside risk.
problem Gap risk in PPI strategies due to jumps in asset price dynamics.
method Optimization problem with S-shaped utility functions, solved via martingale approach in a jump-diffusion framework.
result Determines optimal PPI strategy to maximize expected utility of terminal wealth.
A framework uses a mixture of predictors for semi-supervised inference.
problem Limited labeled data, abundant unlabeled data.
method Mixture of Experts (MOE) for semi-supervised inference.
result MOE-powered inference framework achieves smallest possible variance.
Extends PPI to sequential setting, improving inference over time.
problem Sequential data growth with unlabelled data.
method Prediction-powered confidence sequence procedures using Ville's inequality and the method of mixtures.
result Asymptotically valid uniformly over time, accommodating prior knowledge.
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.
Improved local multivariable regression for better inference with limited data.
problem Limited sample size hampers local polynomial/multivariable regression.
method Prediction-Powered Inference (PPI) algorithm for local multivariable regression.
result Significantly reduces estimation variance without increasing error.
Detection of protein-protein interactions (PPIs) plays a vital role in molecular biology. Particularly, infections are caused by the interactions of host and pathogen proteins. It is important to identify host-pathogen interactions (HPIs) to discover new drugs to counter infectious diseases. Conventional wet lab PPI pr…
New method uses AI predictions as cheaper alternatives to expensive outcomes.
problem Using expensive outcomes for statistical inference.
method Recalibrated prediction-powered inference using machine learning techniques.
result Significant gains in effective sample size over existing PPI proposals.
PAS improves estimation of multiple means using ML predictions and shrinkage.
problem Improving statistical estimates with limited gold-standard data and noisy ML predictions.
method Prediction-Powered Adaptive Shrinkage (PAS) that combines PPI with empirical Bayes shrinkage.
result PAS adapts to the reliability of ML predictions and outperforms traditional methods in large-scale applications.
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.
StratPPI improves prediction-powered inference with stratified sampling.
problem Improving statistical estimates with limited human-labeled data.
method Combining small human-labeled data with large automatic-labeled data, stratifying data for tighter confidence intervals.
result StratPPI provides substantially tighter confidence intervals than unstratified approaches.
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…
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.
Paper presents RGNN for better graph node representation learning.
problem Node representation learning with graph neural networks.
method Recurrent Graph Neural Network (RGNN) with recurrent units.
result RGNN achieves state-of-the-art results on three benchmarks.
New graph representation learning network improves scalability and feature integration.
problem Scalability and feature integration in graph neural networks for large, dense graphs.
method Adaptive sampling of neighbours based on weighted multi-step transition probabilities.
result Comparable or better results on various graph benchmarks.
PPI uses proxy data to improve inference from limited labels across related tasks.
problem Statistical inference with limited labels across multiple related tasks.
method Prediction-powered inference framework that uses cross-task recalibration to improve power and accuracy.
result Cross-task recalibration can substantially reduce confidence interval widths when labels are scarce.
Three years ago we found a statistically reliable link between ConocoPhillips' (NYSE: COP) stock price and the difference between the core and headline CPI in the United States. In this article, the original relationship is revisited with new data available since 2009. The agreement between the observed monthly closing…
Generative Augmented Inference improves AI-generated data for causal inference.
problem Challenges in using AI-generated annotations for reliable causal inference.
method Generative Augmented Inference (GAI) treats AI outputs as informative features for learning true labels, flexibly modeling the relationship using nonparametric methods.
result GAI significantly reduces estimation error and improves confidence interval quality compared to human-only and PPI-based methods.
The worldwide surge of multiresistant microbial strains has propelled the search for alternative treatment options. The study of Protein-Protein Interactions (PPIs) has been a cornerstone in the clarification of complex physiological and pathogenic processes, thus being a priority for the identification of vital compon…
Graph Convolutional Networks (GCNs) have shown significant improvements in semi-supervised learning on graph-structured data. Concurrently, unsupervised learning of graph embeddings has benefited from the information contained in random walks. In this paper, we propose a model: Network of GCNs (N-GCN), which marries th…
Piecewise polynomial interpolation-based gradient descent reduces oracle complexity for smooth loss functions.
problem Optimizing empirical risk minimization loss functions
method Piecewise polynomial interpolation-based gradient descent
result Oracle complexity is reduced for smooth loss functions
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.
PDNAS optimizes GNN architectures for diverse datasets.
problem Inadequate adaptability and combinatorial search space in GNNs.
method Dual architecture search (micro- and macro-architectures) with gradient-based optimization.
result PDNAS finds deeper GNNs with better performance on diverse datasets.
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…
GraphSAINT improves GCN training efficiency and accuracy with graph sampling.
problem Neighbor explosion problem in minibatch training of GCNs.
method GraphSAINT constructs minibatches by sampling the training graph, ensuring fixed well-connected nodes in all layers.
result GraphSAINT achieves new state-of-the-art F1 scores for PPI and Reddit.
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.
PPBoot simplifies prediction-powered inference.
problem Prediction-powered inference problems.
method Bootstrap-based method for arbitrary estimation problems.
result PPBoot often performs nearly identically to PPI(++).
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.
New methods use ML predictions to improve statistical inference.
problem Improving statistical inference using machine learning predictions.
method Prediction-Augmented Trees (PART, PAQ) for reliable statistical analysis.
result PART and PAQ outperform existing methods in various datasets.
Paper establishes statistical inference for performative predictions.
problem Dynamic influence of predictions on their targets.
method End-to-end framework for estimation and inference under performativity.
result Established central limit theorem for performative settings.
Cluster-GCN efficiently trains deep GCNs on large graphs without memory or computational constraints.
problem Training large-scale GCNs is computationally and memory-intensive.
method Cluster-GCN exploits graph clustering to restrict neighborhood search to dense subgraphs, reducing memory and computational requirements.
result Cluster-GCN achieves comparable test accuracy to previous algorithms while being faster and using less memory.
R-AutoEval+ improves model evaluation efficiency and reliability using adaptive synthetic data.
problem Accurate model selection from AI candidates using real-world data is costly and impractical at scale.
method R-AutoEval+ uses adaptive prediction-powered inference to correct bias in autoevaluators while maintaining or improving sample efficiency.
result R-AutoEval+ provides finite-sample reliability guarantees and enhanced sample efficiency compared to conventional methods.