OpenRaiser/Intern-Atlas huggingface dataset:
Multi-Objective-Guided Discrete Flow Matching for Controllable Biological Sequence Design
Venue: arXiv cs.LG 2025
Year: 2025

Designing biological sequences that satisfy multiple, often conflicting, functional and biophysical criteria remains a central challenge in biomolecule engineering. While discrete flow matching models have recently shown promise for efficient sampling in high-dimensional sequence spaces, existing approaches address only single objectives or require continuous embeddings that can distort discrete distributions. We present Multi-Objective-Guided Discrete Flow Matching (MOG-DFM), a general framework to steer any pretrained discrete flow matching generator toward Pareto-efficient trade-offs across multiple scalar objectives. At each sampling step, MOG-DFM computes a hybrid rank-directional score for candidate transitions and applies an adaptive hypercone filter to enforce consistent multi-objective progression. We also trained two unconditional discrete flow matching models, PepDFM for diverse peptide generation and EnhancerDFM for functional enhancer DNA generation, as base generation models for MOG-DFM. We demonstrate MOG-DFM's effectiveness in generating peptide binders optimized across five properties (hemolysis, non-fouling, solubility, half-life, and binding affinity), and in designing DNA sequences with specific enhancer classes and DNA shapes. In total, MOG-DFM proves to be a powerful tool for multi-property-guided biomolecule sequence design.
Physics-informed Multiple-Input Operators for efficient dynamic response prediction of structures
Venue: arXiv cs.LG 2025
Year: 2025

Finite element (FE) modeling is essential for structural analysis but remains computationally intensive, especially under dynamic loading. While operator learning models have shown promise in replicating static structural responses at FEM level accuracy, modeling dynamic behavior remains more challenging. This work presents a Multiple Input Operator Network (MIONet) that incorporates a second trunk network to explicitly encode temporal dynamics, enabling accurate prediction of structural responses under moving loads. Traditional DeepONet architectures using recurrent neural networks (RNNs) are limited by fixed time discretization and struggle to capture continuous dynamics. In contrast, MIONet predicts responses continuously over both space and time, removing the need for step wise modeling. It maps scalar inputs including load type, velocity, spatial mesh, and time steps to full field structural responses. To improve efficiency and enforce physical consistency, we introduce a physics informed loss based on dynamic equilibrium using precomputed mass, damping, and stiffness matrices, without solving the governing PDEs directly. Further, a Schur complement formulation reduces the training domain, significantly cutting computational costs while preserving global accuracy. The model is validated on both a simple beam and the KW-51 bridge, achieving FEM level accuracy within seconds. Compared to GRU based DeepONet, our model offers comparable accuracy with improved temporal continuity and over 100 times faster inference, making it well suited for real-time structural monitoring and digital twin applications.
Minimal Linear Codes Violating the Ashikhmin-Barg Condition from Arbitrary Projective Linear Codes
Venue: arXiv cs.IT 2025
Year: 2025

In recent years, there have been many constructions of minimal linear codes violating the Ashikhmin-Barg condition from Boolean functions, linear codes with few nonzero weights or partial difference sets. In this paper, we first give a general method to transform a minimal code satisfying the Ashikhmin-Barg condition to a minimal code violating the Ashikhmin-Barg condition. Then we give a construction of a minimal code satisfying the Ashikhmin-Barg condition from an arbitrary projective linear code. Hence an arbitrary projective linear code can be transformed to a minimal codes violating the Ashikhmin-Barg condition. Then we give infinite many families of minimal codes violating the Ashikhamin-Barg condition. Weight distributions of constructed minimal codes violating the Ashikhmin-Barg condition in this paper are determined. Many minimal linear codes violating the Ashikhmin-Barg condition with their minimum weights close to the optimal or the best known minimum weights of linear codes are constructed in this paper. Moreover, many infinite families of self-orthogonal binary minimal codes violating the Ashikhmin-Barg condition are also given.
HAMLET: Healthcare-focused Adaptive Multilingual Learning Embedding-based Topic Modeling
Venue: arXiv cs.CL 2025
Year: 2025

Traditional topic models often struggle with contextual nuances and fail to adequately handle polysemy and rare words. This limitation typically results in topics that lack coherence and quality. Large Language Models (LLMs) can mitigate this issue by generating an initial set of topics. However, these raw topics frequently lack refinement and representativeness, which leads to redundancy without lexical similarity and reduced interpretability. This paper introduces HAMLET, a graph-driven architecture for cross-lingual healthcare topic modeling that uses LLMs. The proposed approach leverages neural-enhanced semantic fusion to refine the embeddings of topics generated by the LLM. Instead of relying solely on statistical co-occurrence or human interpretation to extract topics from a document corpus, this method introduces a topic embedding refinement that uses Bidirectional Encoder Representations from Transformers (BERT) and Graph Neural Networks (GNN). After topic generation, a hybrid technique that involves BERT and Sentence-BERT (SBERT) is employed for embedding. The topic representations are further refined using a GNN, which establishes connections between documents, topics, words, similar topics, and similar words. A novel method is introduced to compute similarities. Consequently, the topic embeddings are refined, and the top k topics are extracted. Experiments were conducted using two healthcare datasets, one in English and one in French, from which six sets were derived. The results demonstrate the effectiveness of HAMLET.
Towards Actionable Pedagogical Feedback: A Multi-Perspective Analysis of Mathematics Teaching and Tutoring Dialogue
Venue: arXiv cs.CL 2025
Year: 2025

