OpenRaiser/Intern-Atlas huggingface dataset:
Monte Carlo Tree Diffusion with Multiple Experts for Protein Design
Venue: arXiv cs.LG 2026
Year: 2026

The goal of protein design is to generate amino acid sequences that fold into functional structures with desired properties. Prior methods combining autoregressive language models with Monte Carlo Tree Search (MCTS) struggle with long-range dependencies and suffer from an impractically large search space. We propose MCTD-ME, Monte Carlo Tree Diffusion with Multiple Experts, which integrates masked diffusion models with tree search to enable multi-token planning and efficient exploration under the guidance of multiple experts. Unlike autoregressive planners, MCTD-ME uses biophysical-fidelity-enhanced diffusion denoising as the rollout engine, jointly revising multiple positions and scaling to large sequence spaces. It further leverages experts of varying capacities to enrich exploration, guided by a pLDDT-based masking schedule that targets low-confidence regions while preserving reliable residues. We propose a novel multi-expert selection rule ( PH-UCT-ME) extends Shannon-entropy-based UCT to expert ensembles with mutual information. MCTD-ME achieves superior performance on the CAMEO and PDB benchmarks, excelling in protein design tasks such as inverse folding, folding, and conditional design challenges like motif scaffolding on lead optimization tasks. Our framework is model-agnostic, plug-and-play, and extensible to denovo protein engineering and beyond.
Relational Dissonance in Human-AI Interactions: The Case of Knowledge Work
Venue: arXiv cs.HC 2026
Year: 2026

When AI systems allow human-like communication, they elicit increasingly complex relational responses. Knowledge workers face a particular challenge: They approach these systems as tools while interacting with them in ways that resemble human social interaction. To understand the relational contexts that arise when humans engage with anthropomorphic conversational agents, we need to expand existing human-computer interaction frameworks. Through three workshops with qualitative researchers, we found that the fundamental ontological and relational ambiguities inherent in anthropomorphic conversational agents make it difficult for individuals to maintain consistent relational stances toward them. Our findings indicate that people's articulated positioning toward such agents often differs from the relational dynamics that occur during interactions. We propose the concept of relational dissonance to help researchers, designers, and policymakers recognize the resulting tensions in the development, deployment, and governance of anthropomorphic conversational agents and address the need for relational transparency.
Exploring Synthesizable Chemical Space with Iterative Pathway Refinements
Venue: arXiv cs.LG 2026
Year: 2026

A well-known pitfall of molecular generative models is that they are not guaranteed to generate synthesizable molecules. Existing solutions for this problem often struggle to effectively navigate exponentially large combinatorial space of synthesizable molecules and suffer from poor coverage. To address this problem, we introduce ReaSyn, an iterative generative pathway refinement framework that obtains synthesizable analogs to input molecules by projecting them onto synthesizable space. Specifically, we propose a simple synthetic pathway representation that allows for generating pathways in both bottom-up and top-down traversal of synthetic trees. We design ReaSyn so that both bottom-up and top-down pathways can be sampled with a single unified autoregressive model. ReaSyn can thus iteratively refine subtrees of generated synthetic trees in a bidirectional manner. Further, we introduce a discrete flow model that refines the generated pathway at the entire pathway level with edit operations: insertion, deletion, and substitution. The iterative refinement cycle of (1) bottom-up decoding, (2) top-down decoding, and (3) holistic editing constitutes a powerful pathway reasoning strategy, allowing the model to explore the vast space of synthesizable molecules. Experimentally, ReaSyn achieves the highest reconstruction rate and pathway diversity in synthesizable molecule reconstruction and the highest optimization performance in synthesizable goal-directed molecular optimization, and significantly outperforms previous synthesizable projection methods in synthesizable hit expansion. These results highlight ReaSyn's superior ability to navigate combinatorially-large synthesizable chemical space.
RPG: A Repository Planning Graph for Unified and Scalable Codebase Generation
Venue: arXiv cs.CL 2026
Year: 2026

