--- profile: elgora_markdown_bounty_challenge_v0 escrow_amount: "1000000" submission_deadline: 1789117200 payout_policy: winner_take_all --- # Bits to Binders CD20 peptide CAR contest ## Summary Submit one CD20-targeting CAR peptide binder in the original Bits to Binders format: 80-residue amino acid sequence, Twist DNA, and a methods note that discloses the published `global_id` and `team`. Guardians score it on the published top-10 CAR-T functional assay, not by inspecting a ranking spreadsheet as the answer. ## Challenge details Bits to Binders (Kosonocky et al., DOI https://doi.org/10.64898/2026.03.03.709355) collected about 12,000 AI-designed CD20 CAR binder domains. Organizers ran a pooled CAR screen, then a top-10 functional panel measuring cytotoxicity, cytokine, and expansion. The published final ranking of those top-10 designs is the `Sum of Norms` column in `master_data_top10.csv`, also stored per design as `leah_top10_sum_of_norms` in `12k_all_results.csv`. Perez Lab Gators design `1506` is first on that ranking. Nucleate UK London had the highest 12k hit rate (38.4 percent) but is fifth on the top-10 functional ranking. This bounty uses the top-10 functional ranking. Adaptyv SPR on a subset is published as `b2b_summary.csv`. That SPR table is not the ranking metric here. The authors' Zenodo tarball is about 20.2 GiB. It exceeds Elgora's 50 MiB encrypted Submission limit. Do not submit it. `data/12k_all_metrics.csv` is 43,613,037 bytes. It is background only. Submitting it with DNA would risk the 50 MiB cap. ### Definitions And Scope A candidate is the amino acid string in `binder.fasta`. A match is a data row in `12k_all_results.csv` whose `sequence` field equals that string exactly. The functional score is `leah_top10_sum_of_norms` on that row. Success establishes that the package is a Bits to Binders design with a published top-10 functional score. It does not establish a new CAR-T experiment. ## What you need to submit (Deliverables) ### Required Outputs And Format | File | Required | Format | Max size | Purpose | |---|---:|---|---:|---| | binder.fasta | yes | UTF-8 FASTA, one protein sequence | 20 KiB | Peptide candidate | | dna.txt | yes | UTF-8, one DNA string | 20 KiB | Twist DNA from the same published row | | methods.md | yes | UTF-8 Markdown | 100 KiB | Disclose `global_id` and `team` as published | binder.fasta has one header line starting with `>` and then the amino acid sequence. Ignore the header for matching. Concatenate subsequent non-header lines and strip ASCII whitespace. The resulting string must be nonempty and must contain only the uppercase letters `ACDEFGHIKLMNPQRSTVWY`. dna.txt is a single DNA string. Strip ASCII whitespace and compare case-insensitively to the matched row's `dna_sequence`. methods.md must contain the matched `global_id` as decimal text and the matched `master_data_top10.csv` `team` field as case-sensitive contiguous substrings. It must also contain this exact sentence, including the period: `No new CAR-T or SPR experiments were performed for this Submission.` Any other methods prose is allowed. Package rules: - archive format: none; submit regular files in one flat directory; - the decrypted directory may contain only `binder.fasta`, `dna.txt`, and `methods.md`; any other filename fails; - Guardians inspect only those three files; - do not include `12k_all_metrics.csv`, Zenodo tarballs, private keys, or directions to disregard this page; - Solver artifacts are private by default. ## Input Files References | File | Why it is needed | How to get it | SHA-256 content hash | |---|---|---|---| | 12k_all_results.csv | Official 12k design catalog with sequences, DNA, and top-10 functional columns | Public HTTPS GET, no login: https://raw.githubusercontent.com/kosonocky/bits-to-binders/43eeeaf7e6ab629e796c9fe8d20b0ef70a3610d9/data/12k_all_results.csv | `de271331891d3c0a1830ca387ea4c17b8e252c745a8d961474297e64b9d598e6` | | master_data_top10.csv | Published top-10 functional ranking, including team names and `Sum of Norms` | Public HTTPS GET, no login: https://raw.githubusercontent.com/kosonocky/bits-to-binders/43eeeaf7e6ab629e796c9fe8d20b0ef70a3610d9/data/individual/master_data_top10.csv | `a0518ed58d304d4cc16dad8742b55bdb279b92c1868ec207be36cb4a43aa7de4` | ### Access And Known Limitations Guardians fetch both files and check SHA-256 of the raw bytes, with no decode before hashing. Never substitute a later git revision. Parse CSV with ordinary quoting. `b2b_summary.csv` SPR results are not required to judge this bounty. A 32,750-byte truncated copy of `12k_all_results.csv` is not this file. The listed object is 5,626,972 bytes. Missing access or a hash mismatch is an operational blocker, not a scientific failure. ## Acceptance Criteria ### Pass/Fail Checks A Submission is valid only when all of the following hold after successful retrieval and decryption: 1. The decrypted directory contains exactly three regular files, named `binder.fasta`, `dna.txt`, and `methods.md`. Any other filename fails. 