OpenRaiser/Intern-Atlas huggingface dataset:
A million-scale dataset and generalizable foundation model for nanomaterial-protein interactions
Venue: arXiv cs.LG 2025
Year: 2025

Unlocking the potential of nanomaterials in medicine and environmental science hinges on understanding their interactions with proteins, a complex decision space where AI is poised to make a transformative impact. However, progress has been hindered by limited datasets and the restricted generalizability of existing models. Here, we propose NanoPro-3M, the largest nanomaterial-protein interaction dataset to date, comprising over 3.2 million samples and 37,000 unique proteins. Leveraging this, we present NanoProFormer, a foundational model that predicts nanomaterial-protein affinities through multimodal representation learning, demonstrating strong generalization, handling missing features, and unseen nanomaterials or proteins. We show that multimodal modeling significantly outperforms single-modality approaches and identifies key determinants of corona formation. Furthermore, we demonstrate its applicability to a range of downstream tasks through zero-shot inference and fine-tuning. Together, this work establishes a solid foundation for high-performance and generalized prediction of nanomaterial-protein interaction endpoints, reducing experimental reliance and accelerating various in vitro applications.
Breaking the Illusion of Security via Interpretation: Interpretable Vision Transformer Systems under Attack
Venue: arXiv cs.CR 2025
Year: 2025

Vision transformer (ViT) models, when coupled with interpretation models, are regarded as secure and challenging to deceive, making them well-suited for security-critical domains such as medical applications, autonomous vehicles, drones, and robotics. However, successful attacks on these systems can lead to severe consequences. Recent research on threats targeting ViT models primarily focuses on generating the smallest adversarial perturbations that can deceive the models with high confidence, without considering their impact on model interpretations. Nevertheless, the use of interpretation models can effectively assist in detecting adversarial examples. This study investigates the vulnerability of transformer models to adversarial attacks, even when combined with interpretation models. We propose an attack called "AdViT" that generates adversarial examples capable of misleading both a given transformer model and its coupled interpretation model. Through extensive experiments on various transformer models and two transformer-based interpreters, we demonstrate that AdViT achieves a 100% attack success rate in both white-box and black-box scenarios. In white-box scenarios, it reaches up to 98% misclassification confidence, while in black-box scenarios, it reaches up to 76% misclassification confidence. Remarkably, AdViT consistently generates accurate interpretations in both scenarios, making the adversarial examples more difficult to detect.
WebGuard: Building a Generalizable Guardrail for Web Agents
Venue: arXiv cs.AI 2025
Year: 2025

The rapid development of autonomous web agents powered by Large Language Models (LLMs), while greatly elevating efficiency, exposes the frontier risk of taking unintended or harmful actions. This situation underscores an urgent need for effective safety measures, akin to access controls for human users. To address this critical challenge, we introduce WebGuard, the first comprehensive dataset designed to support the assessment of web agent action risks and facilitate the development of guardrails for real-world online environments. In doing so, WebGuard specifically focuses on predicting the outcome of state-changing actions and contains 4,939 human-annotated actions from 193 websites across 22 diverse domains, including often-overlooked long-tail websites. These actions are categorized using a novel three-tier risk schema: SAFE, LOW, and HIGH. The dataset includes designated training and test splits to support evaluation under diverse generalization settings. Our initial evaluations reveal a concerning deficiency: even frontier LLMs achieve less than 60% accuracy in predicting action outcomes and less than 60% recall in lagging HIGH-risk actions, highlighting the risks of deploying current-generation agents without dedicated safeguards. We therefore investigate fine-tuning specialized guardrail models using WebGuard. We conduct comprehensive evaluations across multiple generalization settings and find that a fine-tuned Qwen2.5VL-7B model yields a substantial improvement in performance, boosting accuracy from 37% to 80% and HIGH-risk action recall from 20% to 76%. Despite these improvements, the performance still falls short of the reliability required for high-stakes deployment, where guardrails must approach near-perfect accuracy and recall.
Language Models as Ontology Encoders
Venue: arXiv cs.AI 2025
Year: 2025