Large language models excel at generating individual functions or single files of code, yet generating complete repositories from scratch remains a fundamental challenge. This capability is key to building coherent software systems from high-level specifications and realizing the full potential of automated code generation. The process requires planning at two levels: deciding what features and modules to build (proposal stage) and defining their implementation details (implementation stage). Current approaches rely on natural language planning, which often produces unclear specifications, misaligned components, and brittle designs due to its inherent ambiguity and lack of structure. To address these limitations, we introduce the Repository Planning Graph (RPG), a structured representation that encodes capabilities, file structures, data flows, and functions in a unified graph. By replacing free-form natural language with an explicit blueprint, RPG enables consistent long-horizon planning for repository generation. Building on RPG, we develop ZeroRepo, a graph-driven framework that operates in three stages: proposal-level planning, implementation-level construction, and graph-guided code generation with test validation. To evaluate, we construct RepoCraft, a benchmark of six real-world projects with 1,052 tasks. On RepoCraft, ZeroRepo produces nearly 36K Code Lines and 445K Code Tokens, on average 3.9$\times$ larger than the strongest baseline (Claude Code), and 68$\times$ larger than other baselines. It achieves 81.5% coverage and 69.7% test accuracy, improving over Claude Code by 27.3 and 35.8 points. Further analysis shows that RPG models complex dependencies, enables more sophisticated planning through near-linear scaling, and improves agent understanding of repositories, thus accelerating localization. Our data and code are available at https://github.com/microsoft/RPG-ZeroRepo.
From Canopy to Ground via ForestGen3D: Learning Cross-Domain Generation of 3D Forest Structure from Aerial-to-Terrestrial LiDAR
Venue: arXiv cs.CV 2026
Year: 2026

The 3D structure of living and non-living components in ecosystems plays a critical role in determining ecological processes and feedbacks from both natural and human-driven disturbances. Anticipating the effects of wildfire, drought, disease, or atmospheric deposition depends on accurate characterization of 3D vegetation structure, yet widespread measurement remains prohibitively expensive and often infeasible. We present ForestGen3D, a cross-domain generative framework that preserves aerial LiDAR (ALS) observed 3D forest structure while inferring missing sub-canopy detail. ForestGen3D is based on conditional denoising diffusion probabilistic models trained on co-registered ALS and terrestrial LiDAR (TLS) data. The model generates realistic TLS-like point clouds that remain spatially consistent with ALS geometry, enabling landscape-scalable reconstruction of full vertical forest structure. We evaluate ForestGen3D at tree, plot, and landscape scales using real-world data from mixed conifer ecosystems, and show through qualitative and quantitative geometric and distributional analyses that it produces high-fidelity reconstructions closely matching TLS reference data in terms of 3D structural similarity and downstream biophysical metrics, including tree height, DBH, crown diameter, and crown volume. We further introduce and demonstrate the expected point containment (EPC) metric which serves as a practical proxy for generation quality in settings where TLS ground truth is unavailable. Our results demonstrate that ForestGen3D enhances the utility of ALS only environments by inferring ecologically plausible sub-canopy structure while faithfully preserving the landscape heterogeneity encoded in ALS observations, thereby providing a richer 3D representation for ecological analysis, structural fuel characterization and related remote sensing applications.
Domain-Specific Constitutional AI: Enhancing Safety in LLM-Powered Mental Health Chatbots
Venue: arXiv cs.AI 2026
Year: 2026

Mental health applications have emerged as a critical area in computational health, driven by rising global rates of mental illness, the integration of AI in psychological care, and the need for scalable solutions in underserved communities. These include therapy chatbots, crisis detection, and wellness platforms handling sensitive data, requiring specialized AI safety beyond general safeguards due to emotional vulnerability, risks like misdiagnosis or symptom exacerbation, and precise management of vulnerable states to avoid severe outcomes such as self-harm or loss of trust. Despite AI safety advances, general safeguards inadequately address mental health-specific challenges, including crisis intervention accuracy to avert escalations, therapeutic guideline adherence to prevent misinformation, scale limitations in resource-constrained settings, and adaptation to nuanced dialogues where generics may introduce biases or miss distress signals. We introduce an approach to apply Constitutional AI training with domain-specific mental health principles for safe, domain-adapted CAI systems in computational mental health applications.
Bayesian Ego-graph Inference for Networked Multi-Agent Reinforcement Learning
Venue: arXiv cs.MA 2026
Year: 2026

