OpenRaiser/Intern-Atlas huggingface dataset:
Bidirectional Hierarchical Protein Multi-Modal Representation Learning
Venue: arXiv cs.LG 2025
Year: 2025

Protein representation learning is critical for numerous biological tasks. Recently, large transformer-based protein language models (pLMs) pretrained on large scale protein sequences have demonstrated significant success in sequence-based tasks. However, pLMs lack structural context. Conversely, graph neural networks (GNNs) designed to leverage 3D structural information have shown promising generalization in protein-related prediction tasks, but their effectiveness is often constrained by the scarcity of labeled structural data. Recognizing that sequence and structural representations are complementary perspectives of the same protein entity, we propose a multimodal bidirectional hierarchical fusion framework to effectively merge these modalities. Our framework employs attention and gating mechanisms to enable effective interaction between pLMs-generated sequential representations and GNN-extracted structural features, improving information exchange and enhancement across layers of the neural network. This bidirectional and hierarchical (Bi-Hierarchical) fusion approach leverages the strengths of both modalities to capture richer and more comprehensive protein representations. Based on the framework, we further introduce local Bi-Hierarchical Fusion with gating and global Bi-Hierarchical Fusion with multihead self-attention approaches. Our method demonstrates consistent improvements over strong baselines and existing fusion techniques in a variety of protein representation learning benchmarks, including enzyme EC classification, model quality assessment, protein-ligand binding affinity prediction, protein-protein binding site prediction, and B cell epitopes prediction. Our method establishes a new state-of-the-art for multimodal protein representation learning, emphasizing the efficacy of Bi-Hierarchical Fusion in bridging sequence and structural modalities.
Bottom-Up Scattering Information Perception Network for SAR target recognition
Venue: arXiv cs.CV 2025
Year: 2025

Deep learning methods based synthetic aperture radar (SAR) image target recognition tasks have been widely studied currently. The existing deep methods are insufficient to perceive and mine the scattering information of SAR images, resulting in performance bottlenecks and poor robustness of the algorithms. To this end, this paper proposes a novel bottom-up scattering information perception network for more interpretable target recognition by constructing the proprietary interpretation network for SAR images. Firstly, the localized scattering perceptron is proposed to replace the backbone feature extractor based on CNN networks to deeply mine the underlying scattering information of the target. Then, an unsupervised scattering part feature extraction model is proposed to robustly characterize the target scattering part information and provide fine-grained target representation. Finally, by aggregating the knowledge of target parts to form the complete target description, the interpretability and discriminative ability of the model is improved. We perform experiments on the FAST-Vehicle dataset and the SAR-ACD dataset to validate the performance of the proposed method.
ELT-Bench: An End-to-End Benchmark for Evaluating AI Agents on ELT Pipelines
Venue: arXiv cs.DB 2025
Year: 2025

Practitioners are increasingly turning to Extract-Load-Transform (ELT) pipelines with the widespread adoption of cloud data warehouses. However, designing these pipelines often involves significant manual work to ensure correctness. Recent advances in AI-based methods, which have shown strong capabilities in data tasks, such as text-to-SQL, present an opportunity to alleviate manual efforts in developing ELT pipelines. Unfortunately, current benchmarks in data engineering only evaluate isolated tasks, such as using data tools and writing data transformation queries, leaving a significant gap in evaluating AI agents for generating end-to-end ELT pipelines. To fill this gap, we introduce ELT-Bench, an end-to-end benchmark designed to assess the capabilities of AI agents to build ELT pipelines. ELT-Bench consists of 100 pipelines, including 835 source tables and 203 data models across various domains. By simulating realistic scenarios involving the integration of diverse data sources and the use of popular data tools, ELT-Bench evaluates AI agents' abilities in handling complex data engineering workflows. AI agents must interact with databases and data tools, write code and SQL queries, and orchestrate every pipeline stage. We evaluate two representative code agent frameworks, Spider-Agent and SWE-Agent, using six popular Large Language Models (LLMs) on ELT-Bench. The highest-performing agent, Spider-Agent Claude-3.7-Sonnet with extended thinking, correctly generates only 3.9% of data models, with an average cost of $4.30 and 89.3 steps per pipeline. Our experimental results demonstrate the challenges of ELT-Bench and highlight the need for a more advanced AI agent to reduce manual effort in ELT workflows. Our code and data are available at https://github.com/uiuc-kang-lab/ELT-Bench.
BIASINSPECTOR: Detecting Bias in Structured Data through LLM Agents
Venue: arXiv cs.AI 2025
Year: 2025