Effective feedback is essential for refining instructional practices in mathematics education, and researchers often turn to advanced natural language processing (NLP) models to analyze classroom dialogues from multiple perspectives. However, utterance-level discourse analysis encounters two primary challenges: (1) multifunctionality, where a single utterance may serve multiple purposes that a single tag cannot capture, and (2) the exclusion of many utterances from domain-specific discourse move classifications, leading to their omission in feedback. To address these challenges, we proposed a multi-perspective discourse analysis that integrates domain-specific talk moves with dialogue act (using the flattened multi-functional SWBD-MASL schema with 43 tags) and discourse relation (applying Segmented Discourse Representation Theory with 16 relations). Our top-down analysis framework enables a comprehensive understanding of utterances that contain talk moves, as well as utterances that do not contain talk moves. This is applied to two mathematics education datasets: TalkMoves (teaching) and SAGA22 (tutoring). Through distributional unigram analysis, sequential talk move analysis, and multi-view deep dive, we discovered meaningful discourse patterns, and revealed the vital role of utterances without talk moves, demonstrating that these utterances, far from being mere fillers, serve crucial functions in guiding, acknowledging, and structuring classroom discourse. These insights underscore the importance of incorporating discourse relations and dialogue acts into AI-assisted education systems to enhance feedback and create more responsive learning environments. Our framework may prove helpful for providing human educator feedback, but also aiding in the development of AI agents that can effectively emulate the roles of both educators and students.
A Generative Re-ranking Model for List-level Multi-objective Optimization at Taobao
Venue: arXiv cs.IR 2025
Year: 2025

E-commerce recommendation systems aim to generate ordered lists of items for customers, optimizing multiple business objectives, such as clicks, conversions and Gross Merchandise Volume (GMV). Traditional multi-objective optimization methods like formulas or Learning-to-rank (LTR) models take effect at item-level, neglecting dynamic user intent and contextual item interactions. List-level multi-objective optimization in the re-ranking stage can overcome this limitation, but most current re-ranking models focus more on accuracy improvement with context. In addition, re-ranking is faced with the challenges of time complexity and diversity. In light of this, we propose a novel end-to-end generative re-ranking model named Sequential Ordered Regression Transformer-Generator (SORT-Gen) for the less-studied list-level multi-objective optimization problem. Specifically, SORT-Gen is divided into two parts: 1)Sequential Ordered Regression Transformer innovatively uses Transformer and ordered regression to accurately estimate multi-objective values for variable-length sub-lists. 2)Mask-Driven Fast Generation Algorithm combines multi-objective candidate queues, efficient item selection and diversity mechanism into model inference, providing a fast online list generation method. Comprehensive online experiments demonstrate that SORT-Gen brings +4.13% CLCK and +8.10% GMV for Baiyibutie, a notable Mini-app of Taobao. Currently, SORT-Gen has been successfully deployed in multiple scenarios of Taobao App, serving for a vast number of users.
Measuring General Intelligence with Generated Games
Venue: arXiv cs.AI 2025
Year: 2025

We present gg-bench, a collection of game environments designed to evaluate general reasoning capabilities in language models. Unlike most static benchmarks, gg-bench is a data generating process where new evaluation instances can be generated at will. In particular, gg-bench is synthetically generated by (1) using a large language model (LLM) to generate natural language descriptions of novel games, (2) using the LLM to implement each game in code as a Gym environment, and (3) training reinforcement learning (RL) agents via self-play on the generated games. We evaluate language models by their winrate against these RL agents by prompting models with the game description, current board state, and a list of valid moves, after which models output the moves they wish to take. gg-bench is challenging: state-of-the-art LLMs such as GPT-4o and Claude 3.7 Sonnet achieve winrates of 7-9% on gg-bench using in-context learning, while reasoning models such as o1, o3-mini and DeepSeek-R1 achieve average winrates of 31-36%. We release the generated games, data generation process, and evaluation code in order to support future modeling work and expansion of our benchmark.
Compression, Regularity, Randomness and Emergent Structure: Rethinking Physical Complexity in the Data-Driven Era
Venue: arXiv cs.LG 2025
Year: 2025