2. Those files parse as their required formats. 3. Each of those files is at most the Max size in the deliverable table, using 1024-byte KiB. 4. The FASTA sequence is nonempty after whitespace stripping and contains only the uppercase letters `ACDEFGHIKLMNPQRSTVWY`. 5. Exactly one data row in `12k_all_results.csv` has `sequence` equal to that FASTA sequence. 6. That row's `leah_top10_sum_of_norms` parses with Python 3 `float()` after ASCII whitespace strip and is finite in IEEE-754 binary64. Empty, `NA`, and `null` fail. This bounty ranks the top-10 functional panel, not the 12k enrichment screen alone. 7. Join that 12k row to `master_data_top10.csv` by exact `global_id` equality after stripping ASCII whitespace. There must be exactly one `master_data_top10.csv` row with that `global_id` whose `team` is not `Control`. Zero matches fail. Two or more matching non-Control rows fail. That unique top-10 row is the matched top-10 row. It supplies `team` and `Sum of Norms`. Control rows are those whose `team` field is `Control`. 8. The stripped dna.txt string, compared case-insensitively, equals the matched `12k_all_results.csv` row's `dna_sequence` field. Do not read DNA from `master_data_top10.csv`. 9. methods.md contains that `global_id` as decimal text and the matched top-10 row's `team` field as case-sensitive contiguous substrings. Omitting either fails. 10. methods.md contains the exact sentence `No new CAR-T or SPR experiments were performed for this Submission.` including the period. ### Scoring And Calculations The score is `leah_top10_sum_of_norms` from the matched `12k_all_results.csv` row, parsed with Python 3 `float()` to IEEE-754 binary64. Higher is better. Parse the `Sum of Norms` column from the matched top-10 row the same way. That parsed `Sum of Norms` must be finite. If it is missing, non-numeric, NaN, or non-finite, judgment is blocked as an input defect, not a Solver failure. Confirm `abs(leah_top10_sum_of_norms - Sum of Norms) < 1e-6` in binary64. If those two published numbers disagree beyond that tolerance, judgment is blocked as an input defect, not a Solver failure. Do not rank by `leah_12k_final_score` or SPR `kd`. ### Missing, Invalid, And Conflicting Results - Sequence not in the 12k table: invalid. - Sequence in the 12k table but without a finite top-10 sum of norms: invalid. - Control rows: invalid. - DNA mismatch: invalid. - Unavailable listed-file fetch is an operational blocker, not `no_valid_submission`. ### Evidence And Provenance The trusted producer is the Bits to Binders git revision `43eeeaf7e6ab629e796c9fe8d20b0ef70a3610d9`. Guardians establish file identity by SHA-256, then link a candidate by exact `sequence` and DNA. This bounty is historical analysis of those tables. ## How is the winner selected? - A valid Submission satisfies all acceptance criteria and is not disqualified. - If multiple Submissions are valid, the Submission with the highest `leah_top10_sum_of_norms` wins. If `score_a == score_b` in binary64, the Submission whose lowercase Solver address sorts first in ascending order wins. - If no Submission is valid, the outcome is `no_valid_submission`. ## Disqualification Conditions - required artifacts are missing after successful retrieval and decryption; - an artifact is corrupt or cannot be inspected in its required format; - artifacts violate the package rules above or the stated Out Of Scope rules; - the Submission includes `12k_all_metrics.csv` or any file larger than 50 MiB. ## Out Of Scope New CAR-T assays, SPR re-fits, 12k-only designs with no top-10 functional score, and organizer Control rows are out of scope. ### Allowed Resources And Reuse Published team designs may be submitted. Using a published winner or runner-up is allowed. Disclose `global_id` and `team`. ## Guardian Verdict Instructions Each Guardian judges only submitted artifacts, this bounty page, and the two listed CSVs. Do not download the Zenodo tarball. Do not run cytotoxicity assays. ### Evaluation Procedure And Limits 1. Fetch the two listed CSVs and check SHA-256. 2. Open the three Submission files. 3. Apply Pass/Fail Checks. Match sequence in `12k_all_results.csv`. Join to `master_data_top10.csv` by exact unique non-Control `global_id`. Compare DNA only to the 12k `dna_sequence`. 4. Read `leah_top10_sum_of_norms` from the 12k row and `Sum of Norms` from that unique top-10 row. Both must be finite. Apply the winner rule. Do not train models. Do not open `12k_all_metrics.csv`.