CRONOS: A Multimodal Sequential Clinical Decision-Making Benchmark in Oncology

CRONOS is a benchmark designed to evaluate the reasoning capabilities of multimodal large language models (LLMs) in complex clinical decision-making scenarios. It focuses on two core challenges in oncology: multimodal integration (e.g., pathology, genomics, radiology) and longitudinal reasoning across patient timelines. The benchmark includes agentic tasks requiring interaction with external foundation model-based tools and datasets.

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🛠 Getting Started

To install all required dependencies, simply run:

bash setup.sh

Note: If you want to evaluate the agent on IHC data, you will need to additionally clone and install TRIDENT from source.

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⚙️ Configuration

Before running the benchmark, configure your paths and credentials in:

neurips25/configs/base.yaml

The config file specifies paths to datasets, tool credentials, and output directories. Below, we provide guidance for acquiring the necessary external datasets.

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📁 Datasets

HANCOCK (Multimodal Tissue Microarrays)

The HANCOCK dataset contains SVS-format tissue micro arrays (TMAs). To prepare it:

1. Follow the original HANCOCK GitHub repository to extract tiles and compute cell densities using QuPath.
2. Reproduce our ABMIL training by extracting tumor centers and cell density measurements for Blocks 1 and 2.
3. Download the dataset files from the HANCOCK project page to replicate the question curation used in the benchmark.

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MSK-CHORD (Longitudinal Genomic Profiles)

The MSK-CHORD dataset is available on cBioPortal. To use it:

• Download the ZIP archive from the cBioPortal page.
• Extract it and update the dataset path in base.yaml.

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DrugBank API

To enable the DrugBank tool for longitudinal drug lookups:

1. Register for a DrugBank account.
2. Apply for a license to access their API.
3. Download and locally host the dataset following their documentation.
4. Update your API path and credentials in the config file.

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📑 Agent Logs

We provide full logs of agent interactions for all models evaluated in the paper:

• agent_logs_hancock/: Multimodal evaluation logs (HANCOCK)
• agent_logs_msk/: Longitudinal evaluation logs (MSK-CHORD)

Each log includes all agent–LLM conversations, intermediate reasoning steps, and generated answers.

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▶️ Running the Benchmark

Make sure you have:

• Installed dependencies
• Configured Hugging Face access tokens (for model download)
• Set paths in base.yaml

To run an evaluation with Qwen/Qwen2.5-VL-7B-Instruct on the HANCOCK dataset:

python -m neurips25.benchmarks.run_agent_benchmark \
  --doctor_model "Qwen/Qwen2.5-VL-7B-Instruct" \
  --output_dir "./agent_logs_hancock/" \
  --dataset "hancock"

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