arXiv:2609.36679v1 Announce Type: new Abstract: Machine learning engineering (MLE) agents have made substantial progress, but learning through ML experimentation remains costly in time and computatio...
arXiv:2606. 16517v1 Announce Type: new Abstract: Scientific reasoning models for biology combine language models with foundation models trained on multimodal biological data, including DNA, RNA, and proteins.
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.
The paper introduces OmicsBench, a new reasoning benchmark for multi‑omics sequences that includes 1,160 expert‑validated questions across DNA regulation, RNA processing, and protein function tasks, requiring traceable evidence chains. Evaluation of 17 large language models shows that scientific LLMs, while more accurate in classification, often lack valid evidence, suggesting shortcut learning. To address this, the authors propose tool‑augmented on‑policy distillation (TA‑OPD), a post‑training method that improves both evidence grounding and predictive performance across five Qwen3.5 models of varying sizes.
arXiv:2609.36641v1 Announce Type: cross Abstract: Process reward models (PRMs) have become a key component for LLMs, as their step-level feedback supports both post-training and test-time reasoning....
UniToolCall introduces a unified framework for tool-use in large language model agents, standardizing toolset construction, dataset generation, and evaluation. The framework aggregates over 22,000 tools and creates a hybrid training corpus of more than 390,000 instances by combining ten public datasets with synthetically generated, structurally controlled trajectories. It models diverse interaction patterns—single‑hop vs. multi‑hop, single‑turn vs. multi‑turn, serial vs. parallel execution—and adds an Anchor Linkage mechanism to enforce cross‑turn dependencies, while converting seven public benchmarks into a common Query–Action–Observation–Answer format for fine‑grained evaluation.
arXiv:2607. 00531v1 Announce Type: cross Abstract: Scientific reasoning is an increasingly important capability of large language models, yet improving the robustness and efficiency of training such reasoning remains a key open challenge.
arXiv:2606. 18961v1 Announce Type: new Abstract: Protein language models (PLMs) have emerged as powerful tools for controllable biomolecular design, yet their post-training adaptation typically relies on costly wet-lab validation or curated preference datasets.
The paper introduces Proof-of-Use (PoU), a reinforcement learning framework designed to prevent tool‑call hacking in deep research agents. PoU enforces evidence grounding by requiring agents to cite normalized evidence identifiers and uses a multi‑objective reward system that includes progressive process rewards, an answer‑support alignment reward, and a curriculum‑style adaptive reward mixing. Experiments demonstrate that PoU effectively mitigates tool‑call hacking and promotes robust, adaptive tool usage even under domain and tool shifts.
The paper introduces a self‑supervised framework called software‑in‑the‑loop reconstruction (SWR) that automatically generates reference outputs and verification targets for terminal agents by leveraging existing scientific software workflows. SWR executes multiple input configurations, partitions cases into public observations and hidden evaluations, and uses a hierarchical verifier to assess agent‑generated programs against hidden workflow outputs. The authors demonstrate the approach on 500 workflows across six domains, achieving significant performance gains on the Terminal‑Bench 2 benchmark with the Qwen3.8‑Max and Qwen3.8‑27B models.
arXiv:2606. 04970v1 Announce Type: cross Abstract: We envision a proactive multi-modal assistant system which gives users real-time step-by-step guidance on a procedural task, autonomously deciding \textit{when} to interrupt, and \textit{how} to coach.
Protein language models (PLMs) have emerged as powerful tools for controllable biomolecular design, yet their post-training adaptation typically relies on costly wet-lab validation or curated preference datasets. To overcome this supervision bottleneck, we introduce unsupervised reward optimization of PLMs, a comprehensive framework for steerable protein generation without ground-truth labels.