OpenRaiser/Intern-Atlas huggingface dataset:
HyperHELM: Hyperbolic Hierarchy Encoding for mRNA Language Modeling
Venue: arXiv cs.LG 2025
Year: 2025

Language models are increasingly applied to biological sequences like proteins and mRNA, yet their default Euclidean geometry may mismatch the hierarchical structures inherent to biological data. While hyperbolic geometry provides a better alternative for accommodating hierarchical data, it has yet to find a way into language modeling for mRNA sequences. In this work, we introduce HyperHELM, a framework that implements masked language model pre-training in hyperbolic space for mRNA sequences. Using a hybrid design with hyperbolic layers atop Euclidean backbone, HyperHELM aligns learned representations with the biological hierarchy defined by the relationship between mRNA and amino acids. Across multiple multi-species datasets, it outperforms Euclidean baselines on 9 out of 10 tasks involving property prediction, with 10% improvement on average, and excels in out-of-distribution generalization to long and low-GC content sequences; for antibody region annotation, it surpasses hierarchy-aware Euclidean models by 3% in annotation accuracy. Our results highlight hyperbolic geometry as an effective inductive bias for hierarchical language modeling of mRNA sequences.
CEDex: Cross-Embodiment Dexterous Grasp Generation at Scale from Human-like Contact Representations
Venue: arXiv cs.RO 2025
Year: 2025

Cross-embodiment dexterous grasp synthesis refers to adaptively generating and optimizing grasps for various robotic hands with different morphologies. This capability is crucial for achieving versatile robotic manipulation in diverse environments and requires substantial amounts of reliable and diverse grasp data for effective model training and robust generalization. However, existing approaches either rely on physics-based optimization that lacks human-like kinematic understanding or require extensive manual data collection processes that are limited to anthropomorphic structures. In this paper, we propose CEDex, a novel cross-embodiment dexterous grasp synthesis method at scale that bridges human grasping kinematics and robot kinematics by aligning robot kinematic models with generated human-like contact representations. Given an object's point cloud and an arbitrary robotic hand model, CEDex first generates human-like contact representations using a Conditional Variational Auto-encoder pretrained on human contact data. It then performs kinematic human contact alignment through topological merging to consolidate multiple human hand parts into unified robot components, followed by a signed distance field-based grasp optimization with physics-aware constraints. Using CEDex, we construct the largest cross-embodiment grasp dataset to date, comprising 500K objects across four gripper types with 20M total grasps. Extensive experiments show that CEDex outperforms state-of-the-art approaches and our dataset benefits cross-embodiment grasp learning with high-quality diverse grasps.
CoTune: Co-evolutionary Configuration Tuning
Venue: arXiv cs.SE 2025
Year: 2025

To automatically tune configurations for the best possible system performance (e.g., runtime or throughput), much work has been focused on designing intelligent heuristics in a tuner. However, existing tuner designs have mostly ignored the presence of complex performance requirements (e.g., the latency shall ideally be 2 seconds), but simply assume that better performance is always more preferred. This would not only waste valuable information in a requirement but might also consume extensive resources to tune for a goal with little gain. Yet, prior studies have shown that simply incorporating the requirement as a tuning objective is problematic since the requirement might be too strict, harming convergence; or its highly diverse satisfactions might lead to premature convergence. In this paper, we propose CoTune, a tool that takes the information of a given target performance requirement into account through co-evolution. CoTune is unique in the sense that it creates an auxiliary performance requirement to be co-evolved with the configurations, which assists the target performance requirement when it becomes ineffective or even misleading, hence allowing the tuning to be guided by the requirement while being robust to its harm. Experiment results on 162 cases (nine systems and 18 requirements) reveal that CoTune considerably outperforms existing tuners, ranking as the best for 90% cases (against the 0%--35% for other tuners) with up to 2.9x overall improvements, while doing so under a much better efficiency.
Circuit-Aware Reward Training: A Mechanistic Framework for Longtail Robustness in RLHF
Venue: arXiv cs.LG 2025
Year: 2025

