kermt-finetune

name	kermt-finetune
description	Finetune a pretrained KERMT encoder on a labeled CSV. The skill validates the input checkpoint (must be a pretrain ckpt — grover_base / cmim / hybrid), validates the labeled CSV, prepares the data (clean + features + optional split), then launches main.py finetune inside the kermt container (detached for hours-scale runs). Hyperparameters come from agent/config/defaults_finetune.json with per-flag CLI override.
license	Apache-2.0 OR CC-BY-4.0
compatibility	Requires docker, nvidia-container-toolkit, and a CUDA-capable NVIDIA GPU. Designed for Claude Code, Codex, and Nemotron.
metadata	{"classification":"workflow-skill","risk_tier":"skill"}

kermt-finetune

Finetune a pretrained KERMT encoder on a user-supplied labeled CSV. The skill is the workflow orchestrator: validate ckpt, validate data, prepare data, launch the runner detached, return a run directory + container name.

Hardware requirements

• GPUs: 1 (single-GPU). Finetune does not DDP; if you have multiple GPUs visible, pass --gpus 0 (or whichever id) to select one. Multi-GPU finetune is not currently supported.
• VRAM: ≥ 8 GB for the default batch_size 32 configuration. Lower VRAM works at smaller batch sizes — pass --batch-size N to override.
• Disk: a few GB per run (checkpoint + features + logs).
• Driver / CUDA: any host supporting CUDA 12.6 (the kermt image base). kermt-setup validates this up-front.

Inputs

Required:

• --ckpt <path> — input pretrain checkpoint (grover_base / cmim / hybrid). The validator refuses already-finetuned ckpts with a redirect to kermt-infer.
• --csv <path> — labeled CSV. First column is smiles; every other column is a target.

Optional:

• --dataset-type {regression | classification | multiclass} — default regression (from defaults_finetune.json). Drives loss, metric defaults, and head initialization. For classification tasks pass --dataset-type classification.

• --targets COL [COL ...] — explicit target column names. If omitted, the validator auto-detects numeric non-smiles columns and the skill confirms with the user before proceeding.

• --val-csv <path> and --test-csv <path> — user-provided val + test splits. Either pass both or pass neither (the skill auto-splits using the configured --split-type).

• --split-type {random | scaffold_balanced | index_predetermined} — default scaffold_balanced from defaults_finetune.json.

  • random and scaffold_balanced: build the val/test split internally from the train CSV. No --val-csv / --test-csv needed.
  • index_predetermined: requires pre-split CSVs passed via --val-csv + --test-csv (and, separately, per-fold index files — see kermt/util/utils.split_data). Use this when the dataset ships its own canonical split (e.g. tests/data/Biogen_for_grover/scaffold/ balance/<endpoint>/{train,val,test}.csv).

• --metric NAME — mae (regression default), auc (classification default), or any name kermt.util.metrics.get_metric_func accepts.

• --epochs N / --batch-size N / --init-lr F / --max-lr F / --final-lr F / --warmup-epochs F / --weight-decay F / --dropout F / --bond-drop-rate F / --dist-coff F / --early-stop-epoch N / --seed N — training-hyperparameter overrides. Anything not given is filled from agent/config/defaults_finetune.json.

• --ffn-hidden-size N / --ffn-num-layers N — shared FFN trunk dims.

• --ffn-num-task-specific-layers N / --ffn-task-specific-hidden-size H — per-target FFN heads (default 0 = off; useful for heterogeneous multi-target finetunes). Both must be set together when N > 0.

• --ensemble-size N / --num-folds N — multi-model / k-fold CV. Default 1 each.

• --gpus 0 — single GPU id (default 0). Passing more than one is rejected.

• --from-prepare <dir> — skip the prepare step and reuse an existing prepare_data.json in <dir>. Useful when iterating on hyperparameters.

Workflow

Let $KERMT_REPO be the path to your kermt repo checkout, and assume kermt-setup has built kermt:latest. All paths below are on the host; the helper bind-mounts them at known container paths.

