Enumerating Tool Choices Beats Sampling Them in Genomic Reasoning

Full-Group Policy Optimization evaluates every possible tool subset, improving accuracy while reducing reward-model calls and unnecessary tool use.

PaperTop Universitycs.AIarXiv:2609.10221v1
Haoyue Liu · Xiaoyu Ma · Ye Chen · Zhichao Wang · Xiaoying Tang

The Chinese University of Hong Kong, Shenzhen · Shenzhen Future Network of Intelligence Institute (FNii-Shenzhen) · Xi’an Jiaotong University

Research Digest··2 min read
Liu et al. replace sampled reinforcement-learning updates with exact optimization over the complete, enumerable set of genomic tool combinations. Across five frozen reasoners and three benchmarks, their method outperformed GRPO in all 15 experimental settings, by 6.75 percentage points on average.

What they did

The authors developed Full-Group Policy Optimization (FGPO) for settings where a policy selects tools for a frozen reasoning model and every possible tool subset can be enumerated. Rather than estimate expected reward from a small group of sampled subsets, FGPO scores the full action space during each policy update.

They also precomputed rewards for every question–tool-subset pair, creating an exhaustive lookup table that removes frozen-reasoner inference from the training loop. FGPO and GRPO were compared across five frozen reasoners and three genomic reasoning benchmarks.

Key findings

  • FGPO outperformed GRPO in all 15 reasoner–benchmark combinations, with an average gain of 6.75 percentage points and a maximum gain of 14.20 points.
  • Under GRPO, questions producing no learning signal rose from 0.2% with a uniform reference policy to 20.8% after training, as the policy increasingly resampled identical subsets and group-normalized advantages collapsed.
  • A standard on-demand GRPO schedule would require 2.4 times as many frozen-reasoner reward evaluations as FGPO's exhaustive precomputation.
  • On GenomeQA, FGPO reduced the mean number of tools invoked per question from 2.36 to 1.40.

Why it matters

The results challenge the default use of sampled policy optimization when an agent's action space is small enough to enumerate. In specialist domains with a limited tool catalog, exact expectations can provide denser training signals, avoid duplicate-sampling pathologies, and produce more selective tool-use policies.

Caveats

FGPO depends on the complete tool-subset space being tractable and on rewards being precomputable for a frozen reasoner. Its storage and upfront evaluation costs may become prohibitive with larger, dynamic tool catalogs, while the reported evidence is confined to genomic benchmarks and does not establish similar gains in other scientific domains or with jointly trained reasoners.

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