Self-supervised method predicts clean signal and noise distribution from noisy images.
problem Blind denoising and noise estimation in biomedical images with limited clean data.
method Two neural networks jointly predict clean signal and noise distribution from noisy observations.
result Significantly outperforms state-of-the-art algorithms on six biomedical image datasets.
SiMLR reduces complex biomedical data into simpler, interpretable forms.
problem Handling high-dimensional biomedical data for better understanding and prediction.
method Similarity-driven multi-view linear reconstruction (SiMLR) with novel objective function and regularization.
result SiMLR outperforms other methods in various biomedical datasets.
SMM improves signal recovery from noisy data.
problem Estimating signals from noisy and scaled observations.
method Spiked mixture model (SMM) with EM algorithm.
result SMM outperforms GMM in signal recovery.
High throughput biomedical measurements normally capture multiple overlaid biologically relevant signals and often also signals representing different types of technical artefacts like e.g. batch effects. Signal identification and decomposition are accordingly main objectives in statistical biomedical modeling and data…
Logistic regression with wavelets achieves bacterial infection detection accuracy.
problem Interpreting complex biomedical signal models for high-stakes decisions.
method Wavelet features and knockoff variables for feature selection.
result Logistic regression outperforms neural networks in bacterial infection detection.
Two case studies reveal hidden biases and confounders in machine learning models of biomedical data.
problem Hidden biases and confounders in machine learning models of biomedical data.
method Two case studies examining biases and confounders in machine learning models of biomedical data.
result Prediction models performed well but hidden biases and confounders were revealed.
Coherent Multiplex analyzes real-time wavelet coherence among multiple signals.
problem Identifying and visualizing coherence among multiple time series.
method Fast spectral similarity based on cosine similarity metrics of Fourier-transformed signals and sparse time-frequency wavelet coherence.
result Scalable real-time system for low-latency inference and monitoring of inter-signal relationships.
Paper proposes a k-NN classifier for detecting spike-and-wave seizures in EEG.
problem Early detection of epileptic seizures in EEG signals.
method Uses t-location-scale distribution and k-nearest neighbors classifier.
result Demonstrates improved classification accuracy, sensitivity, and specificity on real data.
New method detects spike-and-wave epileptiform discharges using Kendall's Tau-b.
problem Detecting spike-and-wave epileptiform discharges in EEG signals.
method Proposes a new method based on Kendall's Tau-b coefficient.
result High Specificity and rule in (SpPIn) for spike-and-wave discharge detection.
SODA optimizes data augmentation allocation for deep learning models.
problem Inefficient allocation of data augmentation budget in deep neural networks.
method Online learning to dynamically allocate data augmentation budget during training.
result Optimized data augmentation can save computation time and promote greener machine learning.
Paper introduces rational Gaussian wavelets for efficient signal approximation.
problem Efficiently approximating complex signals with few coefficients.
method Continuous wavelet transform using rational Gaussian wavelets with adjustable parameters.
result Proposed rational Gaussian wavelets provide accurate signal approximations.
Stein-Encoder isolates genetic signals in multi-modal biomedical data.
problem Integration of high-dimensional genomic data with clinical data obscures genetic predictive impact.
method White-box supervised framework using Stein's method and residualization.
result Stein-Encoder improves predictive accuracy and reveals specific biological mechanisms.
Using different sources of information to support automated extracting of relations between biomedical concepts contributes to the development of our understanding of biological systems. The primary comprehensive source of these relations is biomedical literature. Several relation extraction approaches have been propos…
Efficient GP framework for scalable non-stationary processes.
problem Heavy memory and computational requirements in Gaussian process regression for large data sets.
method Exploits structure in the kernel matrix, uses multiple sets of non-equidistant inducing points, and employs Toeplitz and Kronecker structure for efficient inference.
result Demonstrated scalability on numerical examples and large biomedical datasets.
VDA improves disentanglement of latent representations in complex signals.
problem Learning disentangled and interpretable representations in nonstationary, high-dimensional time-evolving signals.
method Variational decomposition autoencoding (VDA) framework, incorporating signal decomposition, contrastive self-supervised task, and variational prior approximation.
result DecVAEs surpass state-of-the-art VAE-based methods in disentanglement quality and generalization.
