Smooth KANs improve model reliability in computational biomedicine.
problem Limited convergence of KANs in representing generic smooth functions.
method Introducing smooth, structurally informed KANs that can approximate MLPs in specific function classes.
result Smooth KANs can achieve equivalence to MLPs in specific function classes, enhancing model reliability and performance.
Statistical boosting algorithms have triggered a lot of research during the last decade. They combine a powerful machine-learning approach with classical statistical modelling, offering various practical advantages like automated variable selection and implicit regularization of effect estimates. They are extremely fle…
A new landmark sampling method improves TDA performance on biomedical data.
problem Improving landmark samplers for pseudometric spaces with varying density and multiplicities.
method Proposes 'lastfirst' procedure based on ranked distances, proving landmarks have desired properties.
result lastfirst outperforms maxmin on homology detection tasks and comparable on prediction tasks.
Object detection is a computer vision field that has applications in several contexts ranging from biomedicine and agriculture to security. In the last years, several deep learning techniques have greatly improved object detection models. Among those techniques, we can highlight the YOLO approach, that allows the const…
In multi-label text classification, each textual document can be assigned with one or more labels. Due to this nature, the multi-label text classification task is often considered to be more challenging compared to the binary or multi-class text classification problems. As an important task with broad applications in b…
Causal processes in biomedicine may contain cycles, evolve over time or differ between populations. However, many graphical models cannot accommodate these conditions. We propose to model causation using a mixture of directed cyclic graphs (DAGs), where the joint distribution in a population follows a DAG at any single…
In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While c…
Safe learning of stochastic dynamics with safety constraints.
problem Learning controlled stochastic dynamics with safety constraints.
method Iterative expansion of a safe control set using kernel-based confidence bounds.
result The method ensures safe exploration and efficient estimation of system dynamics.
CEGA addresses GNN security by enabling cost-effective model acquisition.
problem Vulnerability of Graph Neural Networks (GNNs) to model extraction attacks (MEAs).
method Proposes an adaptive node querying strategy to refine node selection over multiple learning cycles.
result Demonstrates superior performance in accuracy, fidelity, and F1 score under strict query-size constraints.
Scalable model learns from mixed data groups.
problem Heterogeneous data affecting predictive models and interpretability.
method Joint learning of feature distributions, regression models, and latent group labels.
result Effective in high dimensions, combining data reduction and re-weighting.
This Perspective provides examples of current and future applications of deep learning in pharmacogenomics, including: (1) identification of novel regulatory variants located in noncoding domains and their function as applied to pharmacoepigenomics; (2) patient stratification from medical records; and (3) prediction of…
Since the beginning of the 21st century, the size, breadth, and granularity of data in biology and medicine has grown rapidly. In the example of neuroscience, studies with thousands of subjects are becoming more common, which provide extensive phenotyping on the behavioral, neural, and genomic level with hundreds of va…
Proposes Genetic Thompson Sampling for multi-armed bandits, improving performance in nonstationary settings.
problem Improving sequential decision making tasks of online learning agents using multi-armed bandits.
method Integrates genetic principles into Thompson Sampling for multi-armed bandits.
result Significantly outperforms baselines in nonstationary settings.
DGM learns graph structure for better graph neural network performance.
problem Graphs are often unknown or noisy, limiting graph neural network performance.
method DGM learns graph structure from data, improving performance in transductive and inductive settings.
result DGM achieves state-of-the-art results across various domains.
Many of the current scientific advances in the life sciences have their origin in the intensive use of data for knowledge discovery. In no area this is so clear as in bioinformatics, led by technological breakthroughs in data acquisition technologies. It has been argued that bioinformatics could quickly become the fiel…
SurvSet offers a repository of 76 T2E datasets for ML benchmarking.
problem Lack of open-source T2E dataset repositories for ML benchmarking.
method Consistent formatting of datasets for various ML algorithms and statistical methods.
result SurvSet provides a comprehensive resource for T2E analysis.
New method controls false edge detections in Gaussian graphical models.
problem High false edge detections in well-established estimators.
method Nodewise variable selection approach to control false discovery rate.
result Significant gain in performance compared to competing methods.
