README.md

---
license: other
pretty_name: SciModelingBench Design-Bench Data
tags:
- benchmark
- scientific-machine-learning
- black-box-optimization
- agent
configs:
- config_name: tfbind8
  data_files:
  - split: six6_ref_r1
    path: data/tfbind8/six6_ref_r1.parquet
- config_name: cell_dag_nas
  data_files:
  - split: architectures
    path: data/cell_dag_nas/architectures.parquet
- config_name: hopper_controller
  data_files:
  - split: policies
    path: data/hopper_controller/policies.parquet
- config_name: superconductor
  data_files:
  - split: composition_groups
    path: data/superconductor/composition_groups.parquet
- config_name: tfbind10_pho4
  data_files:
  - split: observations
    path: data/tfbind10_pho4/observations.parquet
- config_name: utr_mrl_egfp_unmodified
  data_files:
  - split: measurements
    path: data/utr_mrl_egfp_unmodified/measurements.parquet
- config_name: gfp
  data_files:
  - split: protein_genotypes
    path: data/gfp/protein_genotypes.parquet
- config_name: drugmatrix_clinical_pathology
  data_files:
  - split: observations
    path: data/drugmatrix_clinical_pathology/observations.parquet
---

<p align="center">
  <img
    src="https://raw.githubusercontent.com/xukp20/sci-modeling-bench/main/assets/sci-modeling-bench-logo.png"
    alt="SciModelingBench logo"
    width="135"
  >
</p>

<h1 align="center">SciModelingBench Design-Bench Data</h1>

<p align="center">
  <strong>Canonical, provenance-tracked observations for scientific modeling and design Tasks.</strong>
</p>

<p align="center">
  <a href="https://github.com/xukp20/sci-modeling-bench">GitHub</a>
  &nbsp;&middot;&nbsp;
  <a href="https://pypi.org/project/sci-modeling-bench/">Python Package</a>
  &nbsp;&middot;&nbsp;
  <a href="https://github.com/xukp20/sci-modeling-bench/tree/main/docs">Documentation</a>
  &nbsp;&middot;&nbsp;
  <a href="https://huggingface.co/sci-modeling-bench">Organization</a>
</p>

This repository stores the scientific observation layer used by the
SciModelingBench Design-Bench suite. The Python package supplies validators,
Agent-visible Protocols, trusted Objectives, submission contracts, and Task
metrics. Data and evaluation logic are versioned separately so experiments can
pin both.

## Quick Start

Load one canonical table with Hugging Face Datasets:

```python
from datasets import load_dataset

observations = load_dataset(
    "sci-modeling-bench/design-bench",
    name="drugmatrix_clinical_pathology",
    split="observations",
)
```

Or construct an end-to-end benchmark Task from the current package release:

```python
from sci_modeling_bench.suites.design_bench import TFBind8BlackBoxOptimizationTask

task = TFBind8BlackBoxOptimizationTask.from_hub()
agent_input = task.build_input()
```

For reproducible work, pass an immutable Hub commit through the suite's
`revision=` argument rather than relying on the current default branch.

## Available Configs

| Config | Scientific object | Canonical rows | Evaluation setting |
|---|---|---:|---|
| `tfbind8` | Complete SIX6 DNA 8-mer binding landscape | 65,536 | Exact lookup; free-form black-box optimization |
| `tfbind10_pho4` | Pho4 BET-seq raw count observations | 4,160,533 | Replicate-count posterior; black-box optimization |
| `utr_mrl_egfp_unmodified` | Synthetic 50-nt 5' UTRs | 318,468 | Measured MRL; compositional pool ranking |
| `gfp` | Sarkisyan GFP protein genotypes | 51,715 | Measured median brightness; pool ranking |
| `superconductor` | Normalized elemental compositions | 15,164 | Measured group-median critical temperature; pool ranking |
| `drugmatrix_clinical_pathology` | Individual-animal rat toxicology observations | 10,605 | Matched-control measured endpoints; pool ranking |
| `cell_dag_nas` | Canonical NASBench-101 cell DAGs | 423,624 | Official repeated NAS records; black-box optimization |
| `hopper_controller` | Structured PPO policy checkpoints | 3,200 | 500 frozen Hopper-v5 rollouts per policy; pool ranking |

Canonical rows are not always the final candidate-pool size. Protocols derive
Agent-visible observations and label-hidden candidates from the pinned table
without persisting candidate ranks or evaluator-only labels.