Detecting biases in structured data is a complex and time-consuming task. Existing automated techniques are limited in diversity of data types and heavily reliant on human case-by-case handling, resulting in a lack of generalizability. Currently, large language model (LLM)-based agents have made significant progress in data science, but their ability to detect data biases is still insufficiently explored. To address this gap, we introduce the first end-to-end, multi-agent synergy framework, BIASINSPECTOR, designed for automatic bias detection in structured data based on specific user requirements. It first develops a multi-stage plan to analyze user-specified bias detection tasks and then implements it with a diverse and well-suited set of tools. It delivers detailed results that include explanations and visualizations. To address the lack of a standardized framework for evaluating the capability of LLM agents to detect biases in data, we further propose a comprehensive benchmark that includes multiple evaluation metrics and a large set of test cases. Extensive experiments demonstrate that our framework achieves exceptional overall performance in structured data bias detection, setting a new milestone for fairer data applications.
Don't Lag, RAG: Training-Free Adversarial Detection Using RAG
Venue: arXiv cs.AI 2025
Year: 2025

Adversarial patch attacks pose a major threat to vision systems by embedding localized perturbations that mislead deep models. Traditional defense methods often require retraining or fine-tuning, making them impractical for real-world deployment. We propose a training-free Visual Retrieval-Augmented Generation (VRAG) framework that integrates Vision-Language Models (VLMs) for adversarial patch detection. By retrieving visually similar patches and images that resemble stored attacks in a continuously expanding database, VRAG performs generative reasoning to identify diverse attack types, all without additional training or fine-tuning. We extensively evaluate open-source large-scale VLMs, including Qwen-VL-Plus, Qwen2.5-VL-72B, and UI-TARS-72B-DPO, alongside Gemini-2.0, a closed-source model. Notably, the open-source UI-TARS-72B-DPO model achieves up to 95 percent classification accuracy, setting a new state-of-the-art for open-source adversarial patch detection. Gemini-2.0 attains the highest overall accuracy, 98 percent, but remains closed-source. Experimental results demonstrate VRAG's effectiveness in identifying a variety of adversarial patches with minimal human annotation, paving the way for robust, practical defenses against evolving adversarial patch attacks.
System Log Parsing with Large Language Models: A Review
Venue: arXiv cs.LG 2025
Year: 2025

Log data provides crucial insights for tasks like monitoring, root cause analysis, and anomaly detection. Due to the vast volume of logs, automated log parsing is essential to transform semi-structured log messages into structured representations. Recent advances in large language models (LLMs) have introduced the new research field of LLM-based log parsing. Despite promising results, there is no structured overview of the approaches in this relatively new research field with the earliest advances published in late 2023. This work systematically reviews 29 LLM-based log parsing methods. We benchmark seven of them on public datasets and critically assess their comparability and the reproducibility of their reported results. Our findings summarize the advances of this new research field, with insights on how to report results, which data sets, metrics and which terminology to use, and which inconsistencies to avoid, with code and results made publicly available for transparency.
Inter-event Interval Microscopy for Event Cameras
Venue: arXiv cs.CV 2025
Year: 2025

