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.
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.
RoBERTa outperforms other pre-trained models in NER tasks.
problem Improving Named Entity Recognition (NER) performance.
method Fine-tuning four pre-trained models (BERT, ERNIE, ERNIE2.0-tiny, RoBERTa) on NER task.
result RoBERTa achieved state-of-the-art results on MSRA-2006 dataset.
A new method sorts models to find the best one with minimal risk.
problem Finding the best model with minimal risk among nested models.
method Nested Empirical Risk (NER) and Sorted NER (S-NER) methods.
result The S-NER method selects the true model order and the most parsimonious model.
FGN improves Chinese NER by integrating glyph information and interactive context.
problem Chinese named entity recognition is challenging due to the complexity of characters and their glyphs.
method FGN uses a novel CGS-CNN structure to capture glyph and interactive information, and a sliding window method to fuse BERT and glyph representations.
result FGN achieves state-of-the-art performance on four NER datasets, improving over previous methods.
Deep learning model improves Vietnamese NER accuracy.
problem Vietnamese named entity recognition (NER) accuracy.
method Combining Bi-LSTM and CRF with word embeddings and semantic features.
result Achieved state-of-the-art NER results on VLSP2016 dataset.
Study shows partially-typed NER datasets can match fully-typed ones in model performance.
problem Leveraging multiple partially-typed NER datasets for training models without fully-typed annotations.
method Systematic analysis and controlled experiments comparing partially-typed and fully-typed datasets.
result Models trained with partially-typed annotations can achieve similar performance to those trained with fully-typed annotations.
Paper fine-tunes LLaMA-3-8B for financial NER using instruction and LoRA.
problem LLMs struggle with financial NER, especially differentiating entities and amounts.
method Instruction fine-tuning combined with LoRA for parameter-efficient learning.
result Micro-F1 score of 0.894 on financial NER tasks, outperforming other models.
Paper presents a method to train NER models without labelled data using weak supervision.
problem Dealing with NER performance drop in new domains without labelled data.
method Weak supervision through automatic annotation and hidden Markov model integration.
result Improvement of about 7 percentage points in entity-level F1 scores. The paper introduces uncertainty quantification for NER models.
problem Current NER models lack uncertainty measures, leading to downstream errors.
method Full-Sequence and Subsequence Conformal Prediction framework.
result The method provides formal guarantees about the reliability of model predictions.
Recently, due to the increasing popularity of social media, the necessity for extracting information from informal text types, such as microblog texts, has gained significant attention. In this study, we focused on the Named Entity Recognition (NER) problem on informal text types for Turkish. We utilized a semi-supervi…
State-of-the-art named entity recognition (NER) systems have been improving continuously using neural architectures over the past several years. However, many tasks including NER require large sets of annotated data to achieve such performance. In particular, we focus on NER from clinical notes, which is one of the mos…
Recent approaches based on artificial neural networks (ANNs) have shown promising results for named-entity recognition (NER). In order to achieve high performances, ANNs need to be trained on a large labeled dataset. However, labels might be difficult to obtain for the dataset on which the user wants to perform NER: la…
Improved NER performance on imbalanced data.
problem Highly unbalanced training data in NER tasks.
method Adapted a neural architecture with CRF and BI-LSTM layers, using pre-trained embeddings. Introduced a two-class split to optimize performance.
result Significant improvement in performance for weak classes with minimal training data.
Proposes a method to improve deep active learning for NER tasks.
problem Weaknesses of existing deep active learning algorithms in practice.
method Estimates error decay curves of feature-defined subsets to improve sampling efficiency and robustness.
result Significantly outperforms diversification-based methods for black-box NER taggers and makes sampling more robust to labeling noise.
Improves cross-lingual NER by projecting entities from one language to another.
problem Limited annotated corpora for named entity recognition in many languages.
method Uses machine translation twice: first for sentences, then for entities; matches based on ortho- and phonetic similarity; identifies matches using distributional statistics.
result Improves cross-lingual NER by an average of 4.1 points on 5 diverse languages.
This paper describes an approach for automatic construction of dictionaries for Named Entity Recognition (NER) using large amounts of unlabeled data and a few seed examples. We use Canonical Correlation Analysis (CCA) to obtain lower dimensional embeddings (representations) for candidate phrases and classify these phra…
Named-entity recognition (NER) aims at identifying entities of interest in a text. Artificial neural networks (ANNs) have recently been shown to outperform existing NER systems. However, ANNs remain challenging to use for non-expert users. In this paper, we present NeuroNER, an easy-to-use named-entity recognition tool…
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.
Motivated by the need to automate medical information extraction from free-text radiological reports, we present a bi-directional long short-term memory (BiLSTM) neural network architecture for modelling radiological language. The model has been used to address two NLP tasks: medical named-entity recognition (NER) and …
NERS improves RL by sampling diverse transitions considering local and global contexts.
problem Sampling biases in experience replay lead to redundant transitions.
method Neural Experience Replay Sampler (NERS) that considers both local and global contexts.
result NERS significantly improves RL performance by sampling diverse and meaningful transitions.
State-of-the-art sequence labeling systems traditionally require large amounts of task-specific knowledge in the form of hand-crafted features and data pre-processing. In this paper, we introduce a novel neutral network architecture that benefits from both word- and character-level representations automatically, by usi…
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.
Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical databases. However, though drug interaction is an ideal area for translational research, …
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.
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.
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.
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.
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.
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…
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.
GTI network learns linguistic features for multi-task sequence tagging.
problem Improving neural model performance on multi-task sequence tagging without explicit features.
method GTI network with neural gate modules to learn relations between tasks.
result GTI network outperforms baselines on chunking and NER tasks.
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.
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.
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.
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.