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.
The article improves GP interpolation calibration using conformal prediction.
problem GP interpolation often produces poorly calibrated prediction intervals.
method Integrates conformal prediction with Gaussian process models.
result CP methods enhance prediction interval calibration without sacrificing accuracy.
We investigate the effect of the proportional hazards assumption on prognostic and predictive models of the survival time of patients suffering from amyotrophic lateral sclerosis (ALS). We theoretically compare the underlying model formulations of several variants of survival forests and implementations thereof, includ…
Variant of mSSA improves time series prediction error.
problem Improve prediction error in multivariate time series.
method Introduce spatio-temporal factor model, establish prediction error scaling.
result Prediction error scales as 1 / √(min(N, T)T).
This work provides simple algorithms for multi-class (and multi-label) prediction in settings where both the number of examples n and the data dimension d are relatively large. These robust and parameter free algorithms are essentially iterative least-squares updates and very versatile both in theory and in practice. O…
Stochastic gradient methods are dominant in nonconvex optimization especially for deep models but have low asymptotical convergence due to the fixed smoothness. To address this problem, we propose a simple yet effective method for improving stochastic gradient methods named predictive local smoothness (PLS). First, we …
Predictions can shape outcomes, study helps predict these effects.
problem Understanding how predictions influence real-world outcomes.
method Causal identifiability analysis of prediction-covariate-outcome relationships.
result Standard supervised learning can identify transferable relationships from predictions.
Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We present a provably correct algorithm for learning a PST with approximate suffix…
DW-KNN improves KNN by integrating distance and neighbor reliability for better prediction accuracy.
problem Standard KNN assumes all neighbors are equally reliable, leading to unreliable predictions in heterogeneous feature spaces.
method DW-KNN integrates exponential distance with neighbor validity, providing instance-level interpretability and reducing hyperparameter sensitivity.
result DW-KNN achieves 0.8988 average accuracy, ranks 2nd among six methods, and has the lowest cross-validation variance.
New metrics CWSA and CWSA+ improve model evaluation under confidence thresholds.
problem Lack of metrics capturing model reliability under confidence thresholds.
method Introducing CWSA and CWSA+ metrics that reward confident accuracy and penalize overconfident mistakes.
result CWSA and CWSA+ outperform classical metrics in trust-sensitive tests.
This study reviews decentralized prediction markets, identifying key design variants and open problems.
problem Designing and implementing decentralized prediction markets with desirable properties.
method Modular workflow comprising eight stages: infrastructure, market topic, share structure, pricing, market initialization, trading, resolution, settlement, and archiving. Analysis of design variants and trade-offs.
result Identification of open problems for researchers in the field of decentralized prediction markets.
Transformer models show robustness across domains with domain adversarial training.
problem Domain adaptation from multiple sources with no labeled data.
method Domain adversarial training and mixture of experts.
result Domain adversarial training improves representation but not performance.
New method uses DNN for genetic variant identification, controlling randomness and improving interpretability.
problem Challenges in interpreting deep neural networks for genetic variant identification.
method Interpretable neural network model with controlled variable selection using ensembling, knockoffs, and de-randomization.
result The proposed method leads to more discoveries compared to conventional methods.
We interpret black box predictive models using causal attribution.
problem Interpreting models trained using machine learning in high-stakes applications.
method Estimate causal effects of model inputs on output using observational data.
result Effective interpretation of black box predictive models via causal attribution.
Natural spatiotemporal processes can be highly non-stationary in many ways, e.g. the low-level non-stationarity such as spatial correlations or temporal dependencies of local pixel values; and the high-level variations such as the accumulation, deformation or dissipation of radar echoes in precipitation forecasting. Fr…
As a fundamental problem in many different fields, link prediction aims to estimate the likelihood of an existing link between two nodes based on the observed information. Since this problem is related to many applications ranging from uncovering missing data to predicting the evolution of networks, link prediction has…
Proposes new method for calibrating treatment effect predictors.
problem Calibrating predictors of heterogeneous treatment effects.
method Causal isotonic calibration and cross-calibration.
result Achieves fast calibration rates under weak conditions.
