Datasets:
system stringclasses 3
values | instruction stringlengths 2.17k 41.3k | input stringclasses 1
value | output stringlengths 130 1.26k | source stringclasses 4
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|---|---|---|---|---|
You are a scientific search agent proposing candidate antibody CDRH3 sequences under an iterative Bayesian optimization loop. Return ONLY the JSON action. Never predict binding energy, uncertainty, or rank. | # Task: protein (antibody_sequence)
Direct CDRH3 antibody sequence generation for AntBO. Do not output search functions, code, LocalSearch, NeighborSampling, LatinHyperCubeSampling, or explanations. Generate antibody strings directly.
## Objectives
- binding_energy: minimize - Minimize Absolut binding energy. Lower tr... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "ADGHTKQNPRL", "rationale": null}]}, "summary": null} | protein_direct | |
You are a scientific search agent proposing candidate molecules under an iterative multi-objective Bayesian optimization loop. Return ONLY the JSON action. Never predict docking score, activity, EHVI, uncertainty, or rank. | # Task: smallmol (molecule)
The optimization task is for KRAS G12D small-molecule candidates. The activity objective is based on a target-specific model trained from public KRAS G12D IC50 records, and the docking objective evaluates binding with AutoDock Vina.
Public medicinal-chemistry literature has shown that small... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "CC(C)Oc1ncc(C#N)c2oc(=O)n(CCCN3CCOCC3)c12", "rationale": "recombine pyridine and morpholine"}, {"design": "CN1C(=O)oc2c(C#N)cnc(C3CC3CO)c21", "rationale": "methyl substituent with cyclopropylmethanol"}, {"design": "C1CC1COc1ccc(C#N)c2oc(=O)n(... | smallmol | |
You are a scientific search agent proposing candidate molecules under an iterative multi-objective Bayesian optimization loop. Return ONLY the JSON action. Never predict docking score, activity, EHVI, uncertainty, or rank. | # Task: smallmol (molecule)
The optimization task is for KRAS G12D small-molecule candidates. The activity objective is based on a target-specific model trained from public KRAS G12D IC50 records, and the docking objective evaluates binding with AutoDock Vina.
Public medicinal-chemistry literature has shown that small... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "CC(C)CCc1cc(OC(F)(F)F)sc1C#N", "rationale": "branched alkyl on thiophene"}, {"design": "CCC(C)c1cc(OC(F)(F)F)sc1C#N", "rationale": "sec-butyl thiophene variant"}, {"design": "CC1CC1c1coc(OC(F)(F)F)c1C#N", "rationale": "isoxazole core with cyc... | smallmol | |
You are a scientific search agent proposing candidate molecules under an iterative multi-objective Bayesian optimization loop. Return ONLY the JSON action. Never predict docking score, activity, EHVI, uncertainty, or rank. | # Task: smallmol (molecule)
The optimization task is for KRAS G12D small-molecule candidates. The activity objective is based on a target-specific model trained from public KRAS G12D IC50 records, and the docking objective evaluates binding with AutoDock Vina.
Public medicinal-chemistry literature has shown that small... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "CCCOc1ccc2c(N)nc(C3CCC3C(F)(F)Br)n2c1", "rationale": "cyclobutane replaces cyclopropane"}, {"design": "CCCOc1ccc2c(N)nc(C3CC3C(F)(F)C(F)(F)C(F)(F)C(F)(F)C(F)F)n2c1", "rationale": "longer chain with terminal CHF2"}, {"design": "CCCOc1ccc2c(N)n... | smallmol | |
You are a scientific search agent proposing candidate molecules under an iterative multi-objective Bayesian optimization loop. Return ONLY the JSON action. Never predict docking score, activity, EHVI, uncertainty, or rank. | # Task: smallmol (molecule)
The optimization task is for KRAS G12D small-molecule candidates. The activity objective is based on a target-specific model trained from public KRAS G12D IC50 records, and the docking objective evaluates binding with AutoDock Vina.
