{"id":374,"date":"2025-07-16T19:52:31","date_gmt":"2025-07-16T19:52:31","guid":{"rendered":"https:\/\/carlaconference.org\/?page_id=374"},"modified":"2025-09-22T23:34:12","modified_gmt":"2025-09-22T23:34:12","slug":"biocarla-workshop-challenges-and-advances-in-small-foundation-models-for-biomedical-and-life-sciences","status":"publish","type":"page","link":"https:\/\/carlaconference.org\/biocarla-workshop-challenges-and-advances-in-small-foundation-models-for-biomedical-and-life-sciences\/","title":{"rendered":"BioCARLA Workshop"},"content":{"rendered":"\n

BioCARLA: Challenges and Advances in Small\/Foundation Models for Biomedical and Life Sciences Workshop<\/h2>\n\n\n\n

Workshop Description<\/h2>\n\n\n\n

The 7th edition of BioCARLA continues to serve as a central forum within the CARLA conference series (carlaconference.org), bringing together experts in biology, biomedical engineering, computer science, and AI. This year, the workshop focuses on the growing impact of small and foundation models (FMs) in advancing biomedical research, healthcare innovation, and life science applications. Participants will explore how these models can bridge the gap between cutting-edge machine learning and real-world clinical or biotech needs.
The BioCARLA Workshop, part of the CARLA conference series, is a key forum for researchers applying HPC, machine learning, and big data analytics to bioinformatics and biomedicine. The workshop focuses on two core challenges: 1. Transforming multi-omics and biomedical data into actionable insights using scalable HPC-powered models. 2. Advancing clinical readiness through secure, trustworthy, interpretable, and deployable AI systems.
BioCARLA 2025 will spotlight cutting-edge research and interdisciplinary efforts to develop practical, secure, and accessible computational tools for the biomedical and life sciences.<\/p>\n\n\n\n

Call for papers<\/h2>\n\n\n\n

BioCARLA invites submissions from researchers in biology, biomedicine, and computer science working in multidisciplinary teams or startups. We seek original research that integrates HPC, ML, big data analytics, and large-scale multi-omics datasets. <\/p>\n\n\n\n

Submissions should present novel findings or innovative solutions to current challenges. <\/p>\n\n\n\n

Presentation Formats: <\/strong><\/p>\n\n\n\n

\n

\u25cf Short Paper Presentation: 4\u20138 pages (including references) <\/strong><\/p>\n\n\n\n

\u25cf Poster Presentation: Extended abstract, up to 2 pages (including references) <\/strong><\/p>\n<\/div>\n\n\n\n

\n

<\/p>\n\n\n\n

<\/p>\n\n\n\n

Important Dates: <\/strong><\/p>\n\n\n\n

\n
\n

\u25cf Submission Deadline: August 1, 2025 <\/strong><\/p>\n\n\n\n

\u25cf Notification of Acceptance: August 12, 2025<\/strong><\/p>\n<\/div>\n<\/div><\/div>\n<\/div>\n\n\n\n

Submission Guidelines<\/h2>\n\n\n\n

All submitted works must adhere to the general guidelines for papers and posters outlined for CARLA 2025. (https:\/\/carlaconference.org\/call-papers\/)<\/p>\n\n\n\n

Topics<\/strong><\/h2>\n\n\n\n
    \n
  • Foundation and practical application to integrate Bioinformatics, System Biology, and HPC<\/li>\n\n\n\n
  • Design, implementation, and integration of biological workflow using HPC technologies<\/li>\n\n\n\n
  • Network biological and evolutionary methods for multi-omics integration<\/li>\n\n\n\n
  • Computational support of Bioinformatics analyses in parallel and distributed environments<\/li>\n\n\n\n
  • Best practices in HPC management and development for Bioinformatics and System Biology<\/li>\n\n\n\n
  • HPC, Big Data Analytics and Integration for Multi-Omics Biomedical Data<\/li>\n\n\n\n
  • Bioinformatics training activities – computational genomics, metagenomics, phylogenomic, proteomics, and proteogenomic – applied in HPC technologies<\/li>\n\n\n\n
  • Predictive modeling of risks, diseases, and patients’ outcomes using machine learning and deep learning techniques.<\/li>\n<\/ul>\n\n\n\n

    Chairs<\/h2>\n\n\n\n
      \n
    • John Garcia-Henao, Balgrist University Hospital, Switzerland, John.GarciaHenao@balgrist.ch<\/li>\n\n\n\n
    • Kary Oca\u00f1a, National Laboratory of Scientific Computing, Brazil, karyann@lncc.br<\/li>\n<\/ul>\n\n\n\n

      Workshop Schedule<\/strong><\/p>\n\n\n\n

      09:00 \u2013 09:10
      Introduction \u2014 Dr. John Anderson Garc\u00eda<\/p>\n\n\n\n

      09:10 \u2013 10:00
      Keynote \u2014 Dr. St\u00e9phanie Lopez (Universit\u00e9 C\u00f4te d’Azur, Nice, France)
      From Proof of Concept to Clinical Cockpit: Overcoming Translational Barriers in AI-Driven Medical Devices<\/em><\/p>\n\n\n\n

      10:00 \u2013 10:20
      Invited Talk \u2014 Dr. Carla Osthoff (LNCC, Rio de Janeiro, Brazil)
      HPC Scientific Workflows in Bioinformatics<\/em><\/p>\n\n\n\n

      10:20 \u2013 10:40
      Invited Talk \u2014 MD Mario Miguel Barbosa (Fundaci\u00f3n Valle del Lili Hospital, Colombia)
      AI-Powered Early Prediction of Sepsis Progression in the Emergency Department (ED): Protocol Development<\/em><\/p>\n\n\n\n

