OpenRaiser/Intern-Atlas huggingface dataset:
Explainable Diagnosis Prediction through Neuro-Symbolic Integration
Venue: arXiv cs.LG 2025
Year: 2025

Diagnosis prediction is a critical task in healthcare, where timely and accurate identification of medical conditions can significantly impact patient outcomes. Traditional machine learning and deep learning models have achieved notable success in this domain but often lack interpretability which is a crucial requirement in clinical settings. In this study, we explore the use of neuro-symbolic methods, specifically Logical Neural Networks (LNNs), to develop explainable models for diagnosis prediction. Essentially, we design and implement LNN-based models that integrate domain-specific knowledge through logical rules with learnable thresholds. Our models, particularly $M_{\text{multi-pathway}}$ and $M_{\text{comprehensive}}$, demonstrate superior performance over traditional models such as Logistic Regression, SVM, and Random Forest, achieving higher accuracy (up to 80.52\%) and AUROC scores (up to 0.8457) in the case study of diabetes prediction. The learned weights and thresholds within the LNN models provide direct insights into feature contributions, enhancing interpretability without compromising predictive power. These findings highlight the potential of neuro-symbolic approaches in bridging the gap between accuracy and explainability in healthcare AI applications. By offering transparent and adaptable diagnostic models, our work contributes to the advancement of precision medicine and supports the development of equitable healthcare solutions. Future research will focus on extending these methods to larger and more diverse datasets to further validate their applicability across different medical conditions and populations.
Scale-Invariant Learning-to-Rank
Venue: arXiv cs.LG 2025
Year: 2025

At Expedia, learning-to-rank (LTR) models plays a key role on our website in sorting and presenting information more relevant to users, such as search filters, property rooms, amenities, and images. A major challenge in deploying these models is ensuring consistent feature scaling between training and production data, as discrepancies can lead to unreliable rankings when deployed. Normalization techniques like feature standardization and batch normalization could address these issues but are impractical in production due to latency impacts and the difficulty of distributed real-time inference. To address consistent feature scaling issue, we introduce a scale-invariant LTR framework which combines a deep and a wide neural network to mathematically guarantee scale-invariance in the model at both training and prediction time. We evaluate our framework in simulated real-world scenarios with injected feature scale issues by perturbing the test set at prediction time, and show that even with inconsistent train-test scaling, using framework achieves better performance than without.
A Census-Based Genetic Algorithm for Target Set Selection Problem in Social Networks
Venue: arXiv cs.NE 2025
Year: 2025

This paper considers the Target Set Selection (TSS) Problem in social networks, a fundamental problem in viral marketing. In the TSS problem, a graph and a threshold value for each vertex of the graph are given. We need to find a minimum size vertex subset to "activate" such that all graph vertices are activated at the end of the propagation process. Specifically, we propose a novel approach called "a census-based genetic algorithm" for the TSS problem. In our algorithm, we use the idea of a census to gather and store information about each individual in a population and collect census data from the individuals constructed during the algorithm's execution so that we can achieve greater diversity and avoid premature convergence at locally optimal solutions. We use two distinct census information: (a) for each individual, the algorithm stores how many times it has been identified during the execution (b) for each network node, the algorithm counts how many times it has been included in a solution. The proposed algorithm can also self-adjust by using a parameter specifying the aggressiveness employed in each reproduction method. Additionally, the algorithm is designed to run in a parallelized environment to minimize the computational cost and check each individual's feasibility. Moreover, our algorithm finds the optimal solution in all cases while experimenting on random graphs. Furthermore, we execute the proposed algorithm on 14 large graphs of real-life social network instances from the literature, improving around 9.57 solution size (on average) and 134 vertices (in total) compared to the best solutions obtained in previous studies.
DeepProtein: Deep Learning Library and Benchmark for Protein Sequence Learning
Venue: arXiv cs.LG 2025
Year: 2025