Reinforcement Learning from Human Feedback (RLHF) reward models exhibit systematic failures on longtail distributions, leading to reward hacking and misalignment. We propose a mechanistic interpretability framework that identifies specialized neural circuits responsible for rare-event processing in reward models. Drawing from recent advances showing distributed specialization for rare tokens in language models\citep{liu2025no, liu2025emergent}, we hypothesize that reward models also develop functionally distinct circuits for longtail scenarios. Our theoretical framework establishes formal connections between circuit specialization, reward generalization bounds, and longtail performance. We introduce \textbf{Circuit-Aware Reward Training (CART)}, which uses circuit analysis to guide data augmentation, regularization, and ensemble strategies. This approach provides both theoretical insights into reward model failures and practical interventions for improving longtail robustness.
Beyond Softmax: A Natural Parameterization for Categorical Random Variables
Venue: arXiv cs.LG 2025
Year: 2025

Latent categorical variables are frequently found in deep learning architectures. They can model actions in discrete reinforcement-learning environments, represent categories in latent-variable models, or express relations in graph neural networks. Despite their widespread use, their discrete nature poses significant challenges to gradient-descent learning algorithms. While a substantial body of work has offered improved gradient estimation techniques, we take a complementary approach. Specifically, we: 1) revisit the ubiquitous $\textit{softmax}$ function and demonstrate its limitations from an information-geometric perspective; 2) replace the $\textit{softmax}$ with the $\textit{catnat}$ function, a function composed of a sequence of hierarchical binary splits; we prove that this choice offers significant advantages to gradient descent due to the resulting diagonal Fisher Information Matrix. A rich set of experiments - including graph structure learning, variational autoencoders, and reinforcement learning - empirically show that the proposed function improves the learning efficiency and yields models characterized by consistently higher test performance. $\textit{Catnat}$ is simple to implement and seamlessly integrates into existing codebases. Moreover, it remains compatible with standard training stabilization techniques and, as such, offers a better alternative to the $\textit{softmax}$ function.
Who invented deep residual learning?
Venue: arXiv cs.LG 2025
Year: 2025

Modern AI is based on deep artificial neural networks (NNs). As of 2025, the most cited scientific article of the 21st century is an NN paper on deep residual learning with residual connections. Who invented this? We present a timeline of the evolution of deep residual learning.
Collaborating Vision, Depth, and Thermal Signals for Multi-Modal Tracking: Dataset and Algorithm
Venue: arXiv cs.CV 2025
Year: 2025

Existing multi-modal object tracking approaches primarily focus on dual-modal paradigms, such as RGB-Depth or RGB-Thermal, yet remain challenged in complex scenarios due to limited input modalities. To address this gap, this work introduces a novel multi-modal tracking task that leverages three complementary modalities, including visible RGB, Depth (D), and Thermal Infrared (TIR), aiming to enhance robustness in complex scenarios. To support this task, we construct a new multi-modal tracking dataset, coined RGBDT500, which consists of 500 videos with synchronised frames across the three modalities. Each frame provides spatially aligned RGB, depth, and thermal infrared images with precise object bounding box annotations. Furthermore, we propose a novel multi-modal tracker, dubbed RDTTrack. RDTTrack integrates tri-modal information for robust tracking by leveraging a pretrained RGB-only tracking model and prompt learning techniques. In specific, RDTTrack fuses thermal infrared and depth modalities under a proposed orthogonal projection constraint, then integrates them with RGB signals as prompts for the pre-trained foundation tracking model, effectively harmonising tri-modal complementary cues. The experimental results demonstrate the effectiveness and advantages of the proposed method, showing significant improvements over existing dual-modal approaches in terms of tracking accuracy and robustness in complex scenarios. The dataset and source code are publicly available at https://xuefeng-zhu5.github.io/RGBDT500.
Quantifying Generalisation in Imitation Learning
Venue: arXiv cs.LG 2025
Year: 2025

