Related papers: Development and Validation of MicrobEx: an Open-So…
This study presents OpenExtract, an open-source pipeline for automated data extraction in large-scale systematic literature reviews. The pipeline queries large language models (LLMs) to predict data entries based on relevant sections of…
Background: In the information extraction and natural language processing domain, accessible datasets are crucial to reproduce and compare results. Publicly available implementations and tools can serve as benchmark and facilitate the…
Objective:Develop and validate an algorithm for analyzing the layout of PDF clinical documents to improve the performance of downstream natural language processing tasks. Materials and Methods: We designed an algorithm to process clinical…
Recent advances in bioinformatics have made high-throughput microbiome data widely available, and new statistical tools are required to maximize the information gained from these data. For example, analysis of high-dimensional microbiome…
Annually and globally, over three billion radiography examinations and computer tomography scans result in mostly unstructured radiology reports containing free text. Despite the potential benefits of structured reporting, its adoption is…
Biomedical relation extraction (RE) is the task of automatically identifying and characterizing relations between biomedical concepts from free text. RE is a central task in biomedical natural language processing (NLP) research and plays a…
Automatic infectious disease classification from images can facilitate needed medical diagnoses. Such an approach can identify diseases, like tuberculosis, which remain under-diagnosed due to resource constraints and also novel and emerging…
This work uses the state-of-the-art language model GPT-3 to offer a novel method of information extraction for knowledge base development. The suggested method attempts to solve the difficulties associated with obtaining relevant entities…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
This article presents our steps to integrate complex and partly unstructured medical data into a clinical research database with subsequent decision support. Our main application is an integrated faceted search tool, accompanied by the…
The extraction and analysis of insights from medical data, primarily stored in free-text formats by healthcare workers, presents significant challenges due to its unstructured nature. Medical coding, a crucial process in healthcare, remains…
Despite the growing adoption of electronic health records, many processes still rely on paper documents, reflecting the heterogeneous real-world conditions in which healthcare is delivered. The manual transcription process is time-consuming…
Infectious diseases are a significant public health concern globally, and extracting relevant information from scientific literature can facilitate the development of effective prevention and treatment strategies. However, the large amount…
Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements…
Open-ended survey data constitute an important basis in research as well as for making business decisions. Collecting and manually analysing free-text survey data is generally more costly than collecting and analysing survey data consisting…
We work on the task of automatically designing a treatment plan from the findings included in the medical certificate written by the dentist. To develop an artificial intelligence system that deals with free-form certificates written by…
As part of the SMILK Joint Lab, we studied the use of Natural Language Processing to: (1) enrich knowledge bases and link data on the web, and conversely (2) use this linked data to contribute to the improvement of text analysis and the…
Background and Significance: Selecting cohorts for a clinical trial typically requires costly and time-consuming manual chart reviews resulting in poor participation. To help automate the process, National NLP Clinical Challenges (N2C2)…
Europe's healthcare systems require enhanced interoperability and digitalization, driving a demand for innovative solutions to process legacy clinical data. This paper presents the results of our project, which aims to leverage Large…
The community of different types of microbes present in a biological niche plays a very important role in functioning of the system. The crosstalk or interactions among the different microbes contributes to the building blocks of such…