ESMC

How SubSeq Runs It

• Jobs run /ref/bin/esmc_subseq.py with the ESM runtime.
• Model assets are managed by SubSeq.
• Network access is disabled for jobs, and output is forced to /outputs.

Input

Use typed protein sequence text, one FASTA file, or a folder of FASTA files. Inputs should be unaligned protein sequences using amino-acid letters.

>example
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

Example Arguments

Embedding

embed
--sequence=MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
--name=example
--pool=mean
--batch-size=1

Embedding a Folder

embed
--input-dir=/inputs/fastas
--recursive
--pool=both
--batch-size=1

Scoring

score
--fasta=/inputs/sequences.fasta
--batch-size=1
--max-score-length=1024

Raw API Submit

curl -X POST https://subseq.bio/api/v1/job/submit \
  -H "Authorization: Bearer sk-ss-admin-123" \
  -F program=esmc \
  -F args=embed \
  -F args=--sequence=MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG \
  -F args=--name=example \
  -F args=--pool=mean \
  -F args=--batch-size=1

Arguments

Modes

• embed: extract mean and/or per-token embeddings.
• score: compute masked-token pseudo-likelihood scores.

Input

• --sequence=<protein>: one typed protein sequence.
• --name=<label>: output label for typed sequence input.
• --fasta=/inputs/example.fasta: one FASTA file.
• --input-dir=/inputs/fastas: folder of FASTA files.
• --recursive: search subfolders when using a FASTA folder.

Embeddings

• --pool=mean|tokens|both: write one vector per sequence, per-token vectors, or both. Default: mean.
• --batch-size=<int>: embedding batch size. Default: 1.

Scoring

• --batch-size=<int>: masked-position scoring batch size. Default: 1.
• --max-score-length=<int>: maximum token count for pseudo-likelihood scoring. Default: 1024.

Outputs

• Embeddings: /outputs/embeddings_manifest.json and one or more .npy arrays.
• Scoring: /outputs/scores.tsv, /outputs/scores.json, and per-sequence masked-token detail TSVs.

Submit

Queue a run from New Job -> ESMC.