OWL (Web Ontology Language) ontologies which are able to formally represent complex knowledge and support semantic reasoning have been widely adopted across various domains such as healthcare and bioinformatics. Recently, ontology embeddings have gained wide attention due to its potential to infer plausible new knowledge and approximate complex reasoning. However, existing methods face notable limitations: geometric model-based embeddings typically overlook valuable textual information, resulting in suboptimal performance, while the approaches that incorporate text, which are often based on language models, fail to preserve the logical structure. In this work, we propose a new ontology embedding method OnT, which tunes a Pretrained Language Model (PLM) via geometric modeling in a hyperbolic space for effectively incorporating textual labels and simultaneously preserving class hierarchies and other logical relationships of Description Logic EL. Extensive experiments on four real-world ontologies show that OnT consistently outperforms the baselines including the state-of-the-art across both tasks of prediction and inference of axioms. OnT also demonstrates strong potential in real-world applications, indicated by its robust transfer learning abilities and effectiveness in real cases of constructing a new ontology from SNOMED CT. Data and code are available at https://github.com/HuiYang1997/OnT.
Solo Connection: A Parameter Efficient Fine-Tuning Technique for Transformers
Venue: arXiv cs.LG 2025
Year: 2025

Parameter efficient fine tuning (PEFT) is a versatile and extensible approach for adapting a Large Language Model (LLM) for newer tasks. One of the most prominent PEFT approaches, Low Rank Adaptation (LoRA), primarily focuses on adjusting the attention weight matrices within individual decoder blocks of a Generative Pre trained Transformer (GPT2). In contrast, we introduce Solo Connection a novel method that adapts the representation at the decoder-block level rather than modifying individual weight matrices. Not only does Solo Connection outperform LoRA on E2E natural language generation benchmarks, but it also reduces the number of trainable parameters by 59% relative to LoRA and by more than 99% compared to full fine-tuning of GPT2, an early version of Large Language Models (LLMs). Solo Connection is also motivated by homotopy theory: we introduce a trainable linear transformation that gradually interpolates between a zero vector and the task-specific representation, enabling smooth and stable adaptation over time. While skip connections in the original 12 layer GPT2 are typically confined to individual decoder blocks, subsequent GPT2 variants scale up to 48 layers, and even larger language models can include 128 or more decoder blocks. These expanded architectures underscore the need to revisit how skip connections are employed during fine-tuning. This paper focuses on long skip connections that link outputs of different decoder blocks, potentially enhancing the model's ability to adapt to new tasks while leveraging pre-trained knowledge.
RaMen: Multi-Strategy Multi-Modal Learning for Bundle Construction
Venue: arXiv cs.IR 2025
Year: 2025

Existing studies on bundle construction have relied merely on user feedback via bipartite graphs or enhanced item representations using semantic information. These approaches fail to capture elaborate relations hidden in real-world bundle structures, resulting in suboptimal bundle representations. To overcome this limitation, we propose RaMen, a novel method that provides a holistic multi-strategy approach for bundle construction. RaMen utilizes both intrinsic (characteristics) and extrinsic (collaborative signals) information to model bundle structures through Explicit Strategy-aware Learning (ESL) and Implicit Strategy-aware Learning (ISL). ESL employs task-specific attention mechanisms to encode multi-modal data and direct collaborative relations between items, thereby explicitly capturing essential bundle features. Moreover, ISL computes hyperedge dependencies and hypergraph message passing to uncover shared latent intents among groups of items. Integrating diverse strategies enables RaMen to learn more comprehensive and robust bundle representations. Meanwhile, Multi-strategy Alignment & Discrimination module is employed to facilitate knowledge transfer between learning strategies and ensure discrimination between items/bundles. Extensive experiments demonstrate the effectiveness of RaMen over state-of-the-art models on various domains, justifying valuable insights into complex item set problems.
Text-to-SQL for Enterprise Data Analytics
Venue: arXiv cs.CL 2025
Year: 2025

