# Towards Label-Free Biological Reasoning Synthetic Dataset Creation via Uncertainty Filtering

arXiv: https://arxiv.org/abs/2510.05871 · HTML: https://mlsanity.com/paper/2510.05871/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 19 of its 30 references that are in the map.
- First posted on arXiv 7 Oct 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 19 of 19)

- [RoBERTa: A Robustly Optimized BERT Pretraining Approach](https://mlsanity.com/paper/1907.11692/) (2019)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Self-Instruct: Aligning Language Models with Self-Generated Instructions](https://mlsanity.com/paper/2212.10560/) (2022)
- [STaR: Bootstrapping Reasoning With Reasoning](https://mlsanity.com/paper/2203.14465/) (2022)
- [Automatic Chain of Thought Prompting in Large Language Models](https://mlsanity.com/paper/2210.03493/) (2022)
- [OpenThoughts: Data Recipes for Reasoning Models](https://mlsanity.com/paper/2506.04178/) (2025)
- [A Survey of Confidence Estimation and Calibration in Large Language Models](https://mlsanity.com/paper/2311.08298/) (2023)
- [DeepSeek-Prover: Advancing Theorem Proving in LLMs through Large-Scale Synthetic Data](https://mlsanity.com/paper/2405.14333/) (2024)
- [On Hallucination and Predictive Uncertainty in Conditional Language Generation](https://mlsanity.com/paper/2103.15025/) (2021)
- [Symbolic Chain-of-Thought Distillation: Small Models Can Also "Think" Step-by-Step](https://mlsanity.com/paper/2306.14050/) (2023)
- [Quantifying Uncertainty in Answers from any Language Model and Enhancing their Trustworthiness](https://mlsanity.com/paper/2308.16175/) (2023)
- [CoT-Self-Instruct: Building high-quality synthetic prompts for reasoning and non-reasoning tasks](https://mlsanity.com/paper/2507.23751/) (2025)
- [Uncertainty Quantification for LLMs through Minimum Bayes Risk: Bridging Confidence and Consistency](https://mlsanity.com/paper/2502.04964/) (2025)
- [Contextualizing biological perturbation experiments through language](https://mlsanity.com/paper/2502.21290/) (2025)
- [Towards Agents That Know When They Don't Know: Uncertainty as a Control Signal for Structured Reasoning](https://mlsanity.com/paper/2509.02401/) (2025)
- [Sparks of Tabular Reasoning via Text2SQL Reinforcement Learning](https://mlsanity.com/paper/2505.00016/) (2025)
- [SynthPert: Enhancing LLM Biological Reasoning via Synthetic Reasoning Traces for Cellular Perturbation Prediction](https://mlsanity.com/paper/2509.25346/) (2025)
- [STRuCT-LLM: Unifying Tabular and Graph Reasoning with Reinforcement Learning for Semantic Parsing](https://mlsanity.com/paper/2506.21575/) (2025)

## Built on by (most cited first, 3 of 3)

- [Ambig-DS: A Benchmark for Task-Framing Ambiguity in Data-Science Agents](https://mlsanity.com/paper/2605.09698/) (2026)
- [MechPert: Mechanistic Consensus as an Inductive Bias for Unseen Perturbation Prediction](https://mlsanity.com/paper/2602.13791/) (2026)
- [Measuring Black-Box Confidence via Reasoning Trajectories: Geometry, Coverage, and Verbalization](https://mlsanity.com/paper/2605.06308/) (2026)

## Abstract (arXiv)

Synthetic chain-of-thought (CoT) traces are widely used to train large reasoning models (LRMs), improving generalization by providing step-level supervision. Yet most approaches require ground-truth labels to seed or filter these traces - an expensive bottleneck in domains like biology where wet-lab data are scarce. We propose a label-free alternative: uncertainty-based filtering, which uses a model's own confidence - quantified through established uncertainty metrics like self-consistency and predictive perplexity - as a substitute for external labels. We sample multiple reasoning traces and retain only low-uncertainty subsets. Applied to biological perturbation prediction, a domain where wet-lab labels are especially costly, we show that the filtered subset has higher accuracy, and that supervised fine-tuning (SFT) on uncertainty-filtered data outperforms unfiltered synthetic data, narrows the gap to ground-truth training, and surpasses strong LRM baselines. Ablations show that per-class filtering corrects for class-specific uncertainty scales and that hybrid uncertainty metrics yield higher-quality datasets. Our results suggest that model-internal confidence is a powerful signal for efficient reasoning dataset creation, enabling LRMs in domains where supervision is expensive.