1. Pre-flight: ensure container + system probe.

   $KERMT_REPO/agent/scripts/kermt_container.sh check_system | python -c "
   import json, sys; d = json.load(sys.stdin)
   if not d['ok']:
       print('System check failed:', d['gaps']); sys.exit(1)
   print(f'OK: {len(d[\"gpus\"])} GPU(s); CUDA via container toolkit')
   "
   

   Refuse to proceed if ok: false.

2. Compute run directory.

   RUN_DIR=$KERMT_REPO/runs/finetune_$(date -u +%Y-%m-%dT%H-%M-%SZ)
   

3. Validate the checkpoint.

   $KERMT_REPO/agent/scripts/kermt_container.sh run --ckpt <user-ckpt> -- \
       "python agent/scripts/check_checkpoint.py --mode finetune_init --ckpt /ckpt"
   

   Parse the JSON. Abort on ok: false. The validator rejects already- finetuned ckpts (has_task_ffn: true) with a redirect to kermt-infer.

4. Validate the data.

   $KERMT_REPO/agent/scripts/kermt_container.sh run --data <user-csv> -- \
       "python agent/scripts/check_data.py --mode finetune --csv /data/<basename> [--targets COL1 COL2 ...]"
   

   If --targets was not given by the user, surface auto_detected_targets from the JSON and ask the user to confirm before continuing. Abort on ok: false.

5. Prepare the data (skip if --from-prepare given).

   Pre-flight: check for sibling val.csv / test.csv. Before invoking prepare_data, inspect the parent directory of <user-csv>. If a canonical-looking sibling val.csv (or val_*.csv — common variants include val_T.csv, val_clean.csv) AND a matching test.csv / test_*.csv exist next to the train CSV, the dataset ships its own pre-defined split. In that case set --split-type index_predetermined AND pass --val-csv / --test-csv — otherwise the configured split_type (default scaffold_balanced) will re-split the train CSV from scratch and silently discard the user's val/test files. When in doubt — or when the sibling files use non-canonical suffixes (_T, _v2, etc.) — surface the situation to the user and ask which they want.

   Quoting target names. If any of the --targets column names contain shell metacharacters (>, &, |, (, ), $, etc.), single-quote each one when passing on the CLI to keep the shell from eating part of the name. Example: --targets 'Log_Caco2_Papp_A>B' 'logD'. The CSV header itself is read directly by the downstream trainer and is unaffected, but the prepare_data.json manifest's targets[] field captures whatever the shell delivers — unquoted metacharacters get truncated there.

   Mount note: kermt_container.sh --data <host-csv> mounts the parent directory of <host-csv> at /data. --val-csv and --test-csv must therefore reference files in that same parent directory. If val/test live in a separate directory (e.g. a sibling splits/ folder), mount the parent of all three using --data <dir> on a directory rather than a file.

   $KERMT_REPO/agent/scripts/kermt_container.sh run --data <user-csv> --run-dir $RUN_DIR -- \
       "python agent/scripts/prepare_data.py --mode finetune \\
            --csv /data/<basename> --out /runs/data \\
            --split-type <split_type> \\
            [--val-csv /data/<val-basename> --test-csv /data/<test-basename>] \\
            [--val-frac 0.1 --test-frac 0.1 --seed 0] \\
            --targets <COL1> [COL2 ...]"
   

   Outputs land at $RUN_DIR/data/prepare_data.json. For scaffold_balanced and index_predetermined, prep emits a single clean_full_csv + .npz; the runner passes them through to main.py finetune which calls split_data internally with the user-supplied seed.

6. Estimate runtime + echo applied defaults.

   • Finetune wall time is typically minutes-to-hours on 1 GPU.
   • Surface a summary of every flag that was filled from the defaults vs user-supplied, so the user knows what was assumed. The runner records this in args_applied.
   • Sample message: "Filling from defaults_finetune.json: epochs=30, batch_size=32, split_type=scaffold_balanced. Override any of these with --<flag>."