Deep learning has deeply influenced protein science, enabling breakthroughs in predicting protein properties, higher-order structures, and molecular interactions. This paper introduces DeepProtein, a comprehensive and user-friendly deep learning library tailored for protein-related tasks. It enables researchers to seamlessly address protein data with cutting-edge deep learning models. To assess model performance, we establish a benchmark evaluating different deep learning architectures across multiple protein-related tasks, including protein function prediction, subcellular localization prediction, protein-protein interaction prediction, and protein structure prediction. Furthermore, we introduce DeepProt-T5, a series of fine-tuned Prot-T5-based models that achieve state-of-the-art performance on four benchmark tasks, while demonstrating competitive results on six of others. Comprehensive documentation and tutorials are available which could ensure accessibility and support reproducibility. Built upon the widely used drug discovery library DeepPurpose, DeepProtein is publicly available at https://github.com/jiaqingxie/DeepProtein.
XChainWatcher: Monitoring and Identifying Attacks in Cross-Chain Bridges
Venue: arXiv cs.CR 2025
Year: 2025

Cross-chain bridges are a type of middleware for blockchain interoperability that supports the transfer of assets and data across blockchains. However, several of these bridges have vulnerabilities that have caused 3.2 billion dollars in losses since May 2021. Some studies have revealed the existence of these vulnerabilities, but there is little quantitative research available, and there are no safeguard mechanisms to protect bridges from such attacks. Furthermore, no studies are available on the practices of cross-chain bridges that can cause financial losses. We propose \toolName~(Cross-Chain Watcher), a modular and extensible logic-driven anomaly detector for cross-chain bridges. It operates in three main phases: (1) decoding events and transactions from multiple blockchains, (2) building logic relations from the extracted data, and (3) evaluating these relations against a set of detection rules. Using \toolName, we analyze data from two previously attacked bridges: the Ronin and Nomad bridges. \toolName~was able to successfully identify the transactions that led to losses of \$611M and \$190M (USD) and surpassed the results obtained by a reputable security firm in the latter. We not only uncover successful attacks, but also reveal other anomalies, such as 37 cross-chain transactions (\CCTX) that these bridges should not have accepted, failed attempts to exploit Nomad, over \$7.8M worth of tokens locked on one chain but never released on Ethereum, and \$200K lost by users due to inadequate interaction with bridges. We provide the first open dataset of 81,000 \CCTXS~across three blockchains, capturing more than \$4.2B in token transfers.
TPP-LLM: Modeling Temporal Point Processes by Efficiently Fine-Tuning Large Language Models
Venue: arXiv cs.LG 2025
Year: 2025

Temporal point processes (TPPs) are widely used to model the timing and occurrence of events in domains such as social networks, transportation systems, and e-commerce. In this paper, we introduce TPP-LLM, a novel framework that integrates large language models (LLMs) with TPPs to capture both the semantic and temporal aspects of event sequences. Unlike traditional methods that rely on categorical event type representations, TPP-LLM directly utilizes the textual descriptions of event types, enabling the model to capture rich semantic information embedded in the text. While LLMs excel at understanding event semantics, they are less adept at capturing temporal patterns. To address this, TPP-LLM incorporates temporal embeddings and employs parameter-efficient fine-tuning (PEFT) methods to effectively learn temporal dynamics without extensive retraining. This approach improves both predictive accuracy and computational efficiency. Experimental results across diverse real-world datasets demonstrate that TPP-LLM outperforms state-of-the-art baselines in sequence modeling and event prediction, highlighting the benefits of combining LLMs with TPPs.
A Practical Approach to Underwater Depth and Surface Normals Estimation
Venue: arXiv cs.CV 2025
Year: 2025

