# How Post-Training Shapes Biological Reasoning Models

arXiv: https://arxiv.org/abs/2606.16517 · HTML: https://mlsanity.com/paper/2606.16517/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 44 of its 97 references that are in the map.
- First posted on arXiv 15 Jun 2026.

## Placed in

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

## Builds on (most cited first, 30 of 44)

- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Proximal Policy Optimization Algorithms](https://mlsanity.com/paper/1707.06347/) (2017)
- [LoRA: Low-Rank Adaptation of Large Language Models](https://mlsanity.com/paper/2106.09685/) (2021)
- [Qwen3 Technical Report](https://mlsanity.com/paper/2505.09388/) (2025)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [Training Compute-Optimal Large Language Models](https://mlsanity.com/paper/2203.15556/) (2022)
- [Pythia: A Suite for Analyzing Large Language Models Across Training and Scaling](https://mlsanity.com/paper/2304.01373/) (2023)
- [Don't Stop Pretraining: Adapt Language Models to Domains and Tasks](https://mlsanity.com/paper/2004.10964/) (2020)
- [ZeRO: Memory Optimizations Toward Training Trillion Parameter Models](https://mlsanity.com/paper/1910.02054/) (2019)
- [The FineWeb Datasets: Decanting the Web for the Finest Text Data at Scale](https://mlsanity.com/paper/2406.17557/) (2024)
- [Does Reinforcement Learning Really Incentivize Reasoning Capacity in LLMs Beyond the Base Model?](https://mlsanity.com/paper/2504.13837/) (2025)
- [SFT Memorizes, RL Generalizes: A Comparative Study of Foundation Model Post-training](https://mlsanity.com/paper/2501.17161/) (2025)
- [Understanding the Effects of RLHF on LLM Generalisation and Diversity](https://mlsanity.com/paper/2310.06452/) (2023)
- [OpenThoughts: Data Recipes for Reasoning Models](https://mlsanity.com/paper/2506.04178/) (2025)
- [Reinforcement Learning for Reasoning in Large Language Models with One Training Example](https://mlsanity.com/paper/2504.20571/) (2025)
- [When Scaling Meets LLM Finetuning: The Effect of Data, Model and Finetuning Method](https://mlsanity.com/paper/2402.17193/) (2024)
- [Continual Pre-training of Language Models](https://mlsanity.com/paper/2302.03241/) (2023)
- [ProGen2: Exploring the Boundaries of Protein Language Models](https://mlsanity.com/paper/2206.13517/) (2022)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [Continual Pre-Training of Large Language Models: How to (re)warm your model?](https://mlsanity.com/paper/2308.04014/) (2023)
- [Simple and Scalable Strategies to Continually Pre-train Large Language Models](https://mlsanity.com/paper/2403.08763/) (2024)
- [The Art of Scaling Reinforcement Learning Compute for LLMs](https://mlsanity.com/paper/2510.13786/) (2025)
- [AI-Researcher: Autonomous Scientific Innovation](https://mlsanity.com/paper/2505.18705/) (2025)
- [Reuse, Don't Retrain: A Recipe for Continued Pretraining of Language Models](https://mlsanity.com/paper/2407.07263/) (2024)
- [MegaScience: Pushing the Frontiers of Post-Training Datasets for Science Reasoning](https://mlsanity.com/paper/2507.16812/) (2025)
- [Training a Scientific Reasoning Model for Chemistry](https://mlsanity.com/paper/2506.17238/) (2025)
- [D-CPT Law: Domain-specific Continual Pre-Training Scaling Law for Large Language Models](https://mlsanity.com/paper/2406.01375/) (2024)
- [BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model](https://mlsanity.com/paper/2505.23579/) (2025)

## Built on by (most cited first, 1 of 1)

- [When Do Biological Reasoning Models Use Their Biological Inputs?](https://mlsanity.com/paper/2610.00898/) (2026)

## Abstract (arXiv)

Scientific reasoning models for biology combine language models with foundation models trained on multimodal biological data, including DNA, RNA, and proteins. These models are built through post-training, yet how each stage shapes reasoning and generalization remains poorly understood. We study when post-training improves performance and when it induces over-specialization. Across genomics, transcriptomics, and proteins, we train and evaluate more than 100 biological reasoning models under controlled variation in backbone, continued pre-training (CPT), supervised fine-tuning (SFT), and reinforcement learning (RL), measuring both in-domain (ID) and out-of-domain (OOD) performance. We find that each post-training stage reshapes generalization in a distinct way rather than contributing uniform gains. CPT improves downstream performance by aligning models with biological language. SFT consistently increases ID performance but causes OOD performance to peak early and decline as models fit the training distribution. RL, when applied to strong SFT checkpoints with aligned rewards, improves OOD performance and partially recovers generalization. These results show that biological reasoning does not improve monotonically with additional supervision or compute. Instead, performance depends on how training stages are composed. Under fixed post-training budgets, the strongest ID-OOD trade-off comes from brief SFT, larger RL allocations, and asymmetric adaptation capacity across stages.