Imitation learning benchmarks often lack sufficient variation between training and evaluation, limiting meaningful generalisation assessment. We introduce Labyrinth, a benchmarking environment designed to test generalisation with precise control over structure, start and goal positions, and task complexity. It enables verifiably distinct training, evaluation, and test settings. Labyrinth provides a discrete, fully observable state space and known optimal actions, supporting interpretability and fine-grained evaluation. Its flexible setup allows targeted testing of generalisation factors and includes variants like partial observability, key-and-door tasks, and ice-floor hazards. By enabling controlled, reproducible experiments, Labyrinth advances the evaluation of generalisation in imitation learning and provides a valuable tool for developing more robust agents.
LOVE-R1: Advancing Long Video Understanding with an Adaptive Zoom-in Mechanism via Multi-Step Reasoning
Venue: arXiv cs.CV 2025
Year: 2025

Long video understanding is still challenging for recent Large Video-Language Models (LVLMs) due to the conflict between long-form temporal understanding and detailed spatial perception. LVLMs with a uniform frame sampling mechanism, which samples frames with an equal frame size and fixed sampling rate, inevitably sacrifice either temporal clues or spatial details, resulting in suboptimal solutions. To mitigate this dilemma, we propose LOVE-R1, a model that can adaptively zoom in on a video clip. The model is first provided with densely sampled frames but in a small resolution. If some spatial details are needed, the model can zoom in on a clip of interest with a large frame resolution based on its reasoning until key visual information is obtained. The whole process is implemented as a multi-step reasoning process. To train the reasoning ability, we first finetune the model on our collected 38k high-quality CoT data and enhance it with decoupled reinforcement finetuning. As outcome rewards can not provide fine-grained process supervision, we decouple multi-step reasoning into multiple single-step reasoning and optimize the internal zoom-in ability explicitly. Experiments on long video understanding benchmarks show that our model with the slow-fast adaptive frame sampling mechanism achieves a great trade-off between sampling density and frame resolutions, and LOVE-R1 outperforms our baseline Qwen2.5-VL by an average of 3.1% points across 4 common long video understanding benchmarks.
UP2You: Fast Reconstruction of Yourself from Unconstrained Photo Collections
Venue: arXiv cs.CV 2025
Year: 2025

We present UP2You, the first tuning-free solution for reconstructing high-fidelity 3D clothed portraits from extremely unconstrained in-the-wild 2D photos. Unlike previous approaches that require "clean" inputs (e.g., full-body images with minimal occlusions, or well-calibrated cross-view captures), UP2You directly processes raw, unstructured photographs, which may vary significantly in pose, viewpoint, cropping, and occlusion. Instead of compressing data into tokens for slow online text-to-3D optimization, we introduce a data rectifier paradigm that efficiently converts unconstrained inputs into clean, orthogonal multi-view images in a single forward pass within seconds, simplifying the 3D reconstruction. Central to UP2You is a pose-correlated feature aggregation module (PCFA), that selectively fuses information from multiple reference images w.r.t. target poses, enabling better identity preservation and nearly constant memory footprint, with more observations. We also introduce a perceiver-based multi-reference shape predictor, removing the need for pre-captured body templates. Extensive experiments on 4D-Dress, PuzzleIOI, and in-the-wild captures demonstrate that UP2You consistently surpasses previous methods in both geometric accuracy (Chamfer-15%, P2S-18% on PuzzleIOI) and texture fidelity (PSNR-21%, LPIPS-46% on 4D-Dress). UP2You is efficient (1.5 minutes per person), and versatile (supports arbitrary pose control, and training-free multi-garment 3D virtual try-on), making it practical for real-world scenarios where humans are casually captured. Both models and code will be released to facilitate future research on this underexplored task. Project Page: https://zcai0612.github.io/UP2You
Physical Layer Security over Fluid Reconfigurable Intelligent Surface-assisted Communication Systems
Venue: arXiv cs.IT 2025
Year: 2025

