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.
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48 results for “biomedical papers”
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…
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.
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…
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.
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.
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.
A Review on Modern Computational Optimal Transport Methods with Applications in Biomedical Researchstat.ML
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.
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.
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.
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.
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.
Building Diversified Multiple Trees for Classification in High Dimensional Noisy Biomedical Datacs.LG
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…
MedCAT extracts valuable medical information from unstructured text.
problem Extracting structured information from unstructured biomedical documents.
method Unsupervised machine learning for disambiguation of entities.
result Improved entity detection and linking compared to existing tools.
Proposes a new Lasso method with performance constraints.
problem No control over prediction accuracy for certain individuals.
method Adds quadratic performance constraints to Lasso-based objective functions.
result Defines a constrained sparse regression model through nonlinear optimization.
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.
Validity of Feature Importance in Low-Performing Machine Learning for Tabular Biomedical Datastat.ML
This paper shows feature importance remains valid even in low-performing models.
problem Feature importance validity in low-performing machine learning models for biomedical data.
method Experiments with synthetic and real biomedical datasets to compare feature rank stability under different data reductions.
result Feature importance can be maintained even at low performance levels if data size is adequate.
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.
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…
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.
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.
Biomedical text tagging systems are plagued by the dearth of labeled training data. There have been recent attempts at using pre-trained encoders to deal with this issue. Pre-trained encoder provides representation of the input text which is then fed to task-specific layers for classification. The entire network is fin…
It's easy to fool yourself: Case studies on identifying bias and confounding in bio-medical datasetscs.LG
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.
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: variational Bayesian clustering and variable selection for discrete biomedical datastat.ML
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.
Recently, kernelized locality sensitive hashcodes have been successfully employed as representations of natural language text, especially showing high relevance to biomedical relation extraction tasks. In this paper, we propose to optimize the hashcode representations in a nearly unsupervised manner, in which we only u…
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.
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.
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.
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.
We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological context as descriptions of the species, tissue type and cell type that are associated …
New algorithm improves model generalization in structured biomedical domains.
problem Improving model generalization in structured biomedical domains.
method Proposes a new regret minimization (RGM) algorithm and its structured extension for better performance in diverse environments.
result Significantly outperforms previous state-of-the-art baselines on molecular property prediction, protein homology, and stability prediction.
New algorithm improves causal discovery in biomedical data.
problem Stability and accuracy issues in causal discovery algorithms.
method Exploits temporal structure and tiered background knowledge.
result Increases accuracy in finite samples for causal structure estimation.
M3E2 neural network estimates multiple treatment effects.
problem Estimating effects of multiple treatments simultaneously.
method Multi-task learning neural network model for multiple treatments, continuous and binary.
result M3E2 outperforms baselines in synthetic datasets.
We propose a model for tagging unstructured texts with an arbitrary number of terms drawn from a tree-structured vocabulary (i.e., an ontology). We treat this as a special case of sequence-to-sequence learning in which the decoder begins at the root node of an ontological tree and recursively elects to expand child nod…
In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping chromosomes. A segmentation solution that is fast and automated will enable scaling of co…
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.
Framework for causal discovery using multi-modal data.
problem Failure of representation learning in causal tasks.
method Statistical and computational framework combining representation learning and causal inference.
result Effective use of observational and perturbational data for causal discovery.
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.