Declarative Programming in Biology and Medicine (DeclMed) 2023DeclMed 2023

Declarative Programming in Biology and Medicine (“DeclMed”) is a new interdisciplinary workshop that will explore declarative programming methods / paradigms and their applications in the life sciences and medicine. Given promising advances in using declarative approaches in areas such as precision medicine, bioinformatics, graph querying, modeling, and DNA computing, this workshop aims to advance the use of declarative approaches to solve complex problems in biology or medicine. The workshop will solicit abstracts, papers, tutorials, and presentations (including lightning talks). The two main goals of the workshop are to (1) share and explore new techniques and ideas; and (2) bring together researchers and practitioners from the declarative programming communities with practitioners in precision medicine, bioinformatics, and biomodeling.

Location and date

The workshop will be held on Sept. 9, 2023 at the Westin Hotel in Seattle, Washington, USA. The schedule for the workshop (start time and end time) will be posted here as soon as it is finalized.

Parent conference

DeclMed 2023 is being held as part of the 2023 International Conference on Functional Programming (ICFP) (icfp.sigplan.org). The DeclMed 2023 organizers thank the ICFP 2023 organizers and ACM SIGPLAN for their support.

Topics of interest

Topics include, but are not limited to, applications of declarative programming (including logic/relational programming and functional programming approaches), or ideas about potential applications of declarative programming, in:

• life sciences
• precision medicine (e.g., mediKanren), including diagnosis, treatment, and monitoring
• modeling living systems (e.g., BioASP)
• DNA computing
• synthetic biology
• graph querying, particularly for life sciences applications (e.g., Cypher, SPARQLProg)
• bioinformatics (e.g., BioMake)
• translational science
• biochemical kinetics
• computational neuroscience

Speaker list (tentative as of 8/3/2023)

Keynotes

• Chris Mungall, Lawrence Berkeley National Laboratory – topic TBD
• Tyler Beck, National Center for Advancing Translational Sciences – NCATS’ Biomedical Data Translator - Connecting the Dots
• Matt Might, Precision Medicine Institute at the University of Alabama Birmingham – The Algorithm for Precision Medicine

Presenters

• Sierra Moxon, Lawrence Berkeley National Laboratory – Biolink Model: a Universal Schema for Knowledge Graphs in Clinical, Biomedical, and Translational Science
• Pjotr Prins, University of Tennessee Health Science Center – Why code in Python+C if you can code in Lisp+Zig?
• Jeff Henrikson, Groovescale – Functional Pearl: Signature Memoization for Drug Repurposing
• Peter-Michael Osera, Grinnell College – Towards Higher-level Abstractions for Molecular Programming
• Matthew Hur, University of California Irvine – Modeling Graph-Based Morphology of the Synaptic Spine Head
• (Presenter TBD) – ExEmPLAR (Extracting, Exploring and Embedding Pathways Leading to Actionable Research): A User-friendly Interface for Knowledge Graph Mining.
• Daniel Korn, Every Cure – Aggregating combinatorial biomedical graph ranking results for drug repurposing
• Arun Isaac, University College London – Propagator networks for degenerate computation
• Parisa Kordjamshidi, Michigan State University – Declarative Programming for Designing Neuro-Symbolic Learning Models
• Abdullateef Almudaifer, University of Alabama Birmingham – Addressing Treatment-Relevance in Biomedical Relation Extraction

Registration

Please register through the ICFP website.

Organizers

DeclMed 2023 is being organized by Stephen Ramsey (Oregon State University), Will Byrd (University of Alabama Birmingham), and Matt Might (University of Alabama Birmingham), with reviewing help generously provided by the workshop’s Program Committee. We hope to see you at DeclMed 2023!

Accepted Papers

Call for Papers

We invite you to submit an original research article or experience report for inclusion in the workshop’s non-archival proceedings. If the Program Committee accepts your article into the proceedings, you and your coauthors will be invited to have one of you give a 20-minute oral presentation about your research (in person) during the workshop. As you will see below, we (the DeclMed organizers) have streamlined the requirements to make it as easy as possible for you and your co-authors to prepare and submit your manuscript.

Topics of interest

See the DeclMed 2023 main page.

Manuscript Guidelines

Manuscripts should be written in English (U.S. spelling recommended), should describe original research, and should be no more than 10 pages (US Letter page size) in length. In terms of page layout, we recommend having at least 1 inch margins and and that you select a font size and line-skip size so that there are no more than 5.34 lines per inch, vertically. Including page numbering (in Arabic numerals) in the document footer is recommended. If you are preparing your manuscript in Overleaf, please note that Overleaf by default prepares documents in A4 page size, but you can specify a different page size using the “geometry” package. Please prepare your manuscript as a single PDF document with figures embedded in the manuscript and with a caption immediately adjacent to each figure/table. Your manuscript should begin with a title, series title (“Proceedings of the 2023 ICFP Workshop Declarative Programming in Biology and Medicine”), and an abstract. Please do not include an author list in your manuscript; the workshop will use a double-anonymized peer review process, so no information about authors’ names, institutions, or contact information should be included in the manuscript submitted for review. Please try to ensure that when your figure is embedded into the manuscript at its final scaled size, the scaled font sizes of any text labels are at least the size of the running text in your manuscript (to ensure readability). The recommended location for bibliographic citations is to include them in a section entitled “References” at the end of the manuscript. In preparing your PDF document, if you or your co-authors have the ability to embed fonts in the PDF document, please do so. You are welcome to use the SIGPLAN Proceedings LaTeX template file, but by no means required to do so. If you do use the SIGPLAN template, we recommend using the acmsmall option to the acmart document class. Your manuscript must also have a “Declarations” section, as described below.