This letter investigates the secrecy performance of wireless communication systems assisted by a fluid reconfigurable intelligent surface (FRIS). Unlike conventional reconfigurable intelligent surfaces (RISs) with fixed geometries, FRISs dynamically select a subset of reflective elements based on real-time channel conditions, offering enhanced spatial diversity and adaptability. Using this foundation, we model a secure downlink scenario where a base station communicates with a legitimate user in the presence of an eavesdropper, and the propagation is assisted by a FRIS with a limited number of elements set to the ON state. We analyze the system's secrecy performance under spatial correlation by deriving analytical lower and upper bounds for the secrecy outage probability (SOP) and average secrecy capacity (ASC), respectively. Our results demonstrate that FRIS effectively enables secure communication under spatial correlation. Even with partial activation, FRIS significantly outperforms conventional RISs in enhancing secrecy performance under varying deployment densities and element correlations.
Between Help and Harm: An Evaluation of Mental Health Crisis Handling by LLMs
Venue: arXiv cs.CL 2025
Year: 2025

Large language model-powered chatbots have transformed how people seek information, especially in high-stakes contexts like mental health. Despite their support capabilities, safe detection and response to crises such as suicidal ideation and self-harm are still unclear, hindered by the lack of unified crisis taxonomies and clinical evaluation standards. We address this by creating: (1) a taxonomy of six crisis categories; (2) a dataset of over 2,000 inputs from 12 mental health datasets, classified into these categories; and (3) a clinical response assessment protocol. We also use LLMs to identify crisis inputs and audit five models for response safety and appropriateness. First, we built a clinical-informed crisis taxonomy and evaluation protocol. Next, we curated 2,252 relevant examples from over 239,000 user inputs, then tested three LLMs for automatic classification. In addition, we evaluated five models for the appropriateness of their responses to a user's crisis, graded on a 5-point Likert scale from harmful (1) to appropriate (5). While some models respond reliably to explicit crises, risks still exist. Many outputs, especially in self-harm and suicidal categories, are inappropriate or unsafe. Different models perform variably; some, like gpt-5-nano and deepseek-v3.2-exp, have low harm rates, but others, such as gpt-4o-mini and grok-4-fast, generate more unsafe responses. All models struggle with indirect signals, default replies, and context misalignment. These results highlight the urgent need for better safeguards, crisis detection, and context-aware responses in LLMs. They also show that alignment and safety practices, beyond scale, are crucial for reliable crisis support. Our taxonomy, datasets, and evaluation methods support ongoing AI mental health research, aiming to reduce harm and protect vulnerable users.
Towards Understanding the Shape of Representations in Protein Language Models
Venue: arXiv cs.LG 2025
Year: 2025

While protein language models (PLMs) are one of the most promising avenues of research for future de novo protein design, the way in which they transform sequences to hidden representations, as well as the information encoded in such representations is yet to be fully understood. Several works have attempted to propose interpretability tools for PLMs, but they have focused on understanding how individual sequences are transformed by such models. Therefore, the way in which PLMs transform the whole space of sequences along with their relations is still unknown. In this work we attempt to understand this transformed space of sequences by identifying protein structure and representation with square-root velocity (SRV) representations and graph filtrations. Both approaches naturally lead to a metric space in which pairs of proteins or protein representations can be compared with each other. We analyze different types of proteins from the SCOP dataset and show that the Karcher mean and effective dimension of the SRV shape space follow a non-linear pattern as a function of the layers in ESM2 models of different sizes. Furthermore, we use graph filtrations as a tool to study the context lengths at which models encode the structural features of proteins. We find that PLMs preferentially encode immediate as well as local relations between residues, but start to degrade for larger context lengths. The most structurally faithful encoding tends to occur close to, but before the last layer of the models, indicating that training a folding model ontop of these layers might lead to improved folding performance.
OpenGPT-4o-Image: A Comprehensive Dataset for Advanced Image Generation and Editing
Venue: arXiv cs.CV 2025
Year: 2025