CovRegRF estimates covariance matrix from covariates using random forests.
problem Estimating conditional covariances or correlations among multivariate responses.
method Random forest trees with a custom splitting rule to maximize covariance difference.
result Accurate covariance matrix estimates and controlled Type-1 error.
Clustering consists of grouping together samples giving their similar properties. The problem of modeling simultaneously groups of samples and features is known as Co-Clustering. This paper introduces ROCCO - a Robust Continuous Co-Clustering algorithm. ROCCO is a scalable, hyperparameter-free, easy and ready to use al…
Paper presents a workflow for reliable unsupervised learning in science.
problem Lack of standardization in unsupervised learning workflows for reproducible scientific discoveries.
method Structured workflow including data preparation, modeling, validation, and communication.
result Illustrates the importance of validation in unsupervised learning.
In many applications, observed data are influenced by some combination of latent causes. For example, suppose sensors are placed inside a building to record responses such as temperature, humidity, power consumption and noise levels. These random, observed responses are typically affected by many unobserved, latent fac…
PCA outperforms random projections in retaining second order signals from latent groups.
problem Preserving second order structure in latent groups under unsupervised linear projections.
method Theoretical framework and quasi-exhaustive enumeration of projections.
result PCA outperforms random projections in retaining second order signals across a broad range of data-generating parameters.
A new diffusion model generates novel protein backbones without relying on pretrained networks.
problem Generating novel protein backbones without relying on pretrained networks.
method Developed a SE(3) invariant diffusion model on multiple frames, called FrameDiff.
result Generated designable protein monomers up to 500 amino acids without pretrained networks.
Locally sparse neural networks improve interpretability for biomedical tabular data.
problem Overfitting and lack of interpretability in neural networks for tabular biomedical data.
method Locally sparse neural network with a gating network to select relevant features.
result The method outperforms state-of-the-art models in synthetic and real-world biomedical datasets.
Throughout science and technology, receiver operating characteristic (ROC) curves and associated area under the curve (AUC) measures constitute powerful tools for assessing the predictive abilities of features, markers and tests in binary classification problems. Despite its immense popularity, ROC analysis has been su…
This paper reconstructs complex graph signals using kernel methods on manifolds.
problem Reconstructing complex graph signals from samples on graph vertices.
method Kernel methods on complex manifolds, embedding vertices into higher-dimensional spaces.
result Effective reconstruction of complex graph signals, outperforming conventional methods.
Paper generates synthetic radar signatures for motion classification.
problem Lack of large training datasets for radar-based human activity recognition.
method Adversarial learning for synthetic data generation, kinematic sifting for consistency.
result 93% overall accuracy achieved on diverse aspect angles.
This work abstracts deep neural networks into concept graphs for better interpretability in medical tasks.
problem Lack of interpretability in deep learning models, especially in medical domains.
method Developed a graphical representation of medical image processing models to understand concept-based reasoning.
result Extracted a concept-level graph that reveals the decision-making process of deep learning models.
DeepFRC learns both alignment and classification of functional data in one model.
problem Phase variability in functional data obscures underlying patterns and degrades model performance.
method End-to-end deep learning framework that combines diffeomorphic warping functions and a classifier.
result DeepFRC outperforms state-of-the-art methods in both alignment quality and classification accuracy.
Motivation: Understanding functions of proteins in specific human tissues is essential for insights into disease diagnostics and therapeutics, yet prediction of tissue-specific cellular function remains a critical challenge for biomedicine. Results: Here we present OhmNet, a hierarchy-aware unsupervised node feature le…
GG-SAGE predicts links in directed graphs with attributes, outperforming existing methods.
problem Predicting links in directed graphs with node attributes.
method Gravity-GraphSAGE, a modified GraphSAGE model with a gravity-inspired decoder.
result GG-SAGE outperforms state-of-the-art GDL link prediction techniques.
Quantized-TinyLLaVA reduces communication costs in split learning for multimodal models.
problem High communication costs in split learning for multimodal models.
method Integrates a compression module that quantizes intermediate features into discrete representations before transmission.
result Achieves an approximate 87.5% reduction in communication overhead with 2-bit quantization.
