synthetic biology developers

Abstract: Molecular cloning is one of the most routine wet-lab workflows, yet existing evaluations of language models in biology mostly test knowledge recall or isolated steps rather than end-to-end experimental planning. We introduce BenchBench-Cloning, a benchmark for large language models comprising 65 molecular cloning tasks grounded in sequence records, laboratory notebooks, and published experimental studies. Planning a molecular cloning experiment requires defining a set of constructs needed for a scientific objective and a construction route to produce them. BenchBench-Cloning contains 50 protocol-development tasks, in which agents produce an executable protocol for a specified construct, and 15 construct-design tasks, in which agents determine the constructs a scientific objective calls for. Protocol-development tasks are evaluated by execution in a cloning simulator; construct-design tasks are evaluated with task-specific deterministic checks and, where needed, rubric-based LLM-as-a-judge evaluation. Across eight systems with repeated attempts per task, GPT-6 Astra scores highest at 30.6%, with the others between 8.6% and 22.2%, and the benchmark remains unsaturated under best-of-ten sampling. As integrating individual cloning decisions into complete, valid plans remains challenging even for frontier models, we expect BenchBench-Cloning to serve as a useful benchmark for tracking progress in experimental planning.

Abstract: Generative Flow Networks (GFlowNets) learn a policy that samples compositional objects in proportion to an unnormalized reward $R(x)$. This makes them useful wherever many diverse, high-reward candidates are needed and oracle queries are expensive. In practice, a single GFlowNet often fails to cover all modes of a complex distribution, and the obvious ways to scale compute saturate: larger batches and data-parallel gradient averaging draw every trajectory from one, possibly biased, policy, so extra rollouts rediscover known modes instead of finding new ones. We explore whether this mode-bias problem (mode collapse in the extreme) can be addressed with a population of asynchronously trained policies which divide the state space between them. Mixture of GFlowNets (MoG) replaces the single forward policy with a community of $K$ independent GFlowNets coupled through one jointly trained soft classifier, which assigns each member its own region of the state space through reward shaping. Mixing the members under their learned partition functions provably recovers the target $p(x)\propto R(x)$. MoG exchange (MoGX) also lets the classifier route sampled trajectories: a trajectory the classifier assigns to another member is sent to that member and trained on there, with no importance sampling. We evaluate both methods by keeping the environment-interaction budget fixed while scaling the community size, turning parallel compute into mode coverage without extra oracle calls. On HyperGrid, across six reward landscapes and communities of up to $K{=}64$, MoG and MoGX keep finding new modes as $K$ grows, while data-parallel training saturates. On a genomic ideotype-design task, MoGX covers $39%$ of the $1024$ optima at $K{=}64$, against $31\%$ for independent agents and $20\%$ for data-parallel training. MoG also has a lower per-iteration synchronization cost than data-parallel training.

Abstract: Compact regulatory DNA can free up space in vector payloads, reduce synthesis and assay burden, and expose which sequence features drive predicted activity. Yet most model-based nucleic-acid designers optimize fixed-length sequences through substitutions; they do not ask which bases of an existing functional element can be removed while retaining predicted activity. We define the task of sequence slimming as selecting an exact-length, order-preserving subsequence while retaining activity. Modeled on the design benchmark NucleoBench, we propose a quantitative evaluation for slimming that balances sequence reduction with maintaining function. Each slimmer must return both the subsequence and its source indices, which can be used to verify that the slimmer obeyed task requirements. To our knowledge, this is the first dedicated benchmark of this deletion-only problem. The coding agent Empirical Research Assistant (ERA) then searched over executable designer programs. ERA received the task prompt and a successful substitution-only designer GrAdaBeam as a starting program, and it modified the designer to produce GRADASLIM. We report held-out evaluations for five transcription-factor binding targets, comparing random, greedy, and ERA-guided slimming at 400 and 100 bp. ERA has the highest mean in 9/10 settings. Paired bootstrap intervals for ERA minus greedy are above zero in all five 400-bp settings, below zero in one 100-bp setting, and overlap zero in the remaining four.