Monocular Depth and Surface Normals Estimation (MDSNE) is crucial for tasks such as 3D reconstruction, autonomous navigation, and underwater exploration. Current methods rely either on discriminative models, which struggle with transparent or reflective surfaces, or generative models, which, while accurate, are computationally expensive. This paper presents a novel deep learning model for MDSNE, specifically tailored for underwater environments, using a hybrid architecture that integrates Convolutional Neural Networks (CNNs) with Transformers, leveraging the strengths of both approaches. Training effective MDSNE models is often hampered by noisy real-world datasets and the limited generalization of synthetic datasets. To address this, we generate pseudo-labeled real data using multiple pre-trained MDSNE models. To ensure the quality of this data, we propose the Depth Normal Evaluation and Selection Algorithm (DNESA), which evaluates and selects the most reliable pseudo-labeled samples using domain-specific metrics. A lightweight student model is then trained on this curated dataset. Our model reduces parameters by 90% and training costs by 80%, allowing real-time 3D perception on resource-constrained devices. Key contributions include: a novel and efficient MDSNE model, the DNESA algorithm, a domain-specific data pipeline, and a focus on real-time performance and scalability. Designed for real-world underwater applications, our model facilitates low-cost deployments in underwater robots and autonomous vehicles, bridging the gap between research and practical implementation.
Anchors Aweigh! Sail for Optimal Unified Multi-Modal Representations
Venue: arXiv cs.LG 2025
Year: 2025

A unified representation space in multi-modal learning is essential for effectively integrating diverse data sources, such as text, images, and audio, to enhance efficiency and performance across various downstream tasks. Recent binding methods, such as ImageBind, typically rely on a single, fixed anchor modality for aligning multi-modal data. We mathematically analyze these fixed anchor binding methods and uncover significant limitations: (1) over-reliance on the choice of the anchor modality, (2) inadequate capture of intra-modal information, and (3) failure to account for cross-modal correlation among non-anchored modalities. To address these issues, we propose the need for adaptive anchor binding methods, exemplified by our framework CentroBind. The proposed method uses adaptively adjustable centroid-based anchors generated from all available modalities, leading to a balanced and rich representation space. We theoretically demonstrate that our approach captures three critical properties of multi-modal learning -- intra-modal learning, inter-modal learning, and multi-modal alignment -- while constructing a unified representation that spans all modalities. Experiments on both synthetic and real-world datasets show that adaptive anchor methods such as CentroBind consistently outperform fixed anchor binding methods, verifying our analysis.
DomainHarvester: Harvesting Infrequently Visited Yet Trustworthy Domain Names
Venue: arXiv cs.CR 2025
Year: 2025

In cybersecurity, allow lists play a crucial role in distinguishing safe websites from potential threats. Conventional methods for compiling allow lists, focusing heavily on website popularity, often overlook infrequently visited legitimate domains. This paper introduces DomainHarvester, a system aimed at generating allow lists that include trustworthy yet infrequently visited domains. By adopting an innovative bottom-up methodology that leverages the web's hyperlink structure, DomainHarvester identifies legitimate yet underrepresented domains. The system uses seed URLs to gather domain names, employing machine learning with a Transformer-based approach to assess their trustworthiness. DomainHarvester has developed two distinct allow lists: one with a global focus and another emphasizing local relevance. Compared to six existing top lists, DomainHarvester's allow lists show minimal overlaps, 4\% globally and 0.1\% locally, while significantly reducing the risk of including malicious domains, thereby enhancing security. The contributions of this research are substantial, illuminating the overlooked aspect of trustworthy yet underrepresented domains and introducing DomainHarvester, a system that goes beyond traditional popularity-based metrics. Our methodology enhances the inclusivity and precision of allow lists, offering significant advantages to users and businesses worldwide, especially in non-English speaking regions.
Safe Navigation in Unmapped Environments for Robotic Systems with Input Constraints
Venue: arXiv cs.RO 2025
Year: 2025