New Random Forest variants estimate heterogeneous treatment effects using Wasserstein distances.
problem Estimating heterogeneous treatment effects in complex situations.
method Proposes natural variants of Random Forests using Wasserstein distances.
result Natural variants of Random Forests are well-suited for estimating conditional distributions.
A new method predicts true classes from positive and unlabeled data with additional labeled observations.
problem Predicting true classes from positive and unlabeled data with selection bias.
method Introduces augmented PU prediction, allowing feature-dependent labeling, and compares various empirical Bayes rules.
result The variational autoencoder-based method performs similarly or better than other methods and improves accuracy for unlabeled samples.
A new approach to protein language models combines latent space prediction with masked language modeling.
problem Improving protein language models by predicting amino acid identities at masked positions.
method A variant of masked language modeling that predicts latent targets only at masked positions, retaining the MLM cross-entropy.
result The new approach outperforms pure masked language modeling on 11 out of 16 downstream tasks.
We generalize to the finite-state case the notion of the extreme effect variable Y that accumulates all the effect of a variant variable V observed in changes of another variable X. We conduct theoretical analysis and turn the problem of finding of an effect variable into a problem of a simultaneous decomposition…
Fast and cheaper next generation sequencing technologies will generate unprecedentedly massive and highly-dimensional genomic and epigenomic variation data. In the near future, a routine part of medical record will include the sequenced genomes. A fundamental question is how to efficiently extract genomic and epigenomi…
The (variational) graph auto-encoder and its variants have been popularly used for representation learning on graph-structured data. While the encoder is often a powerful graph convolutional network, the decoder reconstructs the graph structure by only considering two nodes at a time, thus ignoring possible interaction…
We consider problems in which a system receives external \emph{perturbations} from time to time. For instance, the system can be a train network in which particular lines are repeatedly disrupted without warning, having an effect on passenger behavior. The goal is to predict changes in the behavior of the system at par…
Bayesian max-margin models have shown superiority in various practical applications, such as text categorization, collaborative prediction, social network link prediction and crowdsourcing, and they conjoin the flexibility of Bayesian modeling and predictive strengths of max-margin learning. However, Monte Carlo sampli…
Distillation is an effective knowledge-transfer technique that uses predicted distributions of a powerful teacher model as soft targets to train a less-parameterized student model. A pre-trained high capacity teacher, however, is not always available. Recently proposed online variants use the aggregated intermediate pr…
causalKANs provides interpretable treatment effect estimates using neural networks.
problem The opacity of deep neural networks limits their adoption in sensitive domains.
method Proposes causalKANs, a framework that transforms neural estimators into interpretable closed-form formulas.
result causalKANs performs on par with neural baselines in CATE error metrics and offers a favorable accuracy--interpretability trade-off.
We consider a variant of the classic Ski Rental online algorithm with applications to machine learning. In our variant, we allow the skier access to a black-box machine-learning algorithm that provides an estimate of the probability that there will be at most a threshold number of ski-days. We derive a class of optimal…
ShapShift explains shifts in model predictions due to data distribution changes.
problem Prediction shifts caused by changes in input distribution.
method Subgroup Conditional Shapley Values applied to decision trees and ensembles.
result Simple, faithful, and near-complete explanations of prediction shifts across model classes.
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.
Deep generative models (DGMs) are effective on learning multilayered representations of complex data and performing inference of input data by exploring the generative ability. However, it is relatively insufficient to empower the discriminative ability of DGMs on making accurate predictions. This paper presents max-ma…
Deep models improve GWAS by identifying genetic interactions.
problem Missing non-linear interaction effects in GWAS.
method Gradient-based DeepLIFT technique to interpret deep models.
result Known and novel genetic risk factors identified.
Machine learning experiments often mislead due to unmet assumptions.
problem Machine learning experiments with pooled data may not meet necessary assumptions for unbiased causal effect estimation.
method Analysis of assumptions required for unbiased causal effect estimation in machine learning experiments.
result Practical applications of A/B-tests with machine learning models may not yield unbiased estimates of causal effect.
