TCDD: Tool-Calling Dataset for Drug Discovery

TCDD is the domain-specific tool-calling dataset introduced with DrugPilot, an LLM-based parameterized reasoning agent for drug discovery. It contains ShareGPT-style traces in which an assistant interprets a drug-discovery request, selects a tool, supplies its arguments, observes the tool output, and produces a final response. Some traces also demonstrate multi-turn use of the Parameterized Memory Pool (PMP).

The dataset is intended to support supervised fine-tuning and evaluation of three capabilities:

1. selecting an appropriate drug-discovery tool from a natural-language request;
2. extracting domain-specific parameters such as SMILES, protein sequences, cell lines, and property names; and
3. reading from and writing results to DrugPilot's Parameterized Memory Pool.

• Paper: DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery
• Code: wzn99/DrugPilot
• Data file: tool_calling_memory_pool.json

Dataset Viewer and repository statistics

The YAML configuration above explicitly exposes the complete JSON file in the Hugging Face Dataset Viewer as the default configuration and train split. The Viewer is paginated; all records remain available through the page controls or the datasets library.

Statistics below were computed from the file currently published in this repository:

Item	Value
Records	3,098
Conversation messages	17,402
File size	11,643,767 bytes
Columns	conversations, system, tools
Conversation length	4–8 messages
Four-message records	1,843
Six-message records	5
Eight-message records	1,250

The DrugPilot paper describes the benchmark as 2,800 annotated samples, including 2,500 training samples and 300 testing samples. The single artifact currently hosted here contains 3,098 records and does not encode the paper's original train/test membership. For that reason, Hugging Face exposes the full file as one train split; users reproducing the paper should obtain or reconstruct the intended split before comparing benchmark results.

Dataset structure

Each top-level item has three fields:

Field	Type	Description
conversations	list of objects	Ordered dialogue messages. Every message has string fields from and value.
system	string	System instruction that defines the expected tool-calling behavior and output format.
tools	string	A JSON-serialized list of available tool definitions, including names, descriptions, parameters, and required fields.

The from field uses these role labels:

• human: the user's natural-language request;
• function_call: the selected function and arguments, represented as a JSON-like string;
• observation: the tool result and a snapshot of the PMP keys;
• gpt: the assistant's natural-language answer.

An abbreviated record looks like this:

{
  "conversations": [
    {
      "from": "human",
      "value": "Determine the thermodynamic free energy ... MemoryPool(arguments=dict_keys([]))"
    },
    {
      "from": "function_call",
      "value": "{\"name\": \"drug_property_prediction\", \"arguments\": {...}}"
    },
    {
      "from": "observation",
      "value": "{\"task\": ..., \"result\": ...} MemoryPool(arguments=dict_keys([...]))"
    },
    {
      "from": "gpt",
      "value": "The free energy of dissolution ..."
    }
  ],
  "system": "You are a function calling AI model ...",
  "tools": "[{\"name\": \"drug_property_prediction\", ...}]"
}

Tool labels in the published artifact

The paper organizes TCDD around eight representative drug-discovery task families. The current JSON contains the following nine distinct callable labels. Counts refer to function-call messages, not top-level records; multi-turn records can contain more than one call.

Function label	Calls
drug_property_prediction	841
drug_target_affinity_regression_predict	689
drug_cell_response_regression_predict	621
drug_target_classification_predict	503
drug_cell_response_regression_optimization	490
drug_cell_response_regression_generation	449
Retrosynthetic_reaction_pathway_prediction	430
drug_drug_response_predict	290
drug_target_affinity_classification_predict	40

Data creation

According to the paper, TCDD simulates realistic user–assistant interactions across single-turn dialogue, multi-turn workflows, parameter-error correction, and memory-pool updates. The authors varied user-query wording and molecular inputs, and included complete instructions as well as cases with missing or misspelled parameters. The paper describes approximately 50% single-turn samples, 30% multi-turn samples, and 20% parameter-error scenarios in the original benchmark design.

The task content draws on drug-discovery resources listed in the paper, including BACE, BBBP, ESOL, FreeSolv, LIPO, GDSCv2, DAVIS, KIBA, BindingDB, DrugBank, TWOSIDES, ZINC, QM9, and USPTO. See the paper and the source datasets for collection details and original terms.

Loading the data

Install the Hugging Face datasets library and load the repository directly:

from datasets import load_dataset

dataset = load_dataset("lik98/TCDD")
train = dataset["train"]

print(train)
print(train[0]["conversations"])

To parse the serialized tool schema for a record:

import json

tool_schema = json.loads(train[0]["tools"])
print(tool_schema[0]["name"])

The original file can also be downloaded without converting it:

from huggingface_hub import hf_hub_download

path = hf_hub_download(
    repo_id="lik98/TCDD",
    filename="tool_calling_memory_pool.json",
    repo_type="dataset",
)

Intended uses

TCDD may be useful for:

• supervised fine-tuning of tool- or function-calling language models;
• evaluating tool selection, argument extraction, and multi-turn tool use;
• studying structured memory for scientific agents; and
• prototyping drug-discovery assistants that connect language models to specialist tools.

When using TCDD as a benchmark, define and publish the exact split, preprocessing rules, prompt template, and parsing policy used in the experiment.

Limitations and responsible use

• The data is intended for research and engineering, not clinical diagnosis, treatment selection, laboratory safety decisions, or unsupervised real-world drug development.
• Tool observations and assistant responses should not be assumed to be experimentally validated. Molecular strings, protein sequences, numerical outputs, and generated text should be checked with appropriate domain tools and expert review.
• tools is a serialized JSON string rather than a nested column. Most function_call values are also JSON strings, but some contain unescaped backslashes in SMILES notation and are not valid strict JSON. Use a validation or normalization step before calling json.loads on every function-call value.
• The published artifact has no explicit train/validation/test field and its row count differs from the benchmark size reported in the paper. Avoid accidental train–test leakage when creating a new split.
• Source databases may have their own licenses, access conditions, biases, and coverage limitations. Users should review those terms for their intended use.
• Drug-discovery datasets can overrepresent well-studied molecules, targets, cell lines, and assay conditions. Performance on these traces does not establish generalization to novel chemistry or experimental settings.

License

This repository is released under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license (CC BY-NC-SA 4.0). Users are responsible for confirming that their use also complies with the terms of the underlying source datasets.

Citation

If you use TCDD or DrugPilot, please cite:

@article{li2025drugpilot,
  title   = {DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery},
  author  = {Li, Kun and Wu, Zhennan and Wang, Shoupeng and Wu, Jia and Pan, Shirui and Hu, Wenbin},
  journal = {arXiv preprint arXiv:2505.13940},
  year    = {2025},
  doi     = {10.48550/arXiv.2505.13940},
  url     = {https://arxiv.org/abs/2505.13940}
}

Related resources

• DrugPilot repository: https://github.com/wzn99/DrugPilot
• Paper: https://arxiv.org/abs/2505.13940
• Dataset repository: https://huggingface.co/datasets/lik98/TCDD