106 research outputs found
Natural Language Processing – Finding the Missing Link for Oncologic Data, 2022
Oncology like most medical specialties, is undergoing a data revolution at the center of which lie vast and growing amounts of clinical data in unstructured, semi-structured and structed formats. Artificial intelligence approaches are widely employed in research endeavors in an attempt to harness electronic medical records data to advance patient outcomes. The use of clinical oncologic data, although collected on large scale, particularly with the increased implementation of electronic medical records, remains limited due to missing, incorrect or manually entered data in registries and the lack of resource allocation to data curation in real world settings. Natural Language Processing (NLP) may provide an avenue to extract data from electronic medical records and as a result has grown considerably in medicine to be employed for documentation, outcome analysis, phenotyping and clinical trial eligibility. Barriers to NLP persist with inability to aggregate findings across studies due to use of different methods and significant heterogeneity at all levels with important parameters such as patient comorbidities and performance status lacking implementation in AI approaches. The goal of this review is to provide an updated overview of natural language processing (NLP) and the current state of its application in oncology for clinicians and researchers that wish to implement NLP to augment registries and/or advance research projects
Ontology Enrichment from Free-text Clinical Documents: A Comparison of Alternative Approaches
While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships, as well as difficulty in updating the ontology as domain knowledge changes. Methodologies developed in the fields of Natural Language Processing (NLP), Information Extraction (IE), Information Retrieval (IR), and Machine Learning (ML) provide techniques for automating the enrichment of ontology from free-text documents. In this dissertation, I extended these methodologies into biomedical ontology development. First, I reviewed existing methodologies and systems developed in the fields of NLP, IR, and IE, and discussed how existing methods can benefit the development of biomedical ontologies. This previously unconducted review was published in the Journal of Biomedical Informatics. Second, I compared the effectiveness of three methods from two different approaches, the symbolic (the Hearst method) and the statistical (the Church and Lin methods), using clinical free-text documents. Third, I developed a methodological framework for Ontology Learning (OL) evaluation and comparison. This framework permits evaluation of the two types of OL approaches that include three OL methods. The significance of this work is as follows: 1) The results from the comparative study showed the potential of these methods for biomedical ontology enrichment. For the two targeted domains (NCIT and RadLex), the Hearst method revealed an average of 21% and 11% new concept acceptance rates, respectively. The Lin method produced a 74% acceptance rate for NCIT; the Church method, 53%. As a result of this study (published in the Journal of Methods of Information in Medicine), many suggested candidates have been incorporated into the NCIT; 2) The evaluation framework is flexible and general enough that it can analyze the performance of ontology enrichment methods for many domains, thus expediting the process of automation and minimizing the likelihood that key concepts and relationships would be missed as domain knowledge evolves
A Survey on Semantic Processing Techniques
Semantic processing is a fundamental research domain in computational
linguistics. In the era of powerful pre-trained language models and large
language models, the advancement of research in this domain appears to be
decelerating. However, the study of semantics is multi-dimensional in
linguistics. The research depth and breadth of computational semantic
processing can be largely improved with new technologies. In this survey, we
analyzed five semantic processing tasks, e.g., word sense disambiguation,
anaphora resolution, named entity recognition, concept extraction, and
subjectivity detection. We study relevant theoretical research in these fields,
advanced methods, and downstream applications. We connect the surveyed tasks
with downstream applications because this may inspire future scholars to fuse
these low-level semantic processing tasks with high-level natural language
processing tasks. The review of theoretical research may also inspire new tasks
and technologies in the semantic processing domain. Finally, we compare the
different semantic processing techniques and summarize their technical trends,
application trends, and future directions.Comment: Published at Information Fusion, Volume 101, 2024, 101988, ISSN
1566-2535. The equal contribution mark is missed in the published version due
to the publication policies. Please contact Prof. Erik Cambria for detail
PadChest: A large chest x-ray image dataset with multi-label annotated reports
We present a labeled large-scale, high resolution chest x-ray dataset for the
automated exploration of medical images along with their associated reports.
