Related papers: TocBERT: Medical Document Structure Extraction Usi…

This work proposes a novel approach to text categorization -- for unknown categories -- in the context of scientific literature, using Natural Language Processing techniques. The study leverages the power of pre-trained language models,…

Biomedical image segmentation is critical for precise structure delineation and downstream analysis. Traditional methods often struggle with noisy data, while deep learning models such as U-Net have set new benchmarks in segmentation…

Language Models (LMs) such as BERT, have been shown to perform well on the task of identifying Named Entities (NE) in text. A BERT LM is typically used as a classifier to classify individual tokens in the input text, or to classify spans of…

Fluorescence microscopy has become a widely used tool for studying various biological structures of in vivo tissue or cells. However, quantitative analysis of these biological structures remains a challenge due to their complexity which is…

Large pretrained language models (LMs) like BERT have improved performance in many disparate natural language processing (NLP) tasks. However, fine tuning such models requires a large number of training examples for each target task.…

Over the recent years, large pretrained language models (LM) have revolutionized the field of natural language processing (NLP). However, while pretraining on general language has been shown to work very well for common language, it has…

Biomedical named entity recognition (NER) is a fundamental task in text mining of medical documents and has many applications. Deep learning based approaches to this task have been gaining increasing attention in recent years as their…

Most publicly available medical segmentation datasets are only partially labeled, with annotations provided for a subset of anatomical structures. When multiple datasets are combined for training, this incomplete annotation poses…

Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve…

Named entity recognition has been extensively studied on English news texts. However, the transfer to other domains and languages is still a challenging problem. In this paper, we describe the system with which we participated in the first…

Reliable biomedical and clinical retrieval requires more than strong ranking performance: it requires a practical way to find systematic model failures and curate the training evidence needed to correct them. Late-interaction models such as…

Language model (LM) pretraining can learn various knowledge from text corpora, helping downstream tasks. However, existing methods such as BERT model a single document, and do not capture dependencies or knowledge that span across…

The field of clinical natural language processing has been advanced significantly since the introduction of deep learning models. The self-supervised representation learning and the transfer learning paradigm became the methods of choice in…

Weakly-supervised medical image segmentation is a challenging task that aims to reduce the annotation cost while keep the segmentation performance. In this paper, we present a novel framework, SimTxtSeg, that leverages simple text cues to…

The large pre-trained BERT has achieved remarkable performance on Natural Language Processing (NLP) tasks but is also computation and memory expensive. As one of the powerful compression approaches, binarization extremely reduces the…

This paper presents a novel approach to accurately classify the hallmarks of cancer, which is a crucial task in cancer research. Our proposed method utilizes the Bidirectional Encoder Representations from Transformers (BERT) architecture,…

The global pandemic has made it more important than ever to quickly and accurately retrieve relevant scientific literature for effective consumption by researchers in a wide range of fields. We provide an analysis of several multi-label…

Natural language processing (NLP) is becoming an important means for automatic recognition of human traits and states, such as intoxication, presence of psychiatric disorders, presence of airway disorders and states of stress. Such…

Accurate and reliable image segmentation is an essential part of biomedical image analysis. In this paper, we consider the problem of biomedical image segmentation using deep convolutional neural networks. We propose a new end-to-end…

Discourse segmentation, which segments texts into Elementary Discourse Units, is a fundamental step in discourse analysis. Previous discourse segmenters rely on complicated hand-crafted features and are not practical in actual use. In this…