In networked multi-agent reinforcement learning (Networked-MARL), decentralized agents must act under local observability and constrained communication over fixed physical graphs. Existing methods often assume static neighborhoods, limiting adaptability to dynamic or heterogeneous environments. While centralized frameworks can learn dynamic graphs, their reliance on global state access and centralized infrastructure is impractical in real-world decentralized systems. We propose a stochastic graph-based policy for Networked-MARL, where each agent conditions its decision on a sampled subgraph over its local physical neighborhood. Building on this formulation, we introduce BayesG, a decentralized actor-framework that learns sparse, context-aware interaction structures via Bayesian variational inference. Each agent operates over an ego-graph and samples a latent communication mask to guide message passing and policy computation. The variational distribution is trained end-to-end alongside the policy using an evidence lower bound (ELBO) objective, enabling agents to jointly learn both interaction topology and decision-making strategies. BayesG outperforms strong MARL baselines on large-scale traffic control tasks with up to 167 agents, demonstrating superior scalability, efficiency, and performance.
FESTA: Functionally Equivalent Sampling for Trust Assessment of Multimodal LLMs
Venue: arXiv cs.AI 2026
Year: 2026

The accurate trust assessment of multimodal large language models (MLLMs) generated predictions, which can enable selective prediction and improve user confidence, is challenging due to the diverse multi-modal input paradigms. We propose Functionally Equivalent Sampling for Trust Assessment (FESTA), a multimodal input sampling technique for MLLMs, that generates an uncertainty measure based on the equivalent and complementary input samplings. The proposed task-preserving sampling approach for uncertainty quantification expands the input space to probe the consistency (through equivalent samples) and sensitivity (through complementary samples) of the model. FESTA uses only input-output access of the model (black-box), and does not require ground truth (unsupervised). The experiments are conducted with various off-the-shelf multi-modal LLMs, on both visual and audio reasoning tasks. The proposed FESTA uncertainty estimate achieves significant improvement (33.3% relative improvement for vision-LLMs and 29.6% relative improvement for audio-LLMs) in selective prediction performance, based on area-under-receiver-operating-characteristic curve (AUROC) metric in detecting mispredictions. The code implementation is open-sourced.
ISCS: Parameter-Guided Feature Pruning for Resource-Constrained Embodied Perception
Venue: arXiv cs.CV 2026
Year: 2026

Prior studies in embodied AI consistently show that robust perception is critical for human-robot interaction, yet deploying high-fidelity visual models on resource-constrained agents remains challenging due to limited on-device computation power and transmission latency. Exploiting the redundancy in latent representations could improve system efficiency, yet existing approaches often rely on costly dataset-specific ablation tests or heavy entropy models unsuitable for real-time edge-robot collaboration. We propose a generalizable, dataset-agnostic method to identify and selectively transmit structure-critical channels in pretrained encoders. Instead of brute-force empirical evaluations, our approach leverages intrinsic parameter statistics-weight variances and biases-to estimate channel importance. This analysis reveals a consistent organizational structure, termed the Invariant Salient Channel Space (ISCS), where Salient-Core channels capture dominant structures while Salient-Auxiliary channels encode fine visual details. Building on ISCS, we introduce a deterministic static pruning strategy that enables lightweight split-computing. Experiments across different datasets demonstrate that our method achieves a deterministic, ultra-low latency pipeline by bypassing heavy entropy modeling. Our method reduces end-to-end latency, providing a critical speed-accuracy trade-off for resource-constrained human-aware embodied systems.
Temporal Drift in Privacy Recall: Users Misremember From Verbatim Loss to Gist-Based Overexposure
Venue: arXiv cs.HC 2026
Year: 2026

