GPDminer: a tool for extracting named entities and analyzing relations in biological literature.

PURPOSE: The expansion of research across various disciplines has led to a substantial increase in published papers and journals, highlighting the necessity for reliable text mining platforms for database construction and knowledge acquisition. This abstract introduces GPDMiner(Gene, Protein, and Disease Miner), a platform designed for the biomedical domain, addressing the challenges posed by the growing volume of academic papers. METHODS: GPDMiner is a text mining platform that utilizes advanced information retrieval techniques. It operates by searching PubMed for specific queries, extracting and analyzing information relevant to the biomedical field. This system is designed to discern and illustrate relationships between biomedical entities obtained from automated information extraction. RESULTS: The implementation of GPDMiner demonstrates its efficacy in navigating the extensive corpus of biomedical literature. It efficiently retrieves, extracts, and analyzes information, highlighting significant connections between genes, proteins, and diseases. The platform also allows users to save their analytical outcomes in various formats, including Excel and images. CONCLUSION: GPDMiner offers a notable additional functionality among the array of text mining tools available for the biomedical field. This tool presents an effective solution for researchers to navigate and extract relevant information from the vast unstructured texts found in biomedical literature, thereby providing distinctive capabilities that set it apart from existing methodologies. Its application is expected to greatly benefit researchers in this domain, enhancing their capacity for knowledge discovery and data management.

A Study of Projection-Based Attentive Spatial-Temporal Map for Remote Photoplethysmography Measurement.

The photoplethysmography (PPG) signal contains various information that is related to CVD (cardiovascular disease). The remote PPG (rPPG) is a method that can measure a PPG signal using a face image taken with a camera, without a PPG device. Deep learning-based rPPG methods can be classified into three main categories. First, there is a 3D CNN approach that uses a facial image video as input, which focuses on the spatio-temporal changes in the facial video. The second approach is a method that uses a spatio-temporal map (STMap), and the video image is pre-processed using the point where it is easier to analyze changes in blood flow in time order. The last approach uses a preprocessing model with a dichromatic reflection model. This study proposed the concept of an axis projection network (APNET) that complements the drawbacks, in which the 3D CNN method requires significant memory; the STMap method requires a preprocessing method; and the dyschromatic reflection model (DRM) method does not learn long-term temporal characteristics. We also showed that the proposed APNET effectively reduced the network memory size, and that the low-frequency signal was observed in the inferred PPG signal, suggesting that it can provide meaningful results to the study when developing the rPPG algorithm.

Assessment of ROI Selection for Facial Video-Based rPPG.

In general, facial image-based remote photoplethysmography (rPPG) methods use color-based and patch-based region-of-interest (ROI) selection methods to estimate the blood volume pulse (BVP) and beats per minute (BPM). Anatomically, the thickness of the skin is not uniform in all areas of the face, so the same diffuse reflection information cannot be obtained in each area. In recent years, various studies have presented experimental results for their ROIs but did not provide a valid rationale for the proposed regions. In this paper, to see the effect of skin thickness on the accuracy of the rPPG algorithm, we conducted an experiment on 39 anatomically divided facial regions. Experiments were performed with seven algorithms (CHROM, GREEN, ICA, PBV, POS, SSR, and LGI) using the UBFC-rPPG and LGI-PPGI datasets considering 29 selected regions and two adjusted regions out of 39 anatomically classified regions. We proposed a BVP similarity evaluation metric to find a region with high accuracy. We conducted additional experiments on the TOP-5 regions and BOT-5 regions and presented the validity of the proposed ROIs. The TOP-5 regions showed relatively high accuracy compared to the previous algorithm's ROI, suggesting that the anatomical characteristics of the ROI should be considered when developing a facial image-based rPPG algorithm.

EPITRANS: a database that integrates epigenome and transcriptome data.

Epigenetic modifications affect gene expression and thereby govern a wide range of biological processes such as differentiation, development and tumorigenesis. Recent initiatives to define genome-wide DNA methylation and histone modification profiles by microarray and sequencing methods have led to the construction of databases. These databases are repositories for international epigenetic consortiums or provide mining results from PubMed, but do not integrate the epigenetic information with gene expression changes. In order to overcome this limitation, we constructed EPITRANS, a novel database that visualizes the relationships between gene expression and epigenetic modifications. EPITRANS uses combined analysis of epigenetic modification and gene expression to search for cell function-related epigenetic and transcriptomic alterations (Freely available on the web at http://epitrans.org ).