Event cameras, an innovative bio-inspired sensor, differ from traditional cameras by sensing changes in intensity rather than directly perceiving intensity and recording these variations as a continuous stream of "events". The intensity reconstruction from these sparse events has long been a challenging problem. Previous approaches mainly focused on transforming motion-induced events into videos or achieving intensity imaging for static scenes by integrating modulation devices at the event camera acquisition end. In this paper, for the first time, we achieve event-to-intensity conversion using a static event camera for both static and dynamic scenes in fluorescence microscopy. Unlike conventional methods that primarily rely on event integration, the proposed Inter-event Interval Microscopy (IEIM) quantifies the time interval between consecutive events at each pixel. With a fixed threshold in the event camera, the time interval can precisely represent the intensity. At the hardware level, the proposed IEIM integrates a pulse light modulation device within a microscope equipped with an event camera, termed Pulse Modulation-based Event-driven Fluorescence Microscopy. Additionally, we have collected IEIMat dataset under various scenes including high dynamic range and high-speed scenarios. Experimental results on the IEIMat dataset demonstrate that the proposed IEIM achieves superior spatial and temporal resolution, as well as a higher dynamic range, with lower bandwidth compared to other methods. The code and the IEIMat dataset will be made publicly available.
A Taxonomy of Self-Handover
Venue: arXiv cs.RO 2025
Year: 2025

Self-handover, transferring an object between one's own hands, is a common but understudied bimanual action. While it facilitates seamless transitions in complex tasks, the strategies underlying its execution remain largely unexplored. Here, we introduce the first systematic taxonomy of self-handover, derived from manual annotation of over 12 hours of cooking activity performed by 21 participants. Our analysis reveals that self-handover is not merely a passive transition, but a highly coordinated action involving anticipatory adjustments by both hands. As a step toward automated analysis of human manipulation, we further demonstrate the feasibility of classifying self-handover types using a state-of-the-art vision-language model. These findings offer fresh insights into bimanual coordination, underscoring the role of self-handover in enabling smooth task transitions-an ability essential for adaptive dual-arm robotics.
Finding large $k$-colorable induced subgraphs in (bull, chair)-free and (bull,E)-free graphs
Venue: arXiv cs.CC 2025
Year: 2025

We study the Max Partial $k$-Coloring problem, where we are given a vertex-weighted graph, and we ask for a maximum-weight induced subgraph that admits a proper $k$-coloring. For $k=1$ this problem coincides with Maximum Weight Independent Set, and for $k=2$ the problem is equivalent (by complementation) to Minimum Odd Cycle Transversal. Furthermore, it generalizes $k$-Coloring. We show that Max Partial $k$-Coloring on $n$-vertex instances with clique number $ω$ can be solved in time * $n^{\mathcal{O}(kω)}$ if the input graph excludes the bull and the chair as an induced subgraph, * $n^{\mathcal{O}(kω\log n)}$ if the input graph excludes the bull and E as an induced subgraph. This implies that $k$-Coloring can be solved in polynomial time in the former class, and in quasipolynomial-time in the latter one.
Wavelet Policy: Imitation Policy Learning in the Scale Domain with Wavelet Transforms
Venue: arXiv cs.RO 2025
Year: 2025

Recent imitation learning policies, often framed as time series prediction tasks, directly map robotic observations into the action space, such as high-dimensional visual data and proprioception. When deploying at the edge, we found the underutilization of frequency domain analysis in robotic manipulation trajectory prediction leads to neglecting the inherent rhythm information embedded within action sequences, resulting in errors at critical moments. To address this, we reframe imitation learning policies through the lens of time-scale domain and introduce the Wavelet Policy. This novel approach employs wavelet transforms (WT) and new Features Extractor (FE) for feature preprocessing and extracts multi-scale features using the Single Encoder to Multiple Decoder (SE2MD) architecture. Furthermore, to enhance feature mapping in the scale domain and appropriately increase model capacity, we introduce a Learnable Scale Domain Filter (LSDF) after each decoder, improving adaptability under different visual conditions. Our results show that the Wavelet Policy maintaining a comparable parameter count outperforms SOTA end-to-end methods on four challenging simulation robotic arm tasks and real tasks, especially at critical moments and remote settings simultaneously. We release the source code and model checkpoint of simulation task at https://github.com/lurenjia384/Wavelet_Policy.
Batch Aggregation: An Approach to Enhance Text Classification with Correlated Augmented Data
Venue: arXiv cs.CL 2025
Year: 2025

