#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.CV
Streaming Multi-Agent Autoregressive Diffusion Model with World State Registers
Sicheng Mo, Yuheng Li, Ziyang Leng and 2 more
Multi-agent interactive world models should not only generate consistent observations, but also maintain world states that persist across agents and evolve across views. Existing autoregressive video diffusion pipelines carry forward observation history as conditioning context, which makes shared state difficult to maintain in multi-agent and multi-view settings. We present WorldWeaver (W^2), a streaming multi-agent video diffusion model that augments rollout with cross-agent world state registers: learnable tokens that store shared world information, track individual agent status, and are dynamically updated after each generated chunk. We ground these registers with supervision signals spanning individual agent status, global state views including bird's-eye views, and scene text. We further improve the architecture with a Mixture-of-Transformers design that uses separate weights for world state modeling and visual frame modeling. Extensive experiments in two-agent Minecraft video generation show that explicit world-state modeling improves logical consistency and generation quality.
#04Jul 23, 2026
cs.CV
UnDA: Unpaired Domain Alignment for Cross-Modal Knowledge Transfer in Medical Imaging
Rafsan Jany, Shadab Tanjeed Ahmad, Ahsan Bulbul and 3 more
Multimodal based approaches often outperform single modality approaches in downstream tasks as the different modalities provide complementary information, yet acquiring paired clinical data remains a significant challenge in real world scenarios. While cross-modal knowledge distillation addresses this, existing methods often struggle with large modality gaps and the propagation of noise from uncertain source-domain predictions. To overcome these challenges, we propose UnDA, an anchor-guided framework for unpaired cross-modal distillation. Our approach introduces a backbone-agnostic Alignment Module that extracts semantically structured class tokens via an attention based pooling mechanism. To ensure robust knowledge transfer, we propose Uncertainty-Weighted Optimal Transport (UCT-OT), which dynamically weights feature-level alignment based on prediction confidence, effectively suppressing noisy supervision. Furthermore, a per-class ProtoNCE objective maintains stable prototype memories to enforce global discriminability across unpaired batches. Evaluations on representative segmentation tasks under strictly unpaired settings show consistent improvements in accuracy and boundary precision in the target modality, demonstrating that meaningful structural knowledge can be transferred across heterogeneous data sources without paired datasets.
#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