Complexity science offers a wide range of measures for quantifying unpredictability, structure, and information. Yet, a systematic conceptual organization of these measures is still missing. We present a unified framework that locates statistical, algorithmic, and dynamical measures along three axes (regularity, randomness, and complexity) and situates them in a common conceptual space. We map statistical, algorithmic, and dynamical measures into this conceptual space, discussing their computational accessibility and approximability. This taxonomy reveals the deep challenges posed by uncomputability and highlights the emergence of modern data-driven methods (including autoencoders, latent dynamical models, symbolic regression, and physics-informed neural networks) as pragmatic approximations to classical complexity ideals. Latent spaces emerge as operational arenas where regularity extraction, noise management, and structured compression converge, bridging theoretical foundations with practical modeling in high-dimensional systems. We close by outlining implications for physics-informed AI and AI-guided discovery in complex physical systems, arguing that classical questions of complexity remain central to next-generation scientific modeling.
Incomplete In-context Learning
Venue: arXiv cs.CV 2025
Year: 2025

Large vision language models (LVLMs) achieve remarkable performance through Vision In-context Learning (VICL), a process that depends significantly on demonstrations retrieved from an extensive collection of annotated examples (retrieval database). Existing studies often assume that the retrieval database contains annotated examples for all labels. However, in real-world scenarios, delays in database updates or incomplete data annotation may result in the retrieval database containing labeled samples for only a subset of classes. We refer to this phenomenon as an \textbf{incomplete retrieval database} and define the in-context learning under this condition as \textbf{Incomplete In-context Learning (IICL)}. To address this challenge, we propose \textbf{Iterative Judgments and Integrated Prediction (IJIP)}, a two-stage framework designed to mitigate the limitations of IICL. The Iterative Judgments Stage reformulates an \(\boldsymbol{m}\)-class classification problem into a series of \(\boldsymbol{m}\) binary classification tasks, effectively converting the IICL setting into a standard VICL scenario. The Integrated Prediction Stage further refines the classification process by leveraging both the input image and the predictions from the Iterative Judgments Stage to enhance overall classification accuracy. IJIP demonstrates considerable performance across two LVLMs and two datasets under three distinct conditions of label incompleteness, achieving the highest accuracy of 93.9\%. Notably, even in scenarios where labels are fully available, IJIP still achieves the best performance of all six baselines. Furthermore, IJIP can be directly applied to \textbf{Prompt Learning} and is adaptable to the \textbf{text domain}.
Synthetic Similarity Search in Automotive Production
Venue: arXiv cs.CV 2025
Year: 2025

Visual quality inspection in automotive production is essential for ensuring the safety and reliability of vehicles. Computer vision (CV) has become a popular solution for these inspections due to its cost-effectiveness and reliability. However, CV models require large, annotated datasets, which are costly and time-consuming to collect. To reduce the need for extensive training data, we propose a novel image classification pipeline that combines similarity search using a vision-based foundation model with synthetic data. Our approach leverages a DINOv2 model to transform input images into feature vectors, which are then compared to pre-classified reference images using cosine distance measurements. By utilizing synthetic data instead of real images as references, our pipeline achieves high classification accuracy without relying on real data. We evaluate this approach in eight real-world inspection scenarios and demonstrate that it meets the high performance requirements of production environments.
Reconfiguring Multiple Connected Components with Size Multiset Constraints
Venue: arXiv cs.DS 2025
Year: 2025

We propose a novel generalization of Independent Set Reconfiguration (ISR): Connected Components Reconfiguration (CCR). In CCR, we are given a graph $G$, two vertex subsets $A$ and $B$, and a multiset $\mathcal{M}$ of positive integers. The question is whether $A$ and $B$ are reconfigurable under a certain rule, while ensuring that each vertex subset induces connected components whose sizes match the multiset $\mathcal{M}$. ISR is a special case of CCR where $\mathcal{M}$ only contains 1. We also propose new reconfiguration rules: component jumping (CJ) and component sliding (CS), which regard connected components as tokens. Since CCR generalizes ISR, the problem is PSPACE-complete. In contrast, we show three positive results: First, CCR-CS and CCR-CJ are solvable in linear and quadratic time, respectively, when $G$ is a path. Second, we show that CCR-CS is solvable in linear time for cographs. Third, when $\mathcal{M}$ contains only the same elements (i.e., all connected components have the same size), we show that CCR-CJ is solvable in linear time if $G$ is chordal. The second and third results generalize known results for ISR and exhibit an interesting difference between the reconfiguration rules.
Cache-Efficient Posterior Sampling for Reinforcement Learning with LLM-Derived Priors Across Discrete and Continuous Domains
Venue: arXiv cs.LG 2025
Year: 2025

