This study evaluates data pre-processing techniques for class imbalance in biomedical data.
problem Class imbalance in biomedical datasets affects model performance.
method Resampling and feature selection techniques evaluated using SVM, C4.5, LDA, and KNN classifiers.
result Feature Selection outperforms other methods in most cases, especially with SVM.
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.
Unified Bayesian model for multi-modal, small sample size biomedical data classification.
problem Classifying high-dimensional, multi-modal biomedical data with small sample sizes.
method Combines multi-modal data views into a latent space, prunes irrelevant features, and uses dual kernels for small sample size scenarios.
result Outperforms state-of-the-art models and identifies features aligned with existing markers.
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.
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…
It is common that a trained classification model is applied to the operating data that is deviated from the training data because of noise. This paper demonstrates that an ensemble classifier, Diversified Multiple Tree (DMT), is more robust in classifying noisy data than other widely used ensemble methods. DMT is teste…
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…
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…
bioLeak addresses data leakage in biomedical machine learning studies.
problem Data leakage causes optimistic bias in machine learning models for biomedical studies.
method bioLeak provides leakage-aware resampling workflows and model audits in R.
result The package supports various machine learning tasks and can detect leakage mechanisms.
New method uses artificial data to improve biomedical text tagging.
problem Lack of labeled data for biomedical tasks.
method Fine-tuning a pre-trained encoder with additional artificial labeled instances.
result Achieved state-of-the-art performance in PICO annotation.
A rigorous ML pipeline for binary classification in biomedical studies, focusing on pancreatic cancer.
problem Handling bias in ML models for complex biomedical data.
method Customizable ML analysis pipeline with 9 algorithms, hyperparameter optimization, and thorough evaluation.
result Comparison of ML algorithms to ExSTraCS, highlighting interpretability and bias handling.
New DL model handles missing data in biomedical datasets.
problem Handling missing data in modern biomedical datasets.
method Proposed a new DL architecture, dlglm, for generalized linear models.
result Outperforms existing methods in MNAR missingness scenarios.
A novel weighted feature selection method using fuzzy sets improves classification accuracy and stability.
problem Improving feature selection accuracy and stability in machine learning models.
method Combination of four feature selection methods using fuzzy sets and bootstrap.
result Our method achieved significantly higher stability than individual methods.
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…
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.
In biomedical research, many different types of patient data can be collected, such as various types of omics data and medical imaging modalities. Applying multi-view learning to these different sources of information can increase the accuracy of medical classification models compared with single-view procedures. Howev…
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.
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.
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.
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.
A study on optimizing self-attention in tabular data using Optimal Transport.
problem Improving efficiency and accuracy of self-attention in tabular classification tasks.
method Developed an OT-based algorithm to generate class-specific dummy Gaussian distributions and train an MLP.
result Achieved comparable accuracy to Transformers with reduced computational cost and efficiency.
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.
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.
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.
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.
Background: In this paper we present the approaches and methods employed in order to deal with a large scale multi-label semantic indexing task of biomedical papers. This work was mainly implemented within the context of the BioASQ challenge of 2014. Methods: The main contribution of this work is a multi-label ensemble…
Mathematical conditions and practical computations for adversarial robustness measures are established.
problem Existence, uniqueness, and scalability of adversarial robustness measures for AI classifiers.
method Formulated and proven mathematical conditions for existence, uniqueness, and explicit analytical computation of minimal adversarial paths and distances. Practical computation demonstrated on various AI tools and synthetic benchmarks.
result Explicit mathematical conditions and practical computations for adversarial robustness measures are established.
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.
Develops variational Bayesian neural network for complex biomedical applications.
problem High computational cost of Markov Chain Monte Carlo in BNN.
method Variational Bayes inference for posterior consistency and classification accuracy.
result Developed statistical theory for posterior consistency and prediction accuracy.
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.
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…
Machine Learning (ML) helps us to recognize patterns from raw data. ML is used in numerous domains i.e. biomedical, agricultural, food technology, etc. Despite recent technological advancements, there is still room for substantial improvement in prediction. Current ML models are based on classical theories of probabili…
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
spex-LVM infers interpretable latent factors from biomedical data.
problem Inability to learn sparse and interpretable hidden states.
method Factorial latent variable model with sparse priors and domain-relevant annotations.
result Robustly identifies relevant structure in RNA-seq datasets.
Over the years, there has been growing interest in using Machine Learning techniques for biomedical data processing. When tackling these tasks, one needs to bear in mind that biomedical data depends on a variety of characteristics, such as demographic aspects (age, gender, etc) or the acquisition technology, which migh…
Microarray cancer gene expression data comprise of very high dimensions. Reducing the dimensions helps in improving the overall analysis and classification performance. We propose two hybrid techniques, Biogeography - based Optimization - Random Forests (BBO - RF) and BBO - SVM (Support Vector Machines) with gene ranki…
Proposes a novel method to identify complex effects in multi-view datasets.
problem Challenges in analyzing multi-view biomedical datasets with complex interactions.
method Generalized kernel machine approach considering marginal and joint effects of features from different views.
result Effective identification of higher-order composite effects in multi-view datasets.
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.
Extracts roles of authors from biomedical papers.
problem Lack of machine-readable author roles in biomedical papers.
method Statistical analysis of roles, Open Information Extraction, Naïve Bayes approach.
result Extracts roles with precision of 0.68, recall of 0.48, and F1 of 0.57.
Motivation: State-of-the-art biomedical named entity recognition (BioNER) systems often require handcrafted features specific to each entity type, such as genes, chemicals and diseases. Although recent studies explored using neural network models for BioNER to free experts from manual feature engineering, the performan…
Deep learning methods have shown extraordinary potential for analyzing very diverse biomedical data, but their dissemination beyond developers is hindered by important computational hurdles. We introduce ImJoy (https://imjoy.io/), a flexible and open-source browser-based platform designed to facilitate widespread reuse…
VICatMix clusters categorical biomedical data efficiently and selects relevant variables.
problem Efficient clustering of high-dimensional categorical biomedical data.
method Variational Bayesian finite mixture model with variational inference.
result Improves clustering accuracy and variable selection on noisy, high-dimensional data.
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.
Machine learning speeds up FLIM analysis in biomedical research.
problem Complex, slow, and computationally expensive FLIM analysis.
method Machine learning techniques for faster and smarter FLIM data extraction and interpretation.
result Higher accuracy in classifying and segmenting FLIM images compared to conventional methods.
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.