Jaewoo Kang

We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

We investigate algorithms for evaluating sliding window joins over pairs of unbounded streams. We introduce a unit-time-basis cost model to analyze the expected performance of these algorithms. Using this cost model, we propose strategies for maximizing the efficiency of processing joins in three scenarios. First, we consider the case where one stream is much faster than the other. We show that asymmetric combinations of join algorithms, (e.g., hash join on one input, nested-loops join on the ot

Most previous solutions to the schema matching problem rely in some fashion upon identifying "similar" column names in the schemas to be matched, or by recognizing common domains in the data stored in the schemas. While each of these approaches is valuable in many cases, they are not infallible, and there exist instances of the schema matching problem for which they do not even apply. Such problem instances typically arise when the column names in the schemas and the data in the columns are "opa

Several computer aided diagnosis (CAD) systems have been developed for mammography. They are widely used in certain countries such as the U.S. where mammography studies are conducted more frequently; however, they are not yet globally employed for clinical use due to their inconsistent performance, which can be attributed to their reliance on hand-crafted features. It is difficult to use hand-crafted features for mammogram images that vary due to factors such as the breast density of patients an

Detecting drug-drug interactions (DDI) is important because information on DDIs can help prevent adverse effects from drug combinations. Since there are many new DDI-related papers published in the biomedical domain, manually extracting DDI information from the literature is a laborious task. However, text mining can be used to find DDIs in the biomedical literature. Among the recently developed neural networks, we use a Recursive Neural Network to improve the performance of DDI extraction. Our

Supplementary data are available at Bioinformatics online.

As the volume of publications rapidly increases, searching for relevant information from the literature becomes more challenging. To complement standard search engines such as PubMed, it is desirable to have an advanced search tool that directly returns relevant biomedical entities such as targets, drugs, and mutations rather than a long list of articles. Some existing tools submit a query to PubMed and process retrieved abstracts to extract information at query time, resulting in a slow respons

We propose a nuclei segmentation method based on DCNNs for histopathology images. The proposed method which uses Mask R-CNN with color normalization and multiple inference post-processing provides robust nuclei segmentation results. Our method also can facilitate downstream nuclei morphological analyses as it provides high-quality features extracted from histopathology images.

Supplementary data are available at Bioinformatics online.

In this article, we describe our system for the CHEMPROT task of the BioCreative VI challenge. Although considerable research on the named entity recognition of genes and drugs has been conducted, there is limited research on extracting relationships between them. Extracting relations between chemical compounds and genes from the literature is an important element in pharmacological and clinical research. The CHEMPROT task of BioCreative VI aims to promote the development of text mining systems

Jinhyuk Lee, Mujeen Sung, Jaewoo Kang, Danqi Chen. Proceedings of the 59th Annual Meeting of the Association for Computational Linguistics and the 11th International Joint Conference on Natural Language Processing (Volume 1: Long Papers). 2021.

Recent studies suggest that the deregulation of pathways, rather than individual genes, may be critical in triggering carcinogenesis. The pathway deregulation is often caused by the simultaneous deregulation of more than one gene in the pathway. This suggests that robust gene pair combinations may exploit the underlying bio-molecular reactions that are relevant to the pathway deregulation and thus they could provide better biomarkers for cancer, as compared to individual genes. In order to valid