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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
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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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