Public medicinal-chemistry literature has shown that small... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "CCCOc1ccc2c(N)nc(C3CC3C(F)(F)C(F)(F)C(F)(F)Cl)n2c1", "rationale": "chlorine end on perfluoro chain"}, {"design": "CCCCOc1ccc2c(N)nc(C3CC3C(F)(F)C(F)(F)C(F)(F)Br)n2c1", "rationale": "butoxy chain with longer fluorinated tail"}, {"design": "CCC... | smallmol | |
You are a scientific search agent proposing candidate antibody CDRH3 sequences under an iterative Bayesian optimization loop. Return ONLY the JSON action. Never predict binding energy, uncertainty, or rank. | # Task: protein (antibody_sequence)
Pure LLM baseline for CDRH3 sequence proposal.
## Objectives
- binding_energy: minimize - Minimize Absolut energy. Lower true score is better.
## Design space (current state - you may act on it)
Representation: complete_design
Active parameters (the surrogate models only these; `c... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "HGPVKPEETRN", "rationale": null}]}, "summary": null} | protein_acq | |
You are a scientific search agent proposing candidate antibody CDRH3 sequences under an iterative Bayesian optimization loop. Return ONLY the JSON action. Never predict binding energy, uncertainty, or rank. | # Task: protein (antibody_sequence)
Pure LLM baseline for CDRH3 sequence proposal.
## Objectives
- binding_energy: minimize - Minimize Absolut energy. Lower true score is better.
## Design space (current state - you may act on it)
Representation: complete_design
Active parameters (the surrogate models only these; `c... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "SQNPWTMPLIH", "rationale": null}]}, "summary": null} | protein_acq | |
You are a scientific search agent proposing candidate molecules under an iterative multi-objective Bayesian optimization loop. Return ONLY the JSON action. Never predict docking score, activity, EHVI, uncertainty, or rank. | # Task: smallmol (molecule)
The optimization task is for KRAS G12D small-molecule candidates. The activity objective is based on a target-specific model trained from public KRAS G12D IC50 records, and the docking objective evaluates binding with AutoDock Vina.
Public medicinal-chemistry literature has shown that small... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "N#Cc1ccc(OCC(C)C)c2[nH]c(=O)oc12", "rationale": "vary smaller scaffold with alkyl"}, {"design": "CC(C)(C)Oc1cc(C#N)c(C#N)c2oc(=O)n(CCC#N)c12", "rationale": "tert-butyl variant of core"}, {"design": "CC(C)Oc1cc(C#N)c(C#N)c2oc(=O)n(C#N)c12", "r... | smallmol | |
You are a scientific search agent proposing candidate molecules under an iterative multi-objective Bayesian optimization loop. Return ONLY the JSON action. Never predict docking score, activity, EHVI, uncertainty, or rank. | # Task: smallmol (molecule)
The optimization task is for KRAS G12D small-molecule candidates. The activity objective is based on a target-specific model trained from public KRAS G12D IC50 records, and the docking objective evaluates binding with AutoDock Vina.
Public medicinal-chemistry literature has shown that small... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "CC(=O)c1csc(C2CCCCC2)n1", "rationale": "thiazole methyl ketone cyclohexyl"}, {"design": "CNS(=O)(=O)c1csc(C2CC2)n1", "rationale": "thiazole sulfonamide cyclopropyl"}, {"design": "NS(=O)(=O)c1c[nH]c(C2CCCC2)n1", "rationale": "imidazole sulfona... | smallmol | |
You are a scientific search agent proposing candidate molecules under an iterative multi-objective Bayesian optimization loop. Return ONLY the JSON action. Never predict docking score, activity, EHVI, uncertainty, or rank. | # Task: smallmol (molecule)
The optimization task is for KRAS G12D small-molecule candidates. The activity objective is based on a target-specific model trained from public KRAS G12D IC50 records, and the docking objective evaluates binding with AutoDock Vina.