With social media content traversing the different platforms, occasionally resurfacing after periods of time, users are increasingly prone to unintended disclosure resulting from a misremembered acceptance of privacy. Context collapse and interface cues are two factors considered by prior researchers, yet we know less about how time-lapse basically alters recall of past audiences destined for exposure. Likewise, the design space for mitigating this temporal exposure risk remains underexplored. Our work theorizes temporal drift in privacy recall as verbatim memory of prior settings blowing apart and eventually settling with gist-based heuristics, which more often than not select an audience larger than the original one. Grounded in memory research, contextual integrity, and usable privacy, we examine why such a drift occurs, why it tends to bias toward broader sharing, and how it compounds upon repeat exposure. Following that, we suggest provenance-forward interface schemes and a risk-based evaluation framework that mutates recall into recognition. The merit of our work lies in establishing a temporal awareness of privacy design as an essential safety rail against inadvertent overexposure.
Generalized Momenta-Based Koopman Formalism for Robust Control of Euler-Lagrangian Systems
Venue: arXiv cs.RO 2026
Year: 2026

This paper presents a novel Koopman operator formulation for Euler Lagrangian dynamics that employs an implicit generalized momentum-based state space representation, which decouples a known linear actuation channel from state dependent dynamics and makes the system more amenable to linear Koopman modeling. By leveraging this structural separation, the proposed formulation only requires to learn the unactuated dynamics rather than the complete actuation dependent system, thereby significantly reducing the number of learnable parameters, improving data efficiency, and lowering overall model complexity. In contrast, conventional explicit formulations inherently couple inputs with the state dependent terms in a nonlinear manner, making them more suitable for bilinear Koopman models, which are more computationally expensive to train and deploy. Notably, the proposed scheme enables the formulation of linear models that achieve superior prediction performance compared to conventional bilinear models while remaining substantially more efficient. To realize this framework, we present two neural network architectures that construct Koopman embeddings from actuated or unactuated data, enabling flexible and efficient modeling across different tasks. Robustness is ensured through the integration of a linear Generalized Extended State Observer (GESO), which explicitly estimates disturbances and compensates for them in real time. The combined momentum-based Koopman and GESO framework is validated through comprehensive trajectory tracking simulations and experiments on robotic manipulators, demonstrating superior accuracy, robustness, and learning efficiency relative to state of the art alternatives.
Better Late Than Never: Meta-Evaluation of Latency Metrics for Simultaneous Speech-to-Text Translation
Venue: arXiv cs.CL 2026
Year: 2026

Simultaneous speech-to-text translation systems must balance translation quality with latency. Although quality evaluation is well established, latency measurement remains a challenge. Existing metrics produce inconsistent results, especially in short-form settings with artificial presegmentation. We present the first comprehensive meta-evaluation of latency metrics across language pairs and systems. We uncover a structural bias in current metrics related to segmentation. We introduce YAAL (Yet Another Average Lagging) for a more accurate short-form evaluation and LongYAAL for unsegmented audio. We propose SoftSegmenter, a resegmentation tool based on soft word-level alignment. We show that YAAL and LongYAAL, together with SoftSegmenter, outperform popular latency metrics, enabling more reliable assessments of short- and long-form simultaneous speech translation systems. We implement all artifacts within the OmniSTEval toolkit: https://github.com/pe-trik/OmniSTEval.
Filling in the Clinical Gaps in Benchmark: Case for HealthBench for the Japanese medical system
Venue: arXiv cs.CL 2026
Year: 2026