The introduction of large language models has brought rapid progress on Text-to-SQL benchmarks, but it is not yet easy to build a working enterprise solution. In this paper, we present insights from building an internal chatbot that enables LinkedIn's product managers, engineers, and operations teams to self-serve data insights from a large, dynamic data lake. Our approach features three components. First, we construct a knowledge graph that captures up-to-date semantics by indexing database metadata, historical query logs, wikis, and code. We apply clustering to identify relevant tables for each team or product area. Second, we build a Text-to-SQL agent that retrieves and ranks context from the knowledge graph, writes a query, and automatically corrects hallucinations and syntax errors. Third, we build an interactive chatbot that supports various user intents, from data discovery to query writing to debugging, and displays responses in rich UI elements to encourage follow-up chats. Our chatbot has over 300 weekly users. Expert review shows that 53% of its responses are correct or close to correct on an internal benchmark set. Through ablation studies, we identify the most important knowledge graph and modeling components, offering a practical path for developing enterprise Text-to-SQL solutions.
Training oscillator Ising machines to assign the dynamic stability of their equilibrium points
Venue: arXiv cs.NE 2025
Year: 2025

We propose a neural network model, which, with appropriate assignment of the stability of its equilibrium points (EPs), achieves Hopfield-like associative memory. The oscillator Ising machine (OIM) is an ideal candidates for such a model, as all its $0/π$ binary EPs are structurally stable with their dynamic stability tunable by the coupling weights. Traditional Hopfield-based models store the desired patterns by designing the coupling weights between neurons. The design of coupling weights should simultaneously take into account both the existence and the dynamic stability of the EPs for the storage of the desired patterns. For OIMs, since all $0/π$ binary EPs are structurally stable, the design of the coupling weights needs only to focus on assigning appropriate stability for the $0/π$ binary EPs according to the desired patterns. In this paper, we establish a connection between the stability and the Hamiltonian energy of EPs for OIMs, and, based on this connection, provide a Hamiltonian-Regularized Eigenvalue Contrastive Method (HRECM) to train the coupling weights of OIMs for assigning appropriate stability to their EPs. Finally, numerical experiments are performed to validate the effectiveness of the proposed method.
Fail Fast, or Ask: Mitigating the Deficiencies of Reasoning LLMs with Human-in-the-Loop Systems Engineering
Venue: arXiv cs.AI 2025
Year: 2025

State-of-the-art reasoning LLMs are powerful problem solvers, but they still occasionally make mistakes. However, adopting AI models in risk-sensitive domains often requires error rates near 0%. To address this gap, we propose collaboration between a reasoning model and a human expert who resolves queries the model cannot confidently answer. We find that quantifying the uncertainty of a reasoning model through the length of its reasoning trace yields an effective basis for deferral to a human, e.g., cutting the error rate of Qwen3 235B-A22B on difficult MATH problems from 3% to less than 1% when deferring 7.5% of queries. However, the high latency of reasoning models still makes them challenging to deploy on use cases with high query volume. To address this challenge, we explore fronting a reasoning model with a large non-reasoning model. We call this modified human-in-the-loop system "Fail Fast, or Ask", since the non-reasoning model may defer difficult queries to the human expert directly ("failing fast"), without incurring the reasoning model's higher latency. We show that this approach yields around 40% latency reduction and about 50% cost savings for DeepSeek R1 while maintaining 90+% area under the accuracy-rejection curve. However, we observe that latency savings are lower than expected because of "latency drag", the phenomenon that processing easier queries with a non-reasoning model pushes the reasoning model's latency distribution towards longer latencies. Broadly, our results suggest that the deficiencies of state-of-the-art reasoning models -- nontrivial error rates and high latency -- can be substantially mitigated through black-box systems engineering, without requiring access to LLM internals.
Personalized Socially Assistive Robots With End-to-End Speech-Language Models For Well-Being Support
Venue: arXiv cs.RO 2025
Year: 2025