This paper presents an approach for navigation and control in unmapped environments under input and state constraints using a composite control barrier function (CBF). We consider the scenario where real-time perception feedback (e.g., LiDAR) is used online to construct a local CBF that models local state constraints (e.g., local safety constraints such as obstacles) in the a priori unmapped environment. The approach employs a soft-maximum function to synthesize a single time-varying CBF from the N most recently obtained local CBFs. Next, the input constraints are transformed into controller-state constraints through the use of control dynamics. Then, we use a soft-minimum function to compose the input constraints with the time-varying CBF that models the a priori unmapped environment. This composition yields a single relaxed CBF, which is used in a constrained optimization to obtain an optimal control that satisfies the state and input constraints. The approach is validated through simulations of a nonholonomic ground robot that is equipped with LiDAR and navigates an unmapped environment. The robot successfully navigates the environment while avoiding the a priori unmapped obstacles and satisfying both speed and input constraints.
Adversarial Decoding: Generating Readable Documents for Adversarial Objectives
Venue: arXiv cs.CL 2025
Year: 2025

We design, implement, and evaluate adversarial decoding, a new, generic text generation technique that produces readable documents for different adversarial objectives. Prior methods either produce easily detectable gibberish, or cannot handle objectives that include embedding similarity. In particular, they only work for direct attacks (such as jailbreaking) and cannot produce adversarial text for realistic indirect injection, e.g., documents that (1) are retrieved in RAG systems in response to broad classes of queries, and also (2) adversarially influence subsequent generation. We also show that fluency (low perplexity) is not sufficient to evade filtering. We measure the effectiveness of adversarial decoding for different objectives, including RAG poisoning, jailbreaking, and evasion of defensive filters, and demonstrate that it outperforms existing methods while producing readable adversarial documents.
GraphIC: A Graph-Based In-Context Example Retrieval Model for Multi-Step Reasoning
Venue: arXiv cs.AI 2025
Year: 2025

In-context learning (ICL) enhances large language models (LLMs) by incorporating demonstration examples, yet its effectiveness heavily depends on the quality of selected examples. Current methods typically use text embeddings to measure semantic similarity, which often introduces bias in multi-step reasoning tasks. This occurs because text embeddings contain irrelevant semantic information and lack deeper reasoning structures. To address this, we propose GraphIC, a graph-based retrieval model that leverages reasoning-aware representation and specialized similarity metric for in-context example retrieval. GraphIC first constructs thought graphs-directed, node-attributed graphs that explicitly model reasoning steps and their dependencies-for candidate examples and queries. This approach filters out superficial semantics while preserving essential reasoning processes. Next, GraphIC retrieves examples using a novel similarity metric tailored for these graphs, capturing sequential reasoning patterns and asymmetry between examples. Comprehensive evaluations across mathematical reasoning, code generation, and logical reasoning tasks demonstrate that GraphIC outperforms 10 baseline methods. Our results highlight the importance of reasoning-aware retrieval in ICL, offering a robust solution for enhancing LLM performance in multi-step reasoning scenarios.
CodePMP: Scalable Preference Model Pretraining for Large Language Model Reasoning
Venue: arXiv cs.AI 2025
Year: 2025

Large language models (LLMs) have made significant progress in natural language understanding and generation, driven by scalable pretraining and advanced finetuning. However, enhancing reasoning abilities in LLMs, particularly via reinforcement learning from human feedback (RLHF), remains challenging due to the scarcity of high-quality preference data, which is labor-intensive to annotate and crucial for reward model (RM) finetuning. To alleviate this issue, we introduce CodePMP, a scalable preference model pretraining (PMP) pipeline that utilizes a large corpus of synthesized code-preference pairs from publicly available high-quality source code. CodePMP improves RM finetuning efficiency by pretraining preference models on large-scale synthesized code-preference pairs. We evaluate CodePMP on mathematical reasoning tasks (GSM8K, MATH) and logical reasoning tasks (ReClor, LogiQA2.0), consistently showing significant improvements in reasoning performance of LLMs and highlighting the importance of scalable preference model pretraining for efficient reward modeling.
SCA: Improve Semantic Consistent in Unrestricted Adversarial Attacks via DDPM Inversion
Venue: arXiv cs.CV 2025
Year: 2025