      10:40 \u2013 11:00
      Invited Talk \u2014 Dr. John Alexander Sanabria (Universidad del Valle, Colombia)
      AI Model Deployment and Real-Time Monitoring Platform for Sepsis Detection<\/em><\/p>\n\n\n\n

      11:00 \u2013 11:30
      Coffee Break<\/p>\n\n\n\n

      11:30 \u2013 11:50
      Invited Talk \u2014 Nicole Arias Espinoza (Centro Nacional de Alta Tecnolog\u00eda, Costa Rica)
      High-Performance Computing for Life Sciences<\/em><\/p>\n\n\n\n

      11:50 \u2013 12:50
      Discussion Panel \u2014 Invited Speakers and Attendees
      From Foundation Models to Biomedical Informatics and Clinical Translation<\/em><\/p>\n\n\n\n

      12:50 \u2013 13:00
      Conclusion \u2014 Dr. John Anderson Garc\u00eda<\/p>\n\n\n\n

      \n\n\n\n

      Keynote: 40 min + 10 min Q&A
      Invited Talk: 15 min + 5 min Q&A
      Discussion Panel: 1 hour<\/p>\n\n\n\n

      <\/p>\n","protected":false},"excerpt":{"rendered":"

      BioCARLA: Challenges and Advances in Small\/Foundation Models for Biomedical and Life Sciences Workshop Workshop Description The 7th edition of BioCARLA continues to serve as a central forum within the CARLA conference series (carlaconference.org), bringing together experts in biology, biomedical engineering, computer science, and AI. This year, the workshop focuses on the growing impact of small and foundation models (FMs) in advancing biomedical research, healthcare innovation, and life science applications. Participants will explore how these models can bridge the gap between cutting-edge machine learning and real-world clinical or biotech needs. The BioCARLA Workshop, part of the CARLA conference series, is a key forum for researchers applying HPC, machine learning, and big data analytics to bioinformatics and biomedicine. The workshop focuses on two core challenges: 1. Transforming multi-omics and biomedical data into actionable insights using scalable HPC-powered models. 2. Advancing clinical readiness through secure, trustworthy, interpretable, and deployable AI systems. BioCARLA 2025 will spotlight cutting-edge research and interdisciplinary efforts to develop practical, secure, and accessible computational tools for the biomedical and life sciences. Call for papers BioCARLA invites submissions from researchers in biology, biomedicine, and computer science working in multidisciplinary teams or startups. We seek original research that integrates HPC, ML, big data analytics, and large-scale multi-omics datasets. Submissions should present novel findings or innovative solutions to current challenges. Presentation Formats: \u25cf Short Paper Presentation: 4\u20138 pages (including references) \u25cf Poster Presentation: Extended abstract, up to 2 pages (including references) Important Dates: \u25cf Submission Deadline: August 1, 2025 \u25cf Notification of Acceptance: August 12, 2025 Submission Guidelines All submitted works must adhere to the general guidelines for papers and posters outlined for CARLA 2025. (https:\/\/carlaconference.org\/call-papers\/) Topics Chairs Workshop Schedule 09:00 \u2013 09:10Introduction \u2014 Dr. John Anderson Garc\u00eda 09:10 \u2013 10:00Keynote \u2014 Dr. St\u00e9phanie Lopez (Universit\u00e9 C\u00f4te d’Azur, Nice, France)From Proof of Concept to Clinical Cockpit: Overcoming Translational Barriers in AI-Driven Medical Devices 10:00 \u2013 10:20Invited Talk \u2014 Dr. Carla Osthoff (LNCC, Rio de Janeiro, Brazil)HPC Scientific Workflows in Bioinformatics 10:20 \u2013 10:40Invited Talk \u2014 MD Mario Miguel Barbosa (Fundaci\u00f3n Valle del Lili Hospital, Colombia)AI-Powered Early Prediction of Sepsis Progression in the Emergency Department (ED): Protocol Development 10:40 \u2013 11:00Invited Talk \u2014 Dr. John Alexander Sanabria (Universidad del Valle, Colombia)AI Model Deployment and Real-Time Monitoring Platform for Sepsis Detection 11:00 \u2013 11:30Coffee Break 11:30 \u2013 11:50Invited Talk \u2014 Nicole Arias Espinoza (Centro Nacional de Alta Tecnolog\u00eda, Costa Rica)High-Performance Computing for Life Sciences 11:50 \u2013 12:50Discussion Panel \u2014 Invited Speakers and AttendeesFrom Foundation Models to Biomedical Informatics and Clinical Translation 12:50 \u2013 13:00Conclusion \u2014 Dr. John Anderson Garc\u00eda Keynote: 40 min + 10 min Q&AInvited Talk: 15 min + 5 min Q&ADiscussion Panel: 1 hour<\/p>\n","protected":false},"author":10,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-374","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/carlaconference.org\/wp-json\/wp\/v2\/pages\/374","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/carlaconference.org\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/carlaconference.org\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/carlaconference.org\/wp-json\/wp\/v2\/users\/10"}],"replies":[{"embeddable":true,"href":"https:\/\/carlaconference.org\/wp-json\/wp\/v2\/comments?post=374"}],"version-history":[{"count":10,"href":"https:\/\/carlaconference.org\/wp-json\/wp\/v2\/pages\/374\/revisions"}],"predecessor-version":[{"id":1352,"href":"https:\/\/carlaconference.org\/wp-json\/wp\/v2\/pages\/374\/revisions\/1352"}],"wp:attachment":[{"href":"https:\/\/carlaconference.org\/wp-json\/wp\/v2\/media?parent=374"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}