Improves biomedical entity linking with latent type modeling.
problem Lack of fine-grained type information for entity disambiguation.
method Jointly models entity disambiguation and latent type learning without direct supervision.
result Significant performance improvements over state-of-the-art techniques.
Novel graph-based method detects R-peaks in noisy ECG signals without preprocessing.
problem Detecting R-peaks in noisy ECG signals for real-time analysis.
method Graph-constrained Changepoint Detection (GCCD) approach.
result GCCD achieves high sensitivity, positive predictivity, and low detection error rate.
SigTime learns interpretable signatures from time series data.
problem Discovering meaningful patterns in time series data with high complexity and limited interpretability.
method Jointly trains two Transformer models using shapelet-based and feature engineering representations.
result Learned shapelets serve as interpretable signatures for time series classification.
Model predicts future term connections in biomedical research.
problem Capturing temporal dynamics and unobserved connections in biomedical term relationships.
method Variational inference model for positive-unlabeled learning on dynamic graphs.
result Model effectively predicts term relationships in real-world datasets.
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.
Model predicts epileptic seizures with high accuracy using EEG signals.
problem Predicting epileptic seizures with high accuracy for diagnosis and treatment.
method Pearson's product-moment correlation coefficient with a linear classifier on generalized Gaussian modeling.
result 100% effectiveness for sensitivity and specificity greater than 83%.
BIOMRC dataset improves MRC performance, especially for non-experts.
problem Improving machine reading comprehension in biomedical texts.
method Developed a new dataset and tested two neural models, along with a BERT-based model.
result BERT-based model outperforms all other methods and reaches expert-level accuracy.
Graph-based framework predicts ADR signals from clinical data.
problem Detecting ADRs in post-market surveillance using clinical data.
method Developed a Drug-disease graph with Graph Neural Network for ADR signal prediction.
result Improved AUROC and AUPRC performance (0.795 and 0.775) compared to other algorithms.
Enhancement attacks can falsely improve machine learning model performance in biomedical research.
problem The trustworthiness of machine learning in biomedical research is threatened by enhancement attacks.
method Developed two techniques to enhance prediction performance with minimal changes to features.
result Falsely improved classifiers' accuracy from 50% to almost 100% while maintaining high feature similarities.
Blind source separation (BSS), i.e., the decoupling of unknown signals that have been mixed in an unknown way, has been a topic of great interest in the signal processing community for the last decade, covering a wide range of applications in such diverse fields as digital communications, pattern recognition, biomedica…
Proposes GFMMD for comparing signals on graphs.
problem Computing distances between distributions on graphs.
method Graph Fourier MMD (GFMMD) using optimal witness functions.
result Analytical solution and embedding of distributions.
Generates biomedical abstracts from titles, years, and keywords.
problem Difficulties in understanding biomedical research papers due to specialized language.
method Conditional transformer-based language model with metadata conditioning.
result Generated abstracts are more relevant and non-trivial than GPT-2.
Review of modern computational optimal transport methods for biomedical applications.
problem Efficient computation of optimal transport for big data.
method Regularization-based and projection-based computational methods.
result Advancements in computational optimal transport methods for biomedical research.
Advances in molecular "omics'" technologies have motivated new methodology for the integration of multiple sources of high-content biomedical data. However, most statistical methods for integrating multiple data matrices only consider data shared vertically (one cohort on multiple platforms) or horizontally (different …
Method integrates logical rules into neural multi-hop reasoning for drug repurposing.
problem Capturing long-range dependencies in biomedical data.
method Combines logical rules with neural multi-hop reasoning using reinforcement learning.
result Our method outperforms baseline methods in drug repurposing tasks.
Paper proposes a new method for imputing missing biomedical data.
problem Missing values in biomedical data.
method Monte Carlo Dropout within Autoencoders.
result The method improves imputation error and predictive similarity.