7. Targets confirmation gate (hard requirement). Before launching the runner, regardless of how the targets list was determined (CLI --targets, auto-detection in step 4, or a user natural-language request like "finetune on Caco2 and HLM"), echo the final targets list to the user with an explicit count: "Will finetune on N target(s): COL1, COL2, ...". If the user's request specified a subset that doesn't match this list (e.g., they asked for 2 tasks via natural language but the list still has 4), treat it as a discrepancy and re-prompt with the diff — never silently proceed on the wrong target set. Wait for explicit confirmation before launching unless --yes was given.

8. Launch the runner detached. (Consistent with the pretrain skills.)

   $KERMT_REPO/agent/scripts/kermt_container.sh run_detached \\
       --name kermt-finetune-<ts> \\
       --ckpt <user-ckpt> --run-dir $RUN_DIR -- \\
       "python agent/scripts/run_finetune_local.py \\
            --ckpt /ckpt \\
            --prepare-manifest /runs/data/prepare_data.json \\
            --dataset-type <type> \\
            --out /runs \\
            [--gpus 0] \\
            [--epochs N --batch-size N --init-lr F ...] \\
            [--ffn-num-task-specific-layers N --ffn-task-specific-hidden-size H]"
   

   Returns the container name + id + log file path.

9. Report to the user. Output a short summary:

   • Container name + id
   • $RUN_DIR/run.json (manifest with cmd_replay + image digest)
   • Log file: $RUN_DIR/logs/finetune.log
   • TensorBoard: $RUN_DIR/logs/tb (open with tensorboard --logdir $RUN_DIR/logs/tb)
   • Final checkpoints land at $RUN_DIR/ckpt/fold_0/model_0/model.pt (best-val) and last_checkpoint.pt (sibling, auto-resume target). Held-out test predictions + metrics land at $RUN_DIR/ckpt/fold_0/test_result.csv. Paths vary with --num-folds / --ensemble-size.
   • To follow progress: kermt-monitor <RUN_DIR> (one-shot) or docker logs -f <container-name> (streaming).
   • To block until the run finishes (useful for short test runs): docker wait <container-name> — prints the exit code on completion.

Hard rules

• Never modify the user's input ckpt. The runner passes its path via --checkpoint_path; task/train.py loads it read-only into the model and attaches a new FFN head. The source file stays untouched.
• Arch comes from the ckpt, not from CLI/defaults. The runner extracts hidden_size, depth, num_attn_head, activation, embedding_output_type, self_attention (+ attn_hidden / attn_out when applicable) from the ckpt's saved_args. There is no --hidden-size flag on this runner.
• Never block on the long-running finetune. The skill launches via run_detached and returns immediately after step 9. Use kermt-monitor.
• Echo applied defaults back to the user. The args_applied field of run.json records every flag's value + source (user / default-config). Surface a one-line summary of every filled-from-default flag so the user knows what was assumed.

Common errors

• finetune_init requires a pretrain ckpt (grover_base / cmim / hybrid) → the ckpt you passed is already finetuned (has task FFN heads). Pick a pretrain ckpt instead, or use kermt-infer if you want to run predictions with the existing finetuned model. To resume a finetune on the SAME dataset, bypass the skill and call python main.py finetune --checkpoint_path <ckpt> ... directly — the agent skill doesn't support resume because saved-task identity can't be machine-verified against the new training data.
• prepare_data manifest reports ok=False → check errors for the failed step (typically clean_smiles or save_features). Fix and re-run.
• ffn_num_task_specific_layers=N>0 but ffn_task_specific_hidden_size is unset → MTL heads need an explicit hidden size. Pass --ffn-task-specific-hidden-size H.
• finetune is single-GPU → multi-GPU finetune is not currently supported; pick a single id.

Replayability

The run.json cmd_replay field is a single-line command that re-runs the finetune with the same inputs, hyperparameters, and arch. To replay inside the kermt container:

$(jq -r .cmd_replay $RUN_DIR/run.json)

If ok_to_replay: false in the manifest (because the kermt repo working tree was dirty at launch time), the replay may not be bit-exact — pin the exact commit via the repo.commit field and git checkout it first.