Rare Disease, Real Kid: The MVA Hackathon 2026

Track 1 Leaderboard

Rankings update automatically each time a valid submission is evaluated. Only the best-scoring submission per team is shown.

How to Submit

Track 1 — Variant Prediction

1. 1
   Prepare your file

   Create a CSV file with one row per proposed causal variant, or proposed compound-heterozygous variant pair. Rank your predictions by your own estimated probability of causal relationship (EPCR) — a number between 0 and 1. An EPCR of 1 means you're fully confident this is the causal variant. An EPCR close to 0 means you're including it as a long-shot or low-confidence guess rather than a serious candidate — there's no fixed "confident enough" cutoff, only your ranking relative to your own other guesses matters for scoring. Coordinates must use GRCh38. Up to 10 candidate rows are accepted — this is one patient, not a cohort, so we're asking for your best-ranked guesses, not an exhaustive list. Flag whether each row is your primary candidate or a secondary/incidental finding using the finding_type column. Secondary or incidental findings won't hurt your automated score — include them if you want them considered.

   ⬇ Download submission template (.csv)

   Field	Type	Description
   proband_id	string	Patient identifier (provided in the dataset)
   chrom_1	string	Chromosome of the first (or only) variant (e.g. chr15)
   pos_1	integer	Base-pair position of the first variant (GRCh38)
   ref_1	string	Reference allele of the first variant
   alt_1	string	Alternate allele of the first variant
   chrom_2	string	Chromosome of the second variant, if proposing a compound-heterozygous pair (leave blank otherwise)
   pos_2	integer	Base-pair position of the second variant (leave blank if not applicable)
   ref_2	string	Reference allele of the second variant (leave blank if not applicable)
   alt_2	string	Alternate allele of the second variant (leave blank if not applicable)
   epcr	float	Estimated probability of causal relationship, in the range (0, 1]
   finding_type	string	Either primary or secondary — flag whether you believe this variant explains the patient's known phenotype, or whether it's a secondary/incidental finding (something unrelated to the primary condition, but still worth surfacing).

2. 2
   Write up your work

   Push your documented, reproducible code to a public GitHub repository. Each model must include a detailed description of your method(s)

4. 3
   Name your files

   Use this naming convention so submissions are easy to track:

   File	Naming pattern	Example
   Track 1 CSV	<teamname>_track1_model<N>.csv	helixsquad_track1_model1.csv
   Methods description	<teamname>_method<N>.txt	helixsquad_track1_method1.txt

   <N> is 1, 2,3,4,5, or 6 matching your Track 1 submission cap, so a team can submit up to 6 distinct models without filename collisions.

5. 4
   Sign in & upload

   Sign in with your Hugging Face account on the leaderboard Space, then submit your CSV file along with your method using the submission form. Teams may submit up to 6 times; only the best-scoring submission counts toward final ranking.

6. 5
   See your score

   Your CSV submission is evaluated automatically using rank points and F-max against the clinically confirmed answer on the leaderboard. Your method(s) will be reviewed separately as part of judging criteria like innovation and scalability.

Track 2 — Drug Repositioning

1. 1
   Write your report

   Prepare a written report (PDF or Markdown) proposing repositioned drug candidates supported by your analysis. Your report should include a characterization of the variant's mechanism — e.g., loss-of-function or gain-of-function, the pathway disrupted, and the downstream biological consequence , as the basis for your repositioning rationale.

2. 2
   Package your work

   Push your documented, reproducible code to a public GitHub repository, and record a 3-minute pitch video walking through your reasoning and proposed candidates.

4. 3
   Name your files

   Use this naming convention so submissions are easy to track:

   File	Naming pattern	Example
   Track 2 report	<teamname>_track2_report.pdf (or .md)	helixsquad_track2_report.pdf
   Pitch video	<teamname>_video.mp4 (or .mov)	helixsquad_pitch_video.mp4

   Track 2 has no model number since only one final submission is accepted per team.

5. 4
   Submit before the deadline

   Upload your report along with your GitHub repo link and video via the submission form. Late submissions cannot be accepted, as materials go directly to human judges for scheduling.

6. 5
   Await judging

   The independent panel reviews all submissions over a ~2–3 month window. Results are announced after the judging period closes.

