| --- |
| license: apache-2.0 |
| language: |
| - en |
| tags: |
| - genomics |
| - tool-calling |
| - function-calling |
| - qwen |
| - mlx |
| pretty_name: CodeXomics-ToolCalling-v1 (V5 training data) |
| --- |
| |
| # CodeXomics-ToolCalling-v1 |
|
|
| This dataset contains the supervised tool-calling trajectories used to fine-tune |
| **CodeXomics-ToolAgent-4B-v1** (internally `qwen3.5:4b-codexomics-tools-v5`) for the CodeXomics |
| genomics workbench (an AI-native genome browser; source: |
| [github.com/Scilence2022/CodeXomics](https://github.com/Scilence2022/CodeXomics)). It is released |
| as the reproducibility artifact for the corresponding paper section and is licensed under |
| Apache-2.0. |
|
|
| ## Contents |
|
|
| - `train.jsonl` — 373 supervised examples |
| - `valid.jsonl` — 123 validation examples |
| - `test.jsonl` — 30 holdout examples |
| - `manifest.json` — dataset schema, eligibility metadata, registry hash, and leakage-control record |
| - `token-stats.json` — render-length statistics per split (3,072-token budget) |
|
|
| Each line is an MLX-LM tool-calling example: a system prompt, a user instruction, and assistant |
| `tool_calls` in the OpenAI function-calling shape. Multi-step examples include the returned tool |
| results and use the cross-round reference syntax `{tool_name.path}`. |
|
|
| ## Composition |
|
|
| | Split | Single-call | Multi-step | Variants | Synthetic chains | Total | |
| | --- | ---: | ---: | ---: | ---: | ---: | |
| | Train | 85 | 18 | 10 | 260 | 373 | |
| | Validation | 66 | 8 | 4 | 45 | 123 | |
| | Test | 21 | 8 | 1 | 0 | 30 | |
|
|
| Source trajectories (678 records) were admitted only after passing: (1) strong-model semantic |
| replay (DeepSeek V4 Flash), (2) fixture executability, (3) state verification for stateful |
| records, and (4) benchmark leakage control. All 172 CodeXomics Benchmark tests are fingerprinted |
| and excluded (`benchmark_scope.use: leakage-gate-only`). |
|
|
| ## Training schema |
|
|
| Six candidate tool schemas per request (gold tool always included), function descriptions truncated |
| to 160 characters, parameter defaults preserved, semantically hard distractors, and a |
| deterministic-randomized gold position. |
|
|
| ## Usage |
|
|
| ```bash |
| huggingface-cli download <this-dataset> --local-dir codexomics-v5-data |
| ``` |
|
|
| ## Citation |
|
|
| ```bibtex |
| @software{codexomics-toolagent-v1, |
| title = {CodeXomics-ToolCalling-v1}, |
| author = {Song, Lifu}, |
| year = {2026}, |
| license = {Apache-2.0}, |
| publisher = {Hugging Face} |
| } |
| ``` |
|
|