Integrating large language models (LLMs) as priors in reinforcement learning (RL) offers significant advantages but comes with substantial computational costs. We present a principled cache-efficient framework for posterior sampling with LLM-derived priors that dramatically reduces these costs while maintaining high performance. At the core of our approach is an adaptive caching mechanism, where cache parameters are meta-optimized using surrogate gradients derived from policy performance. This design enables efficient inference across both discrete text environments (e.g., TextWorld, ALFWorld) and continuous control domains (e.g., MuJoCo), achieving a 3.8--4.7$\times$ reduction in LLM queries and 4.0--12.0$\times$ lower median latencies (85--93\,ms on a consumer GPU) while retaining 96--98\% of uncached performance. Our theoretical analysis provides KL divergence bounds on approximation quality, validated empirically. The framework extends to offline RL, where our CQL-Prior variant improves performance by 14--29\% and reduces training time by 38--40\%. Extensive evaluations across a diverse suite of eight tasks demonstrate the generalizability and practical viability of LLM-guided RL in resource-constrained settings.
Drive Fast, Learn Faster: On-Board RL for High Performance Autonomous Racing
Venue: arXiv cs.RO 2025
Year: 2025

Autonomous racing presents unique challenges due to its non-linear dynamics, the high speed involved, and the critical need for real-time decision-making under dynamic and unpredictable conditions. Most traditional Reinforcement Learning (RL) approaches rely on extensive simulation-based pre-training, which faces crucial challenges in transfer effectively to real-world environments. This paper introduces a robust on-board RL framework for autonomous racing, designed to eliminate the dependency on simulation-based pre-training enabling direct real-world adaptation. The proposed system introduces a refined Soft Actor-Critic (SAC) algorithm, leveraging a residual RL structure to enhance classical controllers in real-time by integrating multi-step Temporal-Difference (TD) learning, an asynchronous training pipeline, and Heuristic Delayed Reward Adjustment (HDRA) to improve sample efficiency and training stability. The framework is validated through extensive experiments on the F1TENTH racing platform, where the residual RL controller consistently outperforms the baseline controllers and achieves up to an 11.5 % reduction in lap times compared to the State-of-the-Art (SotA) with only 20 min of training. Additionally, an End-to-End (E2E) RL controller trained without a baseline controller surpasses the previous best results with sustained on-track learning. These findings position the framework as a robust solution for high-performance autonomous racing and a promising direction for other real-time, dynamic autonomous systems.
SAEN-BGS: Energy-Efficient Spiking AutoEncoder Network for Background Subtraction
Venue: arXiv cs.CV 2025
Year: 2025

Background subtraction (BGS) is utilized to detect moving objects in a video and is commonly employed at the onset of object tracking and human recognition processes. Nevertheless, existing BGS techniques utilizing deep learning still encounter challenges with various background noises in videos, including variations in lighting, shifts in camera angles, and disturbances like air turbulence or swaying trees. To address this problem, we design a spiking autoencoder network, termed SAEN-BGS, based on noise resilience and time-sequence sensitivity of spiking neural networks (SNNs) to enhance the separation of foreground and background. To eliminate unnecessary background noise and preserve the important foreground elements, we begin by creating the continuous spiking conv-and-dconv block, which serves as the fundamental building block for the decoder in SAEN-BGS. Moreover, in striving for enhanced energy efficiency, we introduce a novel self-distillation spiking supervised learning method grounded in ANN-to-SNN frameworks, resulting in decreased power consumption. In extensive experiments conducted on CDnet-2014 and DAVIS-2016 datasets, our approach demonstrates superior segmentation performance relative to other baseline methods, even when challenged by complex scenarios with dynamic backgrounds.
Few-shot Semantic Encoding and Decoding for Video Surveillance
Venue: arXiv cs.CV 2025
Year: 2025

With the continuous increase in the number and resolution of video surveillance cameras, the burden of transmitting and storing surveillance video is growing. Traditional communication methods based on Shannon's theory are facing optimization bottlenecks. Semantic communication, as an emerging communication method, is expected to break through this bottleneck and reduce the storage and transmission consumption of video. Existing semantic decoding methods often require many samples to train the neural network for each scene, which is time-consuming and labor-intensive. In this study, a semantic encoding and decoding method for surveillance video is proposed. First, the sketch was extracted as semantic information, and a sketch compression method was proposed to reduce the bit rate of semantic information. Then, an image translation network was proposed to translate the sketch into a video frame with a reference frame. Finally, a few-shot sketch decoding network was proposed to reconstruct video from sketch. Experimental results showed that the proposed method achieved significantly better video reconstruction performance than baseline methods. The sketch compression method could effectively reduce the storage and transmission consumption of semantic information with little compromise on video quality. The proposed method provides a novel semantic encoding and decoding method that only needs a few training samples for each surveillance scene, thus improving the practicality of the semantic communication system.