Know what to include in your methods write-up

Not sure how much detail to include, or what kind of questions your write-up should answer? Examples of what we're looking for in the methods section such as model description, data sources, how compound-heterozygous or secondary findings were handled, and so on can be found here:

⬇ Methods description examples (.xlsx)

FAQ

Challenge Rules

To participate in this Hackathon, you must review and accept the following terms. Please read carefully and proceed only if you agree to comply with the conditions below.

Terms of Service & Eligibility

• You must abide by the Hugging Face Terms of Service and by these Hackathon Rules.
• You must be 18 years of age or older to participate.
• Each member of your Hackathon team must individually register as a participant and agree to these Hackathon Rules.

Data Privacy & Recontact Restrictions

• You agree that you will not attempt to recontact the data subject, data subject family members, or any points of contact at the MVA Society.
• Your use of the data will comply with all applicable laws, rules, regulations, and professional standards.
• If any unauthorized disclosure of the data occurs or is suspected, you agree to contact Sage Bionetworks' Privacy and Compliance Office via Sage's Help Center.
• You will not release or otherwise grant data access to anyone, and you will establish appropriate safeguards to prevent unauthorized data use.

Hackathon Flow

Registration. Participants must register with Hugging Face and request access to the data, including a valid email address and attestation to accepting these Hackathon Rules.

Hackathon tasks. The Hackathon consists of two tasks:

1. Task 1 — Variant identification: identify the disease-causing variant(s) using genetic variant information and phenotypic presentations. Participants will not be given the NHS-validated disease-causal variants; you will develop computational models and submit a list of variants you believe are causal.
2. Task 2 — Drug repositioning: leveraging the genetic information and variant prediction from Task 1, identify existing market-approved medications whose mechanism of action may target the disease-causing pathway(s) or affect symptoms and improve quality of life.

Team formation.

• Teams are not required.
• Participants may form teams based on skills and interests; teams often combine programmers, designers, and domain experts.

Data & resource provision.

• File types: de-identified genomic data in VCF format (SNPs, indels, structural variants); raw sequencing data optionally in BAM/CRAM. Phenotypic data as standardized HPO terms (e.g., HP:0001250 Seizure, HP:0002904 Hyperbilirubinemia).
• Data size: ~120 GB. A single-subject dataset (one patient) — small in scale, but genomically sensitive; size details are subject to change pending final file export.
• Access: participants request access via Hugging Face's gated-dataset mechanism. Once approved, each participant downloads directly via their own Hugging Face account/token — no data may be emailed, shared via drive, or distributed through any channel outside the Hugging Face access-controlled dataset repo. You must not repost any data on Hugging Face.
• Compute: participants are responsible for their own compute environment and any associated costs; Sage Bionetworks does not provide compute resources for the Hackathon.

Data Deletion

• Data retention after the Hackathon is not permitted for any purpose.
• Participants must delete all copies of the Hackathon dataset from every environment where it was accessed or stored, including:
  • Local machines and personal hard drives (delete files and empty trash/recycle bin);
  • Cloud compute instances and virtual machines (terminate instances and delete associated storage volumes);
  • Notebooks and notebook environments (e.g., Jupyter, Google Colab — delete any cached or downloaded data files);
  • Private code repositories (remove data files from repo history, not only from the working directory);
  • Any intermediate files, derived datasets, or outputs that contain or could reconstruct the original data.
• All data must be deleted within 30 days of Hackathon close. Do not wait until publications or code releases are finalized before deleting the dataset — only the challenge summary preprint and publicly shareable outputs (code, model weights, predictions) may be retained after this deadline.
• All participants must email [team]@synapse.org to confirm data has been deleted from personal compute environments. If you do not confirm, Sage Bionetworks may contact you directly after 30 days.

Presentations & Judging

• Format: each team's submission includes a written report, a GitHub repository (code and workflows, if applicable), and a 3-minute recorded pitch video covering results, methodology, data insights, and proposed solutions.
• Judging panel: a panel of expert judges — including researchers, clinicians, and patient advocates — will review all submissions.
• Timeline: judging takes place over approximately 2–3 months following submission close. Winners are announced at the conclusion of the judging period.
• Format note: presentations are pre-recorded rather than live; there is no live Q&A round in the current design.

Evaluation & Scoring

Track 1 and Track 2 are scored independently, using different methods:

Track 1 — Variant Prediction (automated): scored automatically against the NHS-validated causal variant(s) using rank points and F-max (see the Judging Criteria section of the Overview tab for details). No panel review is involved in this score.