The performance of unified multimodal models for image generation and editing is fundamentally constrained by the quality and comprehensiveness of their training data. While existing datasets have covered basic tasks like style transfer and simple object manipulation, they often lack the systematic structure and challenging scenarios required for real-world applications. To address this bottleneck, we introduce OpenGPT-4o-Image, a large-scale dataset constructed using a novel methodology that combines hierarchical task taxonomy with automated data generation. Our taxonomy not only includes fundamental capabilities such as text rendering and style control but also introduces highly practical yet challenging categories like scientific imagery for chemistry illustrations and complex instruction editing requiring simultaneous execution of multiple operations. Through an automated pipeline leveraging structured resource pools and GPT-4o, we generate 80k high-quality instruction-image pairs with controlled diversity, covering 11 major domains and 51 subtasks. Extensive experiments show that fine-tuning leading models on our dataset achieves significant performance gains across multiple benchmarks, with improvements of up to 18\% on editing tasks (UniWorld-V1 on ImgEdit-Bench) and 13% on generation tasks (Harmon on GenEval). Our work demonstrates that systematic data construction is key to advancing multimodal AI capabilities.
From Code to Action: Hierarchical Learning of Diffusion-VLM Policies
Venue: arXiv cs.RO 2025
Year: 2025

Imitation learning for robotic manipulation often suffers from limited generalization and data scarcity, especially in complex, long-horizon tasks. In this work, we introduce a hierarchical framework that leverages code-generating vision-language models (VLMs) in combination with low-level diffusion policies to effectively imitate and generalize robotic behavior. Our key insight is to treat open-source robotic APIs not only as execution interfaces but also as sources of structured supervision: the associated subtask functions - when exposed - can serve as modular, semantically meaningful labels. We train a VLM to decompose task descriptions into executable subroutines, which are then grounded through a diffusion policy trained to imitate the corresponding robot behavior. To handle the non-Markovian nature of both code execution and certain real-world tasks, such as object swapping, our architecture incorporates a memory mechanism that maintains subtask context across time. We find that this design enables interpretable policy decomposition, improves generalization when compared to flat policies and enables separate evaluation of high-level planning and low-level control.
Trajectory Prediction via Bayesian Intention Inference under Unknown Goals and Kinematics
Venue: arXiv cs.RO 2025
Year: 2025

This work introduces an adaptive Bayesian algorithm for real-time trajectory prediction via intention inference, where a target's intentions and motion characteristics are unknown and subject to change. The method concurrently estimates two critical variables: the target's current intention, modeled as a Markovian latent state, and an intention parameter that describes the target's adherence to a shortest-path policy. By integrating this joint update technique, the algorithm maintains robustness against abrupt intention shifts and unknown motion dynamics. A sampling-based trajectory prediction mechanism then exploits these adaptive estimates to generate probabilistic forecasts with quantified uncertainty. We validate the framework through numerical experiments: Ablation studies of two cases, and a 500-trial Monte Carlo analysis; Hardware demonstrations on quadrotor and quadrupedal platforms. Experimental results demonstrate that the proposed approach significantly outperforms non-adaptive and partially adaptive methods. The method operates in real time around 270 Hz without requiring training or detailed prior knowledge of target behavior, showcasing its applicability in various robotic systems.
Is Sequence Information All You Need for Bayesian Optimization of Antibodies?
Venue: arXiv cs.LG 2025
Year: 2025

Bayesian optimization is a natural candidate for the engineering of antibody therapeutic properties, which is often iterative and expensive. However, finding the optimal choice of surrogate model for optimization over the highly structured antibody space is difficult, and may differ depending on the property being optimized. Moreover, to the best of our knowledge, no prior works have attempted to incorporate structural information into antibody Bayesian optimization. In this work, we explore different approaches to incorporating structural information into Bayesian optimization, and compare them to a variety of sequence-only approaches on two different antibody properties, binding affinity and stability. In addition, we propose the use of a protein language model-based ``soft constraint,'' which helps guide the optimization to promising regions of the space. We find that certain types of structural information improve data efficiency in early optimization rounds for stability, but have equivalent peak performance. Moreover, when incorporating the protein language model soft constraint we find that the data efficiency gap is diminished for affinity and eliminated for stability, resulting in sequence-only methods that match the performance of structure-based methods, raising questions about the necessity of structure in Bayesian optimization for antibodies.