Double-anonymized peer review

DeclMed 2023 will use lightweight double-anonymized reviewing. Submitted manuscripts must omit author names and institutions and reference the authors’ own related work in the third person (e.g., not “we build on our previous work…” but rather “we build on the work of…”). The purpose of double-anonymized review is to help the reviewers come to an unbiased judgment about the suitability of the work for inclusion in the workshop, not to make it impossible for them to discover the authors if they were to try. Nothing should be done in the name of anonymity that weakens the submission or makes the job of reviewing the paper more difficult (e.g., important background references should not be omitted or anonymized).

Declarations

At the end of your manuscript’s running text (i.e., before the “References” section), there should be a section entitled “Declarations”. In that section, you are required to declare the existence of any financial conflicts of interest that are applicable (per COPE guidelines) for the research your manuscript describes, for any of the listed co-authors; if you and your co-authors have no conflicts of interest, you are asked to include a declaration that you do not have any conflicts of interest pertaining to the work described in the article. Additionally, if your research involved human subjects and/or vertebrate animals, you are required to add a sentence declaring that your human subjects and/or vertebrate animal work was carried out with the approval of, or an exemption granted by, your Institutional Review Board and/or Institutional Animal Care and Use Committee. (If your research involved human subjects and/or vertebrate animals and you are unable to include that declaration, then unfortunately, we will be unable to include your work in the proceedings).

Submission

Please submit your manuscript by uploading the PDF at the submission site declmed23.hotcrp.com by the due date (see Key Dates below). If your manuscript is accepted, you will be asked to submit a version including author information, for inclusion in the workshop’s online proceedings.

Proceedings

The DeclMed 2023 proceedings will be published on arXiv.org, by the date of the workshop.

Organizers

See the DeclMed 2023 organizing committee.

Call for Abstracts

We invite you to submit an abstract for inclusion in the workshop’s non-archival proceedings. If the Program Committee accepts your abstract, you and your coauthors will be invited to have one of you give a 10-minute oral presentation about your research (in person) during the workshop. As you will see below, we (the DeclMed organizers) have streamlined the requirements to make it as easy as possible for you and your co-authors to prepare and submit your abstract.

Topics of interest

See the DeclMed 2023 main page.

Abstract Guidelines

Abstracts should be written in English (U.S. spelling recommended), should describe original research, and should be no more than 200 words in length. Your abstract should begin with a title. Please do not include an author list in your abstract; the workshop will use a double-anonymized peer review process, so no information about authors’ names, institutions, or contact information should be included in the abstract submitted for review. You may submit your abstract as a PDF file or as a text file.

Double-anonymized peer review

DeclMed 2023 will use lightweight double-anonymized reviewing. Submitted abstracts must omit author names and institutions and reference the authors’ own related work in the third person (e.g., not “we build on our previous work…” but rather “we build on the work of…”). The purpose of double-anonymized review is to help the reviewers come to an unbiased judgment about the suitability of the work for inclusion in the workshop.

Declarations

If you will be reporting on work for which you have a financial conflict of interest, or if you will be reporting on work that involved human subjects research or vertebrate animal research, at the end of your abstract, you should include a section entitled “Declarations”. In that section, you are asked to declare the existence of any financial conflicts of interest that are applicable (per COPE guidelines) for the research your presentation will describe, for any of the listed co-authors; if you and your co-authors have no conflicts of interest, you are required to include a declaration that you do not have any conflicts of interest pertaining to the work described in the article. Additionally, if your research involved human subjects and/or vertebrate animals, you are required to add a sentence declaring that your human subjects and/or vertebrate animal work was carried out with the approval of, or an exemption granted by, your Institutional Review Board and/or Institutional Animal Care and Use Committee. (If your research involved human subjects and/or vertebrate animals and you are unable to include that declaration, then unfortunately, we will be unable to include your work in the proceedings).

Submission

Please submit your abstract by uploading the PDF or text file at the submission site declmed23.hotcrp.com by the due date (see Key Dates below). If your abstract is accepted, you will be asked to submit a final version including author information, for inclusion in the workshop’s online proceedings.

Proceedings

The DeclMed 2023 proceedings will be published on arXiv.org, by the date of the workshop.

Organizers

See the DeclMed 2023 organizing committee.