Model tags biomedical texts with tree-structured tags.
problem Tagging unstructured texts with an arbitrary number of terms from an ontology.
method Neural tree decoding approach starting from the root node of an ontology.
result Outperforms state-of-the-art approaches on MeSH term assignment.
Extracts biological context from biomedical texts to associate with events.
problem Identifying biological context and associating it with biochemical events in texts.
method Analyzed an annotated corpus and developed classifiers using syntactic, distance, and frequency features.
result Developed and evaluated classifiers for context-event association.
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.
ML-Net improves multi-label text classification in biomedicine.
problem Challenges in multi-label text classification, especially in biomedicine.
method End-to-end deep learning framework combining label prediction and automated label count prediction.
result Significantly outperforms state-of-the-art methods in multi-label classification of biomedical texts.
BioFinBERT analyzes sentiment of biotech press releases and financial text around inflection points.
problem Analyzing sentiment of biotech press releases and financial text around inflection points.
method Finetuning BioBERT on financial datasets to create BioFinBERT for sentiment analysis.
result BioFinBERT accurately analyzes sentiment of biotech press releases and financial text around inflection points.
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.
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.
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.
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…
Paper proposes nearly unsupervised hashcode learning for relation extraction.
problem Relation extraction from text, especially in biomedical domains.
method Optimized hashcode representations learned from data points without class labels, followed by supervised classification.
result Significant accuracy improvements over state-of-the-art methods.
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.
Deep learning models improved sentence similarity in medical records.
problem Improving sentence similarity in electronic medical records.
method Developed models using traditional machine learning and deep learning approaches, pre-trained sentence embeddings on biomedical corpora.
result Ensembled model achieved a Person correlation coefficient of 0.8528.
Model identifies urgent radiology reports with high accuracy.
problem Lack of annotated training data for text analysis.
method Self-supervised contextual language representation using BERT.
result Model achieved 97.0% precision, 93.3% recall, and 95.1% F-measure.
Proposes BONMI for integrating noisy matrices from multi-source data.
problem Integrating noisy matrices from multi-source data with block-wise missingness.
method Exploits orthogonal Procrustes problem to align eigenspaces and completes missing blocks.
result Statistical rate for eigenspace of underlying matrix comparable to independently missing assumption.
Neural networks enhance relation extraction from biomedical literature.
problem Automated extraction of relations between biomedical concepts.
method Use of multichannel architectures in deep neural networks with biomedical ontologies.
result State-of-the-art results in relation extraction tasks.
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.
ImJoy simplifies deep learning for biomedical research.
problem Computational barriers limit deep learning adoption in biomedical research.
method Open-source browser-based platform for deep learning.
result Facilitates widespread reuse of deep learning solutions.
Non-local U-Net improves biomedical image segmentation with fewer parameters and faster computation.
problem Efficiency and effectiveness in biomedical image segmentation using local operators.
method Proposed non-local U-Nets with flexible global aggregation blocks.
result Top performances achieved with fewer parameters and faster computation.
New model improves DDI extraction with 78.5% macro F1-score.
problem Extracting Drug-Drug Interactions from text.
method Attention-Wrapped Hierarchical BLSTMs.
result Model outperforms state-of-the-art with macro F1-score of 0.785.
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.
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.
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.
DISPR uses diffusion models to predict 3D cell shapes from 2D images.
problem Predicting 3D cell shapes from 2D microscopy images.
method Diffusion model trained to predict 3D shapes from 2D microscopy images as a prior.
result Adding DISPR predictions to minority cell classes improves classification accuracy.
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.
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.
Improved NER in biomedical literature using weakly-supervised augmentation.
problem Challenging NER in scientific literature, especially for biomedical entities.
method Weakly-supervised data augmentation with a reference set.
result Iterative model retraining improves NER performance significantly.
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…
Robust biclustering method tackles heavy-tailed data issues.
problem Discovering local correlation in heavy-tailed data.
method Convex biclustering with Huber loss and tuning-free parameter selection.
result Outperforms traditional biclustering methods in heavy-tailed noise.
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.
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.
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.
Originally designed to model text, topic modeling has become a powerful tool for uncovering latent structure in domains including medicine, finance, and vision. The goals for the model vary depending on the application: in some cases, the discovered topics may be used for prediction or some other downstream task. In ot…
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.
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.
Linguistic calibration improves long-form text confidence.
problem LMs hallucinate, leading to suboptimal decisions.
method Defining linguistic calibration, training framework, reinforcement learning.
result Llama 2 7B is significantly more calibrated than baselines.
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…
A new neural network model extends word embedding vectors with MeSH concepts for biomedical semantic similarity.
problem Eliciting semantic similarity between biomedical concepts remains challenging.
method Proposes a MeSH-gram neural network model that extends skip-gram by using MeSH descriptors.
result MeSH-gram outperforms skip-gram and is comparable to best methods but requires more computation and external resources.
BioNAS optimizes deep learning models for biomedical research, revealing new knowledge.
problem Building interpretable deep learning models for biomedical research.
method Neural architecture search with knowledge dissimilarity functions for joint optimization of predictive power and biological knowledge.
result BioNAS optimal models reveal novel knowledge in both simulated and real functional genomics data.
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.