Track 2 — Drug Repositioning (panel-judged): reviewed by the expert judging panel across four weighted criteria:

• Scientific Rigor — 35%
• Patient Impact — 25%
• Innovation — 25%
• Scalability — 15%

A valid submission is completion of either task — Track 1 and Track 2 each accept independent submissions, and teams are welcome to enter one or both. Each submission includes a documented report or CSV (as applicable), a GitHub repository (code/workflows), and a 3-minute recorded pitch video.

Prizes

• Total prize pool: $25,000, sponsored by AWS
• 🥇 1st Place — $12,000
• 🥈 2nd Place — $7,000
• 🥉 3rd Place — $4,000
• 🌟 Innovation / Community Award — $2,000, awarded at judges' discretion to a submission demonstrating exceptional creativity, community impact, or patient-centered design, independent of overall placement

Research Progress & Post-Hackathon Data Handling

• Publications: participants may publish and present on Hackathon results, subject to the embargo policy below.
• Data: all personally identifiable information and raw genomic data must be deleted from participants' systems within 30 days of Hackathon close (see Data Deletion section above). Data hosted on Synapse will be sequestered and inaccessible to external users at that point; the Hugging Face–hosted copy will be removed per the Data Transfer Agreement's deletion policy. Any use of the data beyond the Hackathon's scope requires separate, explicit permission from the donors of the data — this restriction does not lapse over time.
• Results and code: anonymized results — identified variants, statistical analyses, proposed solutions — remain available to the research community via Synapse and/or Hugging Face after the Hackathon ends. Submissions may be rerun by the organizers (Sage Bionetworks, Hugging Face, MVA Society) and are released under a CC-BY license, with participant names shared as part of open-access attribution.
• Leaderboard/landing page visibility: the Hugging Face competition landing page and leaderboard may remain live after close for visibility and recognition, or may be removed by mutual agreement between Sage Bionetworks and Hugging Face.
• Further development: participants are encouraged to continue developing their approaches using publicly available or synthetic datasets — not the original patient data, which must be deleted.

Embargo Policy

• The embargo period begins at Hackathon close and ends upon public posting of the challenge summary report or preprint by the organizing team.
• During the embargo period, participants may not submit manuscripts for peer-reviewed publication that use the challenge dataset.
• Participants are free to publicly share their code, models, and derived outputs (e.g., features, predictions) at any time without restriction.
• Participants may present preliminary findings in conference abstracts, posters, or talks with prior written approval from the organizers.
• Once the challenge summary report or preprint is publicly posted, participants are free to submit independent publications without restriction, provided they follow the Citation and Acknowledgement requirements below.

Submission Reuse & Recontact Consent

• Submission reuse: by registering, participants acknowledge that submissions may be rerun by the Hackathon organizers (Sage Bionetworks, Hugging Face, and the MVA Society). Submissions are subject to a CC-BY license, and your name will be shared as part of the open-access attribution.
• Recontact: by providing your email address and participating, you consent to being recontacted by the Hackathon organizers for purposes related to the Hackathon, including but not limited to follow-up communications, feedback requests, and potential future research opportunities.

Post-Hackathon Information Sharing

• All submitted results will be accessible to the broader research community to foster collaboration and innovation.
• Leading submissions may be prominently featured on Hugging Face, Sage Bionetworks, or Synapse-based websites.
• Follow-up activities such as blog posts, video recaps, and social media highlights may showcase key submissions and behind-the-scenes moments.
• This open-access approach ensures the knowledge generated benefits the broader research community while inspiring future advances in rare disease research.

Citation & Acknowledgement

Any publication, preprint, conference abstract, or public communication arising from participation in this challenge must include the following acknowledgement:

"This work was made possible through the Hackathon, organized by Sage Bionetworks in partnership with the Vall d'Hebron Institute of Oncology (VHIO), the MVA Society, and Hugging Face, with cloud computing support provided by AWS. We are deeply grateful to the patient and family who generously contributed their data and their story to advance research into this ultra-rare disease. We acknowledge their courage and trust in making this challenge possible."

• Data subject privacy: any publication referencing the underlying patient data must not include any information that could re-identify the data subject or their family, beyond what is already publicly available through the family's own blog posts and public communications.
• Dataset citation: the Hackathon dataset must be cited using the reference provided on the challenge Synapse page at the time of publication.