A new experimental design method for combinatorial interventions reduces complexity and improves accuracy.
problem Efficiently conducting all possible combinatorial interventions with multiple treatments and potential interactions.
method Probabilistic factorial experimental design, applying random combinations of treatments and adapting over multiple rounds.
result Optimal dosage of 1/2 for each treatment yields near-optimal design for estimating any k-way interaction model.
cGAP visualizes high-dimensional categorical data with interpretable geometric structure.
problem Lack of visualization tools for high-dimensional categorical data.
method cGAP uses Homogeneity Analysis (HOMALS) to embed data in a 3D space and maps it to colors.
result cGAP reveals coherent clusters, outliers, and local-to-global structure in categorical data.
cGAP visualizes high-dimensional categorical data with interpretable geometric structure.
problem Lack of visualization tools for high-dimensional categorical data.
method cGAP uses Homogeneity Analysis (HOMALS) to embed data in a 3D space and maps it to colors for visualization.
result cGAP reveals coherent clusters, outliers, and local-to-global structure in categorical data.
New method bypasses assumptions for unbiased estimation of complex system interactions.
problem Inferring pair-wise and higher-order interactions from observational data.
method Cross-disciplinary approach using Targeted Learning for unbiased estimation.
result Universal estimator of all-order symmetric interactions without parametric assumptions.
The study examines how much data is needed for generative and vision-language models to make reliable predictions.
problem Ensuring reliable predictions with low data for models used in medical decision support.
method Analyzes uniform convergence bounds for VLM-induced classifiers under low-dimensional semantic representations.
result Finite-sample uniform convergence bounds for accuracy and calibration functionals of VLM-induced classifiers.
FSR efficiently discovers significant patterns with few resampled datasets.
problem Mining significant patterns in transactional data, especially subgroups.
method FSR uses resampling to bound the supremum deviation of quality statistics, providing rigorous guarantees on false discoveries.
result FSR effectively discovers significant subgroups with a small number of resampled datasets.
Measurement noise limits the advantage of nonlinear models over linear models in biomedical prediction
problem Nonlinear models vs. linear models in biomedical prediction
method Measurement reliability
result Measurement noise blurs the population-optimal predictor
Quantum computing speeds up multi-period asset allocation.
problem High computational complexity in classic computing for multi-period asset allocation.
method Applied quantum computing to simulate multi-asset portfolio using historic data.
result Quantum computing offers significant advantages over classical computing in finance.
The paper analyzes the pricing of a new compute futures asset.
problem Uncertainty in AI adoption and pricing of compute capital.
method An asset-pricing framework for compute futures, including synthetic futures pricing.
result Preliminary evidence suggests a positive compute risk premium.
Quantum computing offers energy savings over classical computing.
problem Energy efficiency in computing services.
method Cournot competition model constrained by energy usage.
result Quantum computing firms can outperform classical counterparts in energy efficiency.
The paper introduces reservoir computing models for complex systems.
problem Modeling complex engineering systems using nonlinear autoregression.
method Introduces reservoir computing with output feedback as stationary and ergodic infinite-order nonlinear autoregressive models.
result Demonstrates versatility of classical and quantum reservoir computers in modeling synthetic and real data.
This work makes neural sequence models more efficient by controlling computation.
problem Fixed compute for all examples in neural networks.
method Conditional computation to adapt compute to example complexity.
result Conditional Computation Transformer (CCT) improves efficiency and performance.
Defines computable learning for binary classification over metric spaces.
problem Defines computable PAC learning for binary classification over computable metric spaces.
method Provides sufficient conditions for ERM learners to be computable and bounds the strong Weihrauch degree of an ERM learner.
result Gives a hypothesis class that does not admit any proper computable PAC learner with computable sample function.
Automatic computation speeds up crosscap number calculation for alternating knots.
problem Computing crosscap numbers for alternating knots efficiently.
method Introduced an automatic computation with complexity O(E3). result Crosscap numbers of alternating knots can be computed in O(E3) time. TKFT models computation via smooth vector fields, simulating functions in a single dynamical step.
problem Modeling computation in a single step.
method Established Topological Kleene Field Theory (TKFT) as a new model of computation.
result Any computable function can be simulated in a single go of a dynamical system.
Stochastic reservoir computing is shown to be a universal approximator.
problem Theoretical justification for using stochastic reservoirs in machine learning.
method Investigated stochastic reservoir computing using probabilities of reservoir states as readout.
result Stochastic reservoir computers are universal approximating classes.