This dataset includes more than 160,000 images obtained from 67,000 patients
that were interpreted and reported by radiologists at Hospital San Juan
Hospital (Spain) from 2009 to 2017, covering six different position views and
additional information on image acquisition and patient demography. The reports
were labeled with 174 different radiographic findings, 19 differential
diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and
mapped onto standard Unified Medical Language System (UMLS) terminology. Of
these reports, 27% were manually annotated by trained physicians and the
remaining set was labeled using a supervised method based on a recurrent neural
network with attention mechanisms. The labels generated were then validated in
an independent test set achieving a 0.93 Micro-F1 score. To the best of our
knowledge, this is one of the largest public chest x-ray database suitable for
training supervised models concerning radiographs, and the first to contain
radiographic reports in Spanish. The PadChest dataset can be downloaded from
http://bimcv.cipf.es/bimcv-projects/padchest/
Deep learning in medical imaging and radiation therapy
Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146980/1/mp13264_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146980/2/mp13264.pd
Intelligence artificielle: Les défis actuels et l'action d'Inria - Livre blanc Inria
Livre blanc Inria N°01International audienceInria white papers look at major current challenges in informatics and mathematics and show actions conducted by our project-teams to address these challenges. This document is the first produced by the Strategic Technology Monitoring & Prospective Studies Unit. Thanks to a reactive observation system, this unit plays a lead role in supporting Inria to develop its strategic and scientific orientations. It also enables the institute to anticipate the impact of digital sciences on all social and economic domains. It has been coordinated by Bertrand Braunschweig with contributions from 45 researchers from Inria and from our partners. Special thanks to Peter Sturm for his precise and complete review.Les livres blancs d’Inria examinent les grands défis actuels du numérique et présentent les actions menées par noséquipes-projets pour résoudre ces défis. Ce document est le premier produit par la cellule veille et prospective d’Inria. Cette unité, par l’attention qu’elle porte aux évolutions scientifiques et technologiques, doit jouer un rôle majeur dans la détermination des orientations stratégiques et scientifiques d’Inria. Elle doit également permettre à l’Institut d’anticiper l’impact des sciences du numérique dans tous les domaines sociaux et économiques. Ce livre blanc a été coordonné par Bertrand Braunschweig avec des contributions de 45 chercheurs d’Inria et de ses partenaires. Un grand merci à Peter Sturm pour sa relecture précise et complète. Merci également au service STIP du centre de Saclay – Île-de-France pour la correction finale de la version française
Computational Pathology: A Survey Review and The Way Forward
Computational Pathology CPath is an interdisciplinary science that augments
developments of computational approaches to analyze and model medical
histopathology images. The main objective for CPath is to develop
infrastructure and workflows of digital diagnostics as an assistive CAD system
for clinical pathology, facilitating transformational changes in the diagnosis
and treatment of cancer that are mainly address by CPath tools. With
evergrowing developments in deep learning and computer vision algorithms, and
the ease of the data flow from digital pathology, currently CPath is witnessing
a paradigm shift. Despite the sheer volume of engineering and scientific works
being introduced for cancer image analysis, there is still a considerable gap
of adopting and integrating these algorithms in clinical practice. This raises
a significant question regarding the direction and trends that are undertaken
in CPath. In this article we provide a comprehensive review of more than 800
papers to address the challenges faced in problem design all-the-way to the
application and implementation viewpoints. We have catalogued each paper into a
model-card by examining the key works and challenges faced to layout the
current landscape in CPath. We hope this helps the community to locate relevant
works and facilitate understanding of the field's future directions. In a
nutshell, we oversee the CPath developments in cycle of stages which are
required to be cohesively linked together to address the challenges associated
with such multidisciplinary science. We overview this cycle from different
perspectives of data-centric, model-centric, and application-centric problems.
We finally sketch remaining challenges and provide directions for future
technical developments and clinical integration of CPath
(https://github.com/AtlasAnalyticsLab/CPath_Survey).Comment: Accepted in Elsevier Journal of Pathology Informatics (JPI) 202
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