New track on Apache’s only project focused on biomedical informatics features sessions presented by Apache cTAKES community representatives from the Barcelona Supercomputing Center, Boston Children’s Hospital’s Computational Health Informatics Program (CHIP), Children’s Hospital of Philadelphia, Dell EMC, Geisinger Health, Loyola University Chicago, and University of California San Francisco.
ApacheCon, the official conference series of The Apache Software Foundation (ASF), the world’s largest Open Source foundation, announced today its first dedicated track on Apache cTAKES. The track will be held on all three days of the [email protected] virtual conference, taking place online 29 September – 1 October 2020. Registration is free of charge for all participants and is required in advance to participate.
Now in its 22nd year, ApacheCon is the primary gathering of the collective Apache community worldwide, drawing attendees from more than 130 countries. ApacheCon showcases the latest breakthroughs from dozens of Apache projects, upcoming innovations in the Apache Incubator, and sessions on developing community-led Open Source projects “The Apache Way”.
Apache cTAKES (clinical Text Analysis Knowledge Extraction System) is the Open Source natural language processing (NLP) system for information extraction from electronic medical records (EMR) and health-related free-text. cTAKES originated in 2006 by a team of physicians, computer scientists, and software engineers at Mayo Clinic, was submitted to the Apache Incubator in June 2012, led by the Computational Health Informatics Program (CHIP) at Boston Children’s Hospital, and graduated as an Apache Top-Level Project in April 2013. cTAKES is the only Apache project focused on biomedical informatics software, and, during the ASF’s 20th Anniversary celebrations in 2019, was named one of the 20 most influential Apache projects.
cTAKES was built using the Apache UIMA (Unstructured Information Management Architecture) framework and Apache OpenNLP machine-learning based toolkit. cTAKES identifies signals important for the biomedical domain, including types of clinical named entities mapped to various biomedical terminologies/ontologies such as the Unified Medical Language System (UMLS) —drugs, diseases/disorders, signs/symptoms, anatomical sites and procedures along with their associated attributes such as negation, uncertainty, and more. Apache cTAKES components create rich linguistic and semantic annotations that can be utilized by clinical decision support systems and clinical research.
The cTAKES track is organized and presented by members of the Apache cTAKES project and its community. The track introduces new users to its standard features for biomedical text processing software, including the ability to extract concepts such as symptoms, procedures, diagnoses, medications and anatomy with attributes and standard codes. Several advanced presentations will exemplify its modular engineering and its leading-edge machine learning methods. Components implementing these research-driven methods can, for instance, identify complex relations between entities (e.g. anatomical site of a disease) and relations between temporal elements – resulting in the placement of events in a patient timeline. Session presenters include:
- Peter Abramowitsch, University of California San Francisco
- Siamak Barzegar, Barcelona Supercomputing Center, Spain
- Dmitriy Dligach, Loyola University Chicago
- Sean Finan, Computational Health Informatics Program (CHIP) at Boston Children’s Hospital
- Chen Lin, Computational Health Informatics Program (CHIP) at Boston Children’s Hospital
- Jeff Miller, Children’s Hospital of Philadelphia
- Debdipto Misra, Geisinger Health
- Gandhirajan N, Dell EMC
Apache cTAKES can impact patient health at many levels, and presentations at ApacheCon range from “Automated Adverse Drug Event Surveillance in Pediatric Pulmonary Hypertension” to “Extraction of Information on Diagnosis of Stroke” in Spanish to “High Throughput Orchestration” on notes involving COVID-19, amongst others. Track details can are available at https://www.apachecon.com/acah2020/tracks/ctakes.html
In addition to cTAKES, [email protected] features an array of presentations on Apache projects across categories that include Big Data, Community, Content Delivery, Databases, Fintech, Geospatial, Innovation/Incubator, Integration, IoT, Machine Learning, Search, Servers, Software Development, Streaming, and more. A special track in the Mandarin language, as well as select sessions in German, Hindi, and Spanish will be held as well.
ApacheCon keynotes will be delivered by high profile speakers from organizations such as DataStax, IBM, Imply, Instaclustr, NASA Jet Propulsion Laboratory, Oak Ridge National Labs, Red Hat, Tetrate, Two Sigma, and VMWare.
Register today at https://www.apachecon.com/acah2020/ . Select sessions will be recorded and available following the event.
For more information on Apache cTAKES, visit http://ctakes.apache.org/
ApacheCon is the official global conference series of The Apache Software Foundation. Since 1998 ApacheCon has been drawing participants at all levels to explore ”Tomorrow’s Technology Today” across 350+ Apache projects and their diverse communities. ApacheCon showcases the latest developments in ubiquitous Apache projects and emerging innovations through hands-on sessions, keynotes, real-world case studies, trainings, hackathons, community events, and more. ApacheCon events in 2020 have been consolidated to [email protected], a new, virtual conference that takes place online 29 September – 1 October 2020. Registration is free to all, with advance registration required. For more information, visit http://apachecon.com/ and https://twitter.com/ApacheCon .
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CONTACT: Sally Khudairi Vice President The Apache Software Foundation [email protected]
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