How Post-Training Shapes Biological Reasoning Models

Post-training has become a primary driver of recent progress in large reasoning models, and reasoning data are often the key variable determining whether this stage succeeds. Work on post-training reasoning data has grown rapidly, yet this literature remains scattered across dataset papers, reinforcement-learning recipes, reward-model studies, benchmarks, and frontier system reports. This paper is the first primer to synthesize over 150 key public studies and system reports on post-training reasoning data. We organize the field around four questions: what data objects exist, what makes them useful, how they are constructed, and how they scale. Together, this organization provides an attribution framework for future reasoning-data releases and post-training recipes.

The push toward large language models for biology (BioLM) has created a need for training corpora that can endow models with a genuine understanding of biology. However, existing biological resources, such as molecular databases, protein repositories, genomic annotations, single-cell atlases, and pathway databases, are scattered across heterogeneous formats and remain unorganized into a cohesive corpus for language model training. We present TheBioCollection, a 52.6B-token pre-training-scale corpus that converts these disparate resources into a unified, training-ready form spanning small molecules, proteins, genomic sequences, cells, and pathways. Beyond consolidating existing data, TheBioCollection enriches each record with tool-computed biological properties and introduces new instruction tasks for capabilities that current corpora barely cover. We pair the corpus with TheBioCollection-Eval, a matched suite probing recognition, generation, and prediction across molecular, protein, genomic, cellular, and cross-domain settings. Holding the base Gravity-16B-A3B architecture fixed, training on TheBioCollection more than doubles its overall score on TheBioCollection-Eval with gains in every domain, while leaving general linguistic ability nearly intact.

Recent progress in large language models has led to the emergence of reasoning models, which have shown strong performance on complex tasks through specialized fine-tuning procedures. While these methods reliably improve pass@1 accuracy, prior works have observed that they show a coverage shrinkage behavior, where pass@k degrades relative to the base model. In this paper, we investigate the cause of reasoning shrinkage under SFT-based post-training. We hypothesize that this behavior is driven by properties of the fine-tuning data, specifically related to decision points or "forks in the road" scenarios where model encounters indecipherable patterns with multiple valid reasoning paths. To test this hypothesis, we design controlled case studies that simulate such decision-point settings, spanning indecipherable nodes in graph branching, and reasoning modes. By tracking post-training dynamics in these settings, we find that the shrinkage phenomenon is tightly correlated with the prevalence of decision-point scenarios in the training data. We also demonstrate that this shrinkage behavior can be partially mitigated through targeted data synthesis design of decision-points and a more systematic diversity-encouraging decoding mechanism. Our findings identify data-centric factors as a key driver of shrinkage in reasoning models and highlight diversity-aware designs as an effective lever for controlling it. (Data and code for reproducing our experiments are available at https://github.com/psunlpgroup/reasoning_forks )