Systems based on deep neural networks are vulnerable to adversarial attacks. Unrestricted adversarial attacks typically manipulate the semantic content of an image (e.g., color or texture) to create adversarial examples that are both effective and photorealistic. Recent works have utilized the diffusion inversion process to map images into a latent space, where high-level semantics are manipulated by introducing perturbations. However, they often result in substantial semantic distortions in the denoised output and suffer from low efficiency. In this study, we propose a novel framework called Semantic-Consistent Unrestricted Adversarial Attacks (SCA), which employs an inversion method to extract edit-friendly noise maps and utilizes a Multimodal Large Language Model (MLLM) to provide semantic guidance throughout the process. Under the condition of rich semantic information provided by MLLM, we perform the DDPM denoising process of each step using a series of edit-friendly noise maps and leverage DPM Solver++ to accelerate this process, enabling efficient sampling with semantic consistency. Compared to existing methods, our framework enables the efficient generation of adversarial examples that exhibit minimal discernible semantic changes. Consequently, we for the first time introduce Semantic-Consistent Adversarial Examples (SCAE). Extensive experiments and visualizations have demonstrated the high efficiency of SCA, particularly in being on average 12 times faster than the state-of-the-art attacks. Our code can be found at https://github.com/Pan-Zihao/SCA.
Fair Decentralized Learning
Venue: arXiv cs.LG 2025
Year: 2025

Decentralized learning (DL) is an emerging approach that enables nodes to collaboratively train a machine learning model without sharing raw data. In many application domains, such as healthcare, this approach faces challenges due to the high level of heterogeneity in the training data's feature space. Such feature heterogeneity lowers model utility and negatively impacts fairness, particularly for nodes with under-represented training data. In this paper, we introduce \textsc{Facade}, a clustering-based DL algorithm specifically designed for fair model training when the training data exhibits several distinct features. The challenge of \textsc{Facade} is to assign nodes to clusters, one for each feature, based on the similarity in the features of their local data, without requiring individual nodes to know apriori which cluster they belong to. \textsc{Facade} (1) dynamically assigns nodes to their appropriate clusters over time, and (2) enables nodes to collaboratively train a specialized model for each cluster in a fully decentralized manner. We theoretically prove the convergence of \textsc{Facade}, implement our algorithm, and compare it against three state-of-the-art baselines. Our experimental results on three datasets demonstrate the superiority of our approach in terms of model accuracy and fairness compared to all three competitors. Compared to the best-performing baseline, \textsc{Facade} on the CIFAR-10 dataset also reduces communication costs by 32.3\% to reach a target accuracy when cluster sizes are imbalanced.
ColaCare: Enhancing Electronic Health Record Modeling through Large Language Model-Driven Multi-Agent Collaboration
Venue: arXiv cs.LG 2025
Year: 2025

We introduce ColaCare, a framework that enhances Electronic Health Record (EHR) modeling through multi-agent collaboration driven by Large Language Models (LLMs). Our approach seamlessly integrates domain-specific expert models with LLMs to bridge the gap between structured EHR data and text-based reasoning. Inspired by the Multidisciplinary Team (MDT) approach used in clinical settings, ColaCare employs two types of agents: DoctorAgents and a MetaAgent, which collaboratively analyze patient data. Expert models process and generate predictions from numerical EHR data, while LLM agents produce reasoning references and decision-making reports within the MDT-driven collaborative consultation framework. The MetaAgent orchestrates the discussion, facilitating consultations and evidence-based debates among DoctorAgents, simulating diverse expertise in clinical decision-making. We additionally incorporate the Merck Manual of Diagnosis and Therapy (MSD) medical guideline within a retrieval-augmented generation (RAG) module for medical evidence support, addressing the challenge of knowledge currency. Extensive experiments conducted on three EHR datasets demonstrate ColaCare's superior performance in clinical mortality outcome and readmission prediction tasks, underscoring its potential to revolutionize clinical decision support systems and advance personalized precision medicine. All code, case studies and a questionnaire are available at the project website: https://colacare.netlify.app.