Public medicinal-chemistry literature has shown that small... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "N#Cc1ccc(OCC2CC2C)c2[nH]c(=O)oc12", "rationale": "methylcyclopropyl analog of low-vina molecule"}, {"design": "CC(C)Oc1cc(C#N)c(C#N)c2oc(=O)n(CCN3CCOCC3)c12", "rationale": "morpholine side-chain crossover from elite"}, {"design": "CC(C)Oc1cc(... | smallmol | |
You are a scientific search agent proposing candidate antibody CDRH3 sequences under an iterative Bayesian optimization loop. Return ONLY the JSON action. Never predict binding energy, uncertainty, or rank. | # Task: protein (antibody_sequence)
Pure LLM baseline for CDRH3 sequence proposal.
## Objectives
- binding_energy: minimize - Minimize Absolut energy. Lower true score is better.
## Design space (current state - you may act on it)
Representation: complete_design
Active parameters (the surrogate models only these; `c... | {"type": "propose", "reasoning": null, "payload": {"candidates": [{"design": "ANIFEEVLGRY", "rationale": null}]}, "summary": null} | protein_acq |
LDM-TTS-Base-SFT-19K
Supervised fine-tuning (SFT) corpus for Large Discovery Models (LDM): a dataset that distils an acquisition-guided, test-time search policy into a language-model proposer so that a single forward pass emulates a full model-based optimization loop.
Dataset Summary
An LDM couples three components in a recurrent generate → select → evaluate → update
loop: an LLM that proposes candidate experiments, a probabilistic surrogate that maps
observations to a posterior mean and uncertainty, and an acquisition function that selects
the next experiment under that uncertainty. Running this loop at high budget yields
trajectories of proposal decisions; each decision is rendered as one training example.
Fine-tuning on this corpus compiles the expensive search policy into the proposer's weights.
This release provides the direct-action baseline with no chain-of-thought: the target is the emitted action alone, without an accompanying reasoning trace.
Supported Tasks
Examples are pooled from three discovery domains under a shared action schema:
| Domain | Search space | Objective |
|---|---|---|
| AutoResearch (nanoGPT) | training-code and hyperparameter edits | validation bits-per-byte |
| Small molecule | SMILES candidates (KRAS) | Vina docking score and predicted activity |
| Antibody | CDRH3 amino-acid sequences | Absolut binding energy |
Dataset Structure
Each record follows the Alpaca schema:
{
"instruction": "round context: evaluated history, constraints, and task specification",
"input": "",
"output": "{ JSON action }",
"system": "system prompt defining the proposer's role and output contract"
}
instruction— the search state presented to the proposer at one round.output— the emitted action (proposed candidates), with no reasoning trace.- A single training split is provided (
train.jsonl).
Data Collection and Processing
High-budget LDM rollouts were produced by a self-hosted DeepSeek teacher operating inside the LDM framework, filtered by the empirical acquisition-tilted policy, and rendered into the Alpaca schema.
Related Datasets
| Dataset | Reasoning target | Surrogate values in prompt |
|---|---|---|
| LDM-TTS-Base-SFT-19K (this) | direct action, no reasoning | — |
| LDM-CoT-Acq-SFT-16K | chain-of-thought | shown |
| LDM-CoT-SFT-16K | chain-of-thought | withheld |
Intended Use
Full-parameter SFT of an instruction model as a discovery proposer; the intended base is
Qwen/Qwen3.5-9B with the qwen3_5 chat template. The resulting model is deployed inside
the LDM acquisition loop, where the surrogate and acquisition function remain external.
Limitations
- Objective values reflect the specific oracles used during collection (Vina, an activity model, and Absolut) and should not be read as experimental ground truth.
Loading
from datasets import load_dataset
ds = load_dataset("Yangtze-ailab/LDM-TTS-Base-SFT-19K")
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