Natural language processing models often face challenges due to limited labeled data, especially in domain specific areas, e.g., clinical trials. To overcome this, text augmentation techniques are commonly used to increases sample size by transforming the original input data into artificial ones with the label preserved. However, traditional text classification methods ignores the relationship between augmented texts and treats them as independent samples which may introduce classification error. Therefore, we propose a novel approach called 'Batch Aggregation' (BAGG) which explicitly models the dependence of text inputs generated through augmentation by incorporating an additional layer that aggregates results from correlated texts. Through studying multiple benchmark data sets across different domains, we found that BAGG can improve classification accuracy. We also found that the increase of performance with BAGG is more obvious in domain specific data sets, with accuracy improvements of up to 10-29%. Through the analysis of benchmark data, the proposed method addresses limitations of traditional techniques and improves robustness in text classification tasks. Our result demonstrates that BAGG offers more robust results and outperforms traditional approaches when training data is limited.
Multi-level Neural Networks for high-dimensional parametric obstacle problems
Venue: arXiv cs.LG 2025
Year: 2025

A new method to solve computationally challenging (random) parametric obstacle problems is developed and analyzed, where the parameters can influence the related partial differential equation (PDE) and determine the position and surface structure of the obstacle. As governing equation, a stationary elliptic diffusion problem is assumed. The high-dimensional solution of the obstacle problem is approximated by a specifically constructed convolutional neural network (CNN). This novel algorithm is inspired by a finite element constrained multigrid algorithm to represent the parameter to solution map. This has two benefits: First, it allows for efficient practical computations since multi-level data is used as an explicit output of the NN thanks to an appropriate data preprocessing. This improves the efficacy of the training process and subsequently leads to small errors in the natural energy norm. Second, the comparison of the CNN to a multigrid algorithm provides means to carry out a complete a priori convergence and complexity analysis of the proposed NN architecture. Numerical experiments illustrate a state-of-the-art performance for this challenging problem.
CMaP-SAM: Contraction Mapping Prior for SAM-driven Few-shot Segmentation
Venue: arXiv cs.CV 2025
Year: 2025

Few-shot segmentation (FSS) aims to segment new classes using few annotated images. While recent FSS methods have shown considerable improvements by leveraging Segment Anything Model (SAM), they face two critical limitations: insufficient utilization of structural correlations in query images, and significant information loss when converting continuous position priors to discrete point prompts. To address these challenges, we propose CMaP-SAM, a novel framework that introduces contraction mapping theory to optimize position priors for SAM-driven few-shot segmentation. CMaP-SAM consists of three key components: (1) a contraction mapping module that formulates position prior optimization as a Banach contraction mapping with convergence guarantees. This module iteratively refines position priors through pixel-wise structural similarity, generating a converged prior that preserves both semantic guidance from reference images and structural correlations in query images; (2) an adaptive distribution alignment module bridging continuous priors with SAM's binary mask prompt encoder; and (3) a foreground-background decoupled refinement architecture producing accurate final segmentation masks. Extensive experiments demonstrate CMaP-SAM's effectiveness, achieving state-of-the-art performance with 71.1 mIoU on PASCAL-$5^i$ and 56.1 on COCO-$20^i$ datasets. Code is available at https://github.com/Chenfan0206/CMaP-SAM.
On the Performance of an Explainable Language Model on PubMedQA
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) have shown significant abilities in retrieving medical knowledge, reasoning over it and answering medical questions comparably to physicians. However, these models are not interpretable, hallucinate, are difficult to maintain and require enormous compute resources for training and inference. In this paper, we report results from Gyan, an explainable language model based on an alternative architecture, on the PubmedQA data set. The Gyan LLM is a compositional language model and the model is decoupled from knowledge. Gyan is trustable, transparent, does not hallucinate and does not require significant training or compute resources. Gyan is easily transferable across domains. Gyan-4.3 achieves SOTA results on PubmedQA with 87.1% accuracy compared to 82% by MedPrompt based on GPT-4 and 81.8% by Med-PaLM 2 (Google and DeepMind). We will be reporting results for other medical data sets - MedQA, MedMCQA, MMLU - Medicine in the future.
AI for Climate Finance: Agentic Retrieval and Multi-Step Reasoning for Early Warning System Investments
Venue: arXiv cs.CL 2025
Year: 2025