## Trust Model

SciModelingBench does not use one evaluator type for every scientific domain:

- **Exact:** complete tabulated or analytic mappings, such as TFBind8.
- **Measured:** retained experimental observations or repeated simulator
  outcomes, such as GFP, Superconductor, DrugMatrix, and Hopper Controller.
- **Posterior-derived:** deterministic aggregation grounded in raw replicate
  counts, such as TFBind10 Pho4.
- **Legacy learned surrogate:** documented when relevant, but not silently
  treated as experimental truth when more reliable source measurements exist.

An Objective can be exact with respect to a frozen aggregation rule while the
underlying scientific measurement remains noisy. Each config's documentation
states that distinction explicitly.

## Repository Layout

```text
README.md
scimodelingbench.json
data/<config>/<split>.parquet
manifests/<config>.json
provenance/<config>/*.json
```

- `scimodelingbench.json` maps config names to strict semantic manifests.
- `manifests/` defines inputs, targets, context, units, constraints, splits,
  sources, citations, versions, and license identity.
- `provenance/` records source hashes, transformations, release statistics,
  artifact hashes, and setting-specific audits.
- `data/` contains only canonical benchmark tables, not Python code or model
  checkpoints used by the package.

## Documentation And Provenance

| Config | Task documentation | Machine-readable provenance |
|---|---|---|
| `tfbind8` | [TFBind8](https://github.com/xukp20/sci-modeling-bench/blob/main/docs/suites/design-bench/tfbind8.md) | [`six6_ref_r1.json`](provenance/tfbind8/six6_ref_r1.json) |
| `tfbind10_pho4` | [TFBind10 Pho4](https://github.com/xukp20/sci-modeling-bench/blob/main/docs/suites/design-bench/tfbind10-pho4.md) | [`observations.json`](provenance/tfbind10_pho4/observations.json) |
| `utr_mrl_egfp_unmodified` | Not yet published | [`measurements.json`](provenance/utr_mrl_egfp_unmodified/measurements.json) |
| `gfp` | Not yet published | [`protein_genotypes.json`](provenance/gfp/protein_genotypes.json) |
| `superconductor` | [Superconductor](https://github.com/xukp20/sci-modeling-bench/blob/main/docs/suites/design-bench/superconductor.md) | [`composition_groups.json`](provenance/superconductor/composition_groups.json) |
| `drugmatrix_clinical_pathology` | Not yet published | [`observations.json`](provenance/drugmatrix_clinical_pathology/observations.json) |
| `cell_dag_nas` | [CellDAG-NAS](https://github.com/xukp20/sci-modeling-bench/blob/main/docs/suites/design-bench/cell-dag-nas.md) | [`architectures.json`](provenance/cell_dag_nas/architectures.json) |
| `hopper_controller` | [Hopper Controller](https://github.com/xukp20/sci-modeling-bench/blob/main/docs/suites/design-bench/hopper-controller.md) | [`build.json`](provenance/hopper_controller/build.json) |

## Licensing

The shared repository contains artifacts with different upstream terms, so the
root card uses `license: other`. Every config manifest records its own license
identity and source references.

| Config | Manifest license |
|---|---|
| `cell_dag_nas` | Apache-2.0 |
| `gfp` | CC BY 4.0 |
| `hopper_controller` | MIT for source policies; generated rollout provenance is recorded separately |
| `superconductor` | CC BY 4.0 |
| `tfbind10_pho4` | CC BY 4.0 |
| `tfbind8` | Source-specific terms; see manifest and provenance |
| `utr_mrl_egfp_unmodified` | Unknown in the upstream redistribution |
| `drugmatrix_clinical_pathology` | Unknown; the CEBS page does not state a simple artifact redistribution license |

Do not infer a Dataset config's license from the MIT license of the Python
package.

## Evaluation Boundary

Protocols hide evaluator labels through the package API, but these are public
scientific artifacts and may be discoverable outside that API. Controlled
Agent evaluations require an external harness to isolate the full Dataset,
provenance, caches, source checkout, and network according to the intended
setting. Query budgets and iterative feedback policy also belong to that
external harness rather than this data repository.