The paper proposes a new variant of a decision tree, called an Extreme Learning Tree. It consists of an extremely random tree with non-linear data transformation, and a linear observer that provides predictions based on the leaf index where the data samples fall. The proposed method outperforms linear models on a bench…
Paper proposes a method to quantify and explain machine learning uncertainty in predictive process monitoring.
problem Neglect of data-driven estimation, point forecasts without model uncertainty, and lack of explanations.
method Quantile Regression Forests for interval predictions and SHapley Additive Explanations for uncertainty.
result Effective handling of model uncertainty in predictive process monitoring.
Improved DeepONet variants using Transformer cross-conditioning enhance PDE solution efficiency.
problem Solving partial differential equations efficiently and accurately.
method Transformer-inspired DeepONet variants with bidirectional cross-conditioning.
result Improved efficiency and accuracy compared to modified DeepONet, with variant effectiveness tied to PDE characteristics.
Paper introduces conformal prediction for reliable uncertainty quantification in landmark localization.
problem Systematic underestimation of total predictive uncertainty in landmark localization.
method Conformal prediction framework for multi-output regression, generating flexible prediction regions.
result Methods outperform existing approaches in validity and efficiency across 2D and 3D datasets.
Framework uses machine learning to distinguish major COVID-19 variants.
problem Discriminate and visualize associations between major COVID-19 variants based on genome sequences.
method Unsupervised machine learning methods, including k-mer analysis, PCA, t-SNE, UMAP, and agglomerative hierarchical clustering.
result Framework effectively distinguishes between major variants and identifies emerging variants.
Despite the success of ensemble classification methods in multi-class classification problems, ensemble methods based on approaches other than bagging have not been widely explored for multi-label classification problems. The Kalman Filter-based Heuristic Ensemble (KFHE) is an ensemble method that exploits the sensor f…
MIP framework improves urban flow prediction by adapting to distribution shifts.
problem Distribution shifts in urban flow data make prediction models unreliable.
method Memory-enhanced Invariant Prompt learning with learnable memory bank.
result MIP ensures robust predictions by focusing on invariant features.
AlphaZero assesses new chess variants for balance and dynamics.
problem Designing engaging and balanced game rules, especially for chess variants.
method Used AlphaZero to learn near-optimal strategies for nine chess variants.
result AlphaZero reveals novel strategic and tactical patterns in chess variants.
PEC improves class-incremental learning by measuring prediction error.
problem Challenges in class-incremental learning, particularly forgetting and class imbalance.
method Prediction Error-based Classification (PEC) measures prediction error of a model trained on data from a class.
result PEC outperforms other methods in class-incremental learning across multiple benchmarks.
We propose a dynamic edge exchangeable network model that can capture sparse connections observed in real temporal networks, in contrast to existing models which are dense. The model achieved superior link prediction accuracy on multiple data sets when compared to a dynamic variant of the blockmodel, and is able to ext…
Proposes DeGLIF to denoise graph data for label noise robustness.
problem Label noise in graph data makes node classification challenging.
method Uses leave-one-out influence function to denoise graph data.
result DeGLIF improves accuracy in node classification on noisy datasets.
Study the properties of SGD in non-vanishing learning rate regime.
problem Understanding the noise and fluctuation in SGD with finite learning rates.
method Derive exact solvable results for discrete-time SGD in quadratic loss functions.
result Fluctuation caused by discrete-time dynamics is larger than continuous-time theory predicts.
Topological anomaly scores predict return curves in S&P 500 stocks
problem Detecting anomalies in financial time series
method BallMapper, decoder-conditional VAE, Function-on-Function regression
result Anomaly history carries predictive content for return curves
Effective Yau-Tian-Donaldson conjecture for spherical varieties.
problem Finding effective K-stability criteria for spherical varieties.
method Formulated an effective variant of the Yau-Tian-Donaldson conjecture and reviewed effective K-stability criteria for spherical varieties.
result Effective K-stability criteria can be computed given combinatorial data.
Novel CE-method variants reduce local minima convergence with fewer function evaluations.
problem Local minima and expensive function evaluations in optimization.
method Surrogate model-based CE-method variants to reduce local minima convergence.
result Surrogate model-based approach reduces local minima convergence using fewer function evaluations.