---
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}
}
```