AdaCGP learns dynamic graph topology from time series data, improving over existing methods.
problem Learning dynamic graph topology from time-varying signals, especially in real-time applications.
method AdaCGP is a sparsity-aware adaptive algorithm that recursively estimates the Graph Shift Operator (GSO) through variable splitting.
result AdaCGP outperforms state-of-the-art methods in GSO estimation, achieving improvements exceeding 83%.
DISCoVeR learns disentangled representations by separating shared and condition-specific factors.
problem Learning disentangled representations for multi-condition data.
method Dual-latent architecture, parallel reconstructions, max-min objective.
result DISCoVeR achieves improved disentanglement on various datasets.
Privacy-preserving inference for clinical trials using differential privacy.
problem Balancing knowledge sharing and privacy in healthcare data.
method Differential privacy (DP) applied to log-linear belief updates in distributed settings.
result Differentially private, distributed inference methods outperform existing techniques.
Model classifies hand gestures with low EMG samples augmented with noise.
problem Classify hand gestures with limited EMG data.
method Random variance Gaussian noise augmentation, Random Forest, XGBoost.
result High accuracy model for six hand gestures.
Novel method segments heart sound signals using LSTMs with attention.
problem Heart sound segmentation for diagnostic applications.
method Bidirectional LSTMs with attention mechanisms.
result State-of-the-art performance on multiple benchmarks.
The support vector machine (SVM) is a widely used machine learning tool for classification based on statistical learning theory. Given a set of training data, the SVM finds a hyperplane that separates two different classes of data points by the largest distance. While the standard form of SVM uses L2-norm regularizatio…
Flow-based models use ODEs to generate complex data distributions.
problem Generating high-dimensional data with complex probability distributions.
method Flow-based models use invertible mappings governed by ODEs to capture these distributions.
result Flow-based models provide exact likelihood estimation and efficient sampling.
Most existing feature selection methods are insufficient for analytic purposes as soon as high dimensional data or redundant sensor signals are dealt with since features can be selected due to spurious effects or correlations rather than causal effects. To support the finding of causal features in biomedical experiment…
Monitoring the biomedical literature for cases of Adverse Drug Reactions (ADRs) is a critically important and time consuming task in pharmacovigilance. The development of computer assisted approaches to aid this process in different forms has been the subject of many recent works. One particular area that has shown pro…
A multi-task learning model for slot tagging in biomedical domains.
problem Limited labeled data, memory constraints, and domain-specific slot types.
method Multi-task learning using deep bidirectional transformers.
result Outperforms previous state-of-the-art systems in efficiency and effectiveness.
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.
Non-negative blind source separation (non-negative BSS), which is also referred to as non-negative matrix factorization (NMF), is a very active field in domains as different as astrophysics, audio processing or biomedical signal processing. In this context, the efficient retrieval of the sources requires the use of sig…
Method cleans noisy training labels for biomedical data.
problem Accurately labeling biomedical data is challenging.
method Reliability-based training data cleaning with inductive conformal prediction.
result Significant enhancements in classification performance across multiple tasks.
HOoD detects near-out-of-distribution groups in correlated biomedical assays.
problem Detecting near-out-of-distribution cases in biased or incomplete data.
method Projects correlated measurements through a trained model and uses permutation-based hypothesis tests.
result HOoD reliably identifies OoD groups, outperforming other detectors.
Deep learning has shown its great promise in various biomedical image segmentation tasks. Existing models are typically based on U-Net and rely on an encoder-decoder architecture with stacked local operators to aggregate long-range information gradually. However, only using the local operators limits the efficiency and…
Proposes a Bayesian approach for integrating multiple linked matrices.
problem Integrating multiple linked matrices for diverse applications.
method Empirical Bayes Linked Matrix Decomposition (EB-LMD).
result Efficient estimation algorithm with no tuning parameters.
Biomedical data are widely accepted in developing prediction models for identifying a specific tumor, drug discovery and classification of human cancers. However, previous studies usually focused on different classifiers, and overlook the class imbalance problem in real-world biomedical datasets. There are a lack of st…