Tracking financial investments in climate adaptation is a complex and expertise-intensive task, particularly for Early Warning Systems (EWS), which lack standardized financial reporting across multilateral development banks (MDBs) and funds. To address this challenge, we introduce an LLM-based agentic AI system that integrates contextual retrieval, fine-tuning, and multi-step reasoning to extract relevant financial data, classify investments, and ensure compliance with funding guidelines. Our study focuses on a real-world application: tracking EWS investments in the Climate Risk and Early Warning Systems (CREWS) Fund. We analyze 25 MDB project documents and evaluate multiple AI-driven classification methods, including zero-shot and few-shot learning, fine-tuned transformer-based classifiers, chain-of-thought (CoT) prompting, and an agent-based retrieval-augmented generation (RAG) approach. Our results show that the agent-based RAG approach significantly outperforms other methods, achieving 87\% accuracy, 89\% precision, and 83\% recall. Additionally, we contribute a benchmark dataset and expert-annotated corpus, providing a valuable resource for future research in AI-driven financial tracking and climate finance transparency.
SpeakEasy: Enhancing Text-to-Speech Interactions for Expressive Content Creation
Venue: arXiv cs.HC 2025
Year: 2025

Novice content creators often invest significant time recording expressive speech for social media videos. While recent advancements in text-to-speech (TTS) technology can generate highly realistic speech in various languages and accents, many struggle with unintuitive or overly granular TTS interfaces. We propose simplifying TTS generation by allowing users to specify high-level context alongside their script. Our Wizard-of-Oz system, SpeakEasy, leverages user-provided context to inform and influence TTS output, enabling iterative refinement with high-level feedback. This approach was informed by two 8-subject formative studies: one examining content creators' experiences with TTS, and the other drawing on effective strategies from voice actors. Our evaluation shows that participants using SpeakEasy were more successful in generating performances matching their personal standards, without requiring significantly more effort than leading industry interfaces.
From Sound Workflow Nets to LTLf Declarative Specifications by Casting Three Spells
Venue: arXiv cs.LO 2025
Year: 2025

In process management, effective behavior modeling is essential for understanding execution dynamics and identifying potential issues. Two complementary paradigms have emerged in the pursuit of this objective: the imperative approach, representing all allowed runs of a system in a graph-based model, and the declarative one, specifying the rules that a run must not violate in a constraint-based specification. Extensive studies have been conducted on the synergy and comparisons of the two paradigms. To date, though, whether a declarative specification could be systematically derived from an imperative model such that the original behavior was fully preserved (and if so, how) remained an unanswered question. In this paper, we propose a three-fold contribution. (1) We introduce a systematic approach to synthesize declarative process specifications from safe and sound Workflow nets. (2) We prove behavioral equivalence of the input net with the output specification, alongside related guarantees. (3) We experimentally demonstrate the scalability and compactness of our encoding through tests conducted with synthetic and real-world testbeds.