This study investigates the applicability of HealthBench, a large-scale, rubric-based medical benchmark, to the Japanese context. Although robust evaluation frameworks are essential for the safe development of medical LLMs, resources in Japanese are scarce and often consist of translated multiple-choice questions. Our research addresses this issue in two ways. First, we establish a performance baseline by applying a machine-translated version of HealthBench's 5,000 scenarios to evaluate two models: a high-performing multilingual model (GPT-4.1) and a Japanese-native open-source model (LLM-jp-3.1). Secondly, we use an LLM-as-a-Judge approach to systematically classify the benchmark's scenarios and rubric criteria. This allows us to identify 'contextual gaps' where the content is misaligned with Japan's clinical guidelines, healthcare systems or cultural norms. Our findings reveal a modest performance drop in GPT-4.1 due to rubric mismatches, as well as a significant failure in the Japanese-native model, which lacked the required clinical completeness. Furthermore, our classification shows that, despite most scenarios being applicable, a significant proportion of the rubric criteria require localisation. This work underscores the limitations of direct benchmark translation and highlights the urgent need for a context-aware, localised adaptation, a "J-HealthBench", to ensure the reliable and safe evaluation of medical LLMs in Japan.
Flatness is Necessary, Neural Collapse is Not: Rethinking Generalization via Grokking
Venue: arXiv cs.LG 2026
Year: 2026

Neural collapse, i.e., the emergence of highly symmetric, class-wise clustered representations, is frequently observed in deep networks and is often assumed to reflect or enable generalization. In parallel, flatness of the loss landscape has been theoretically and empirically linked to generalization. Yet, the causal role of either phenomenon remains unclear: Are they prerequisites for generalization, or merely by-products of training dynamics? We disentangle these questions using grokking, a training regime in which memorization precedes generalization, allowing us to temporally separate generalization from training dynamics and we find that while both neural collapse and relative flatness emerge near the onset of generalization, only flatness consistently predicts it. Models encouraged to collapse or prevented from collapsing generalize equally well, whereas models regularized away from flat solutions exhibit delayed generalization, resembling grokking, even in architectures and datasets where it does not typically occur. Furthermore, we show theoretically that neural collapse leads to relative flatness under classical assumptions, explaining their empirical co-occurrence. Our results support the view that relative flatness is a potentially necessary and more fundamental property for generalization, and demonstrate how grokking can serve as a powerful probe for isolating its geometric underpinnings.
EigenSafe: A Spectral Framework for Learning-Based Probabilistic Safety Assessment
Venue: arXiv cs.RO 2026
Year: 2026

We present EigenSafe, an operator-theoretic framework for safety assessment of learning-enabled stochastic systems. In many robotic applications, the dynamics are inherently stochastic due to factors such as sensing noise and environmental disturbances, and it is challenging for conventional methods such as Hamilton-Jacobi reachability and control barrier functions to provide a well-calibrated safety critic that is tied to the actual safety probability. We derive a linear operator that governs the dynamic programming principle for safety probability, and find that its dominant eigenpair provides critical safety information for both individual state-action pairs and the overall closed-loop system. The proposed framework learns this dominant eigenpair, which can be used to either inform or constrain policy updates. We demonstrate that the learned eigenpair effectively facilitates safe reinforcement learning. Further, we validate its applicability in enhancing the safety of learned policies from imitation learning through robot manipulation experiments using a UR3 robotic arm in a food preparation task.
Accurate and Efficient Low-Rank Model Merging in Core Space
Venue: arXiv cs.CV 2026
Year: 2026

In this paper, we address the challenges associated with merging low-rank adaptations of large neural networks. With the rise of parameter-efficient adaptation techniques, such as Low-Rank Adaptation (LoRA), model fine-tuning has become more accessible. While fine-tuning models with LoRA is highly efficient, existing merging methods often sacrifice this efficiency by merging fully-sized weight matrices. We propose the Core Space merging framework, which enables the merging of LoRA-adapted models within a common alignment basis, thereby preserving the efficiency of low-rank adaptation while substantially improving accuracy across tasks. We further provide a formal proof that projection into Core Space ensures no loss of information and provide a complexity analysis showing the efficiency gains. Extensive empirical results demonstrate that Core Space significantly improves existing merging techniques and achieves state-of-the-art results on both vision and language tasks while utilizing a fraction of the computational resources. Codebase is available at https://github.com/apanariello4/core-space-merging.