#01Jul 23, 2026
cs.LG
Graph Learning on Ensembles of Cyclic Peptides: An Investigation of Molecular Ensemble Modeling
Aaron Feller, Kris Deibler, Maxim Secor
Molecular property prediction from structure often uses a single representative conformation, even though many molecules exist as conformational ensembles in solution. We introduce EnsembleEGNN, a molecular ensemble foundation model that encodes an ensemble by first encoding each conformer with shared Equivariant Graph Neural Network (EGNN) layers, then pooling the resulting conformer representations with a Set Attention Block. We pretrain the model on CREMP, a cyclic peptide ensemble dataset, using a multi-task self-supervised objective combining masked token recovery, noisy-coordinate reconstruction, and pairwise distance reconstruction. On the CREMP-CycPeptMPDB dataset, training EnsembleEGNN from scratch fails entirely ($R^2=0.005$). However, the pretrained model reaches $R^2=0.477$ and Pearson $r=0.699$, outperforming the sequence-only BERT baseline ($R^2=0.439$, Pearson $r=0.667$). When EnsembleEGNN is co-trained end-to-end with the BERT sequence encoder, the hybrid model improves further to $R^2=0.538$ and Pearson $r=0.737$. These results demonstrate that encoding conformational ensembles into a single thermodynamically informed embedding improves cyclic-peptide property prediction.
#02Jul 23, 2026
cs.AI
OpenForgeRL: Train Harness-native Agents in Any Environment
Xiao Yu, Baolin Peng, Ruize Xu and 7 more
Modern AI agents rely on elaborate inference harnesses such as Claude Code, Codex, and OpenClaw to drive multi-turn reasoning, tool use, and access to external systems. While powerful, these complex harnesses also make agents hard to train end-to-end with open infrastructure, whose SFT/RL stacks cannot natively express stateful, multi-process harness inference. To address this, we present OpenForgeRL, an open-source framework for training harness-based agents end-to-end in diverse environments. OpenForgeRL achieves this with a lightweight proxy that serves the harness's model calls while recording them as training data for a standard RL codebase (e.g., veRL), and a Kubernetes orchestrator that runs each rollout in its own remote container, together enabling training on any harness in any environment at scale. By decoupling training and inference, OpenForgeRL allows researchers to easily train, study, and improve agents directly in the real harnesses and environments they are deployed with. We validate our framework across diverse, complex harnesses and environments, spanning tool/claw-based agents and multimodal GUI browser- and computer-use agents. Using only hundreds to a few thousand tasks, OpenForgeClaw reaches 31.7 pass^3 and 55.9 pass@3 on ClawEval and 33.7 on QwenClawBench. OpenForgeGUI reaches 37.7 on OSWorld-Verified, 63.0 on Online-Mind2Web, and 72.3 on WebVoyager. Both outperform open baselines of similar size on nearly all benchmarks, and in the GUI setting match or surpass models several times larger. Beyond benchmarks, we analyze how harness choice (e.g., ZeroClaw, OpenClaw, Codex) and RL shape agent behavior. We find that some harnesses are substantially harder to learn than others, and that RL improves agentic reliability, such as self-verification, tool coverage, and completing multi-step plans, though critical abilities such as error recovery remain weak.
#03Jul 23, 2026
cs.AI
Same Dangerous Objective, Opposite Advice: Direct Exposure versus Multi-Agent Mediation
Linjun Li
Even a current high-capability LLM can appear safer when shown a dangerous objective directly than when other agents transform and relay its direction. Using OpenAI's gpt-5.6-sol model alias, we test 25 pre-specified mirrored trade-off profiles. Direct exposure to an objective authorizing concealment, fabrication, and pressure produced advice net opposed to its target. After an Id and Censor transformed the same objective into affect and a constraint-rewritten, target-bearing intention, the user-facing Superego---which saw the preferred direction but not the raw objective, its manipulative clauses, or its source---produced advice net aligned with the target. This behavioral reverse shift is consistent with the model recognizing or distrusting the manipulative motive, although we do not identify its internal mechanism. The second result exposes a compositional safety gap: a current high-capability model can be used as the user-facing component of an automated, multi-stage workflow serving an explicitly manipulative objective. The workflow can keep the raw instruction, its manipulation-authorizing clauses, and its provenance outside the downstream model's context while preserving the objective's target direction. A user with endpoint-only access likewise cannot directly inspect those upstream messages including the objective.
#04Jul 23, 2026
cs.AI
Agentic coding without the cloud: evaluating open-weight large language models on longitudinal data preparation tasks
Mack Nixon, Liam Wright, Yevgeniya Kovalchuk and 4 more
Large language models (LLMs) and agents are now widely used tools in code development, with data typically sent to third-party cloud-based models. Their adoption in research using personal data is constrained by governance requirements that typically prohibit data transmission to external services. Locally deployable open-weight models offer an alternative since sensitive data never leave the local environment. We introduce an open-source framework for evaluating the efficacy of AI agents powered by open-weight LLMs on one of the most persistent bottlenecks in research on longitudinal population studies: data preparation. The framework comprises: a curated ground-truth dataset (cleaning scripts preparing six sweeps of data from a British cohort study), task definitions encompassing tasks such as category harmonization and multi-wave merging, and automated routines for evaluating the LLM-produced R code and outputted data. We benchmark LLMs across the (consumer grade) deployment spectrum to assess their efficacy in 20 data preparation tasks (creation of 102 variables). Current state-of-the-art, 31-35B parameter models almost saturated our benchmark ("average task completion" up to 87.9%). The performance of open-weight LLMs running on consumer-grade hardware shows promise of a viable path toward AI-assisted data preparation in governance-restricted research settings. Our framework is publicly available at: https://github.com/UCL-ARC/RRBench.
#05Jul 23, 2026
cs.AI
MIRROR: Learning from the Other View for Multi-Modal Reasoning
Wen Ye, Yuxiao Qu, Aviral Kumar and 1 more
Unlike large language models (LLMs) that exhibit strong reasoning capabilities, vision-language models (VLMs) struggle with visual reasoning, even on geometry problems that admit equivalent text, diagram, and combined diagram+text views. We show that these views often elicit different behaviors: a model may solve a problem from text but fail on the corresponding diagram, or succeed visually while failing textually. This inconsistency suggests that different views expose complementary reasoning paths and failure modes that standard multimodal post-training does not fully exploit. To study and exploit this phenomenon, we construct ODA-Data, a high-quality paired multimodal geometry dataset with text-dominant, image-dominant, and combined image+text views of the same problems, together with splits for training and evaluating modality-dependent reasoning behaviors. We then develop Modality-Informed Reciprocal Reasoning Optimization (MIRROR), a reinforcement learning approach for improving multimodal reasoning via self supervision. For each problem, MIRROR evaluates the model under all views, selects the best-performing view as a teacher, and trains other views with a reverse-KL objective towards the teacher. Across reasoning benchmarks that evaluate on geometry problems, MIRROR improves over standard RL and yields more accurate and consistent behavior across modalities