Socially assistive robots (SARs) have shown great potential for supplementing well-being support. However, prior studies have found that existing dialogue pipelines for SARs remain limited in real-time latency, back-channeling, and personalized speech dialogue. Toward addressing these limitations, we propose using integrated end-to-end speech-language models (SLMs) with SARs. This work 1) evaluated the usability of an SLM-enabled SAR dialogue system through a small user study, and 2) identified remaining limitations through study user feedback to inform future improvements. We conducted a small within-participant user study with university students (N = 11) whose results showed that participants perceived an SLM-enabled SAR system as capable of providing empathetic feedback, natural turn-taking, back-channeling, and adaptive responses. We also found that participants reported the robot's nonverbal behaviors as lacking variability and synchronization with conversation, and the SLM's verbal feedback as generic and repetitive. These findings highlighted the need for real-time robot movement synchronized with conversation, improved prompting or fine-tuning to generate outputs better aligned with mental health practices, and more expressive, adaptive vocal generation.
Inverse Scaling in Test-Time Compute
Venue: arXiv cs.AI 2025
Year: 2025

We construct evaluation tasks where extending the reasoning length of Large Reasoning Models (LRMs) deteriorates performance, exhibiting an inverse scaling relationship between test-time compute and accuracy. Our evaluation tasks span four categories: simple counting tasks with distractors, regression tasks with spurious features, deduction tasks with constraint tracking, and advanced AI risks. We identify five distinct failure modes when models reason for longer: 1) Claude models become increasingly distracted by irrelevant information; 2) OpenAI o-series models resist distractors but overfit to problem framings; 3) models shift from reasonable priors to spurious correlations; 4) all models show difficulties in maintaining focus on complex deductive tasks; and 5) extended reasoning may amplify concerning behaviors, with Claude Sonnet 4 showing increased expressions of self-preservation. These findings suggest that while test-time compute scaling remains promising for improving model capabilities, it may inadvertently reinforce problematic reasoning patterns. Our results demonstrate the importance of evaluating models across diverse reasoning lengths to identify and address these failure modes in LRMs.
Pseudorandomness of Expander Walks via Fourier Analysis on Groups
Venue: arXiv cs.CC 2025
Year: 2025

One approach to study the pseudorandomness properties of walks on expander graphs is to label the vertices of an expander with elements from an alphabet $Σ$, and study the mean of functions over $Σ^n$. We say expander walks $\varepsilon$-fool a function if, for any unbiased labeling of the vertices, the expander walk mean is $\varepsilon$-close to the true mean. We show that: - The class of symmetric functions is $O(|Σ|\cdotλ)$-fooled by expander walks over any generic $λ$-expander, and any alphabet $Σ$ . This generalizes the result of Cohen, Peri, Ta-Shma [STOC'21] which analyzes it for $|Σ| =2$, and exponentially improves the previous bound of $O(|Σ|^{O(|Σ|)}\cdot λ)$, by Golowich and Vadhan [CCC'22]. Additionally, if the expander is a Cayley graph over $\mathbb{Z}_{|Σ|}$, we get a further improved bound of $O(\sqrt{|Σ|}\cdotλ)$. Morever, when $Σ$ is a finite group $G$, we show the following for functions over $G^n$: - The class of symmetric class functions is $O\Big({\frac{\sqrt{|G|}}{D}\cdotλ}\Big)$-fooled by expander walks over "structured" $λ$-expanders, if $G$ is $D$-quasirandom. - We show a lower bound of $Ω(λ)$ for symmetric functions for any finite group $G$ (even for "structured" $λ$-expanders). - We study the Fourier spectrum of a class of non-symmetric functions arising from word maps, and show that they are exponentially fooled by expander walks. Our proof employs Fourier analysis over general groups, which contrasts with earlier works that have studied either the case of $\mathbb{Z}_2$ or $\mathbb{Z}$. This enables us to get quantitatively better bounds even for unstructured sets.
Routine: A Structural Planning Framework for LLM Agent System in Enterprise
Venue: arXiv cs.AI 2025
Year: 2025

The deployment of agent systems in an enterprise environment is often hindered by several challenges: common models lack domain-specific process knowledge, leading to disorganized plans, missing key tools, and poor execution stability. To address this, this paper introduces Routine, a multi-step agent planning framework designed with a clear structure, explicit instructions, and seamless parameter passing to guide the agent's execution module in performing multi-step tool-calling tasks with high stability. In evaluations conducted within a real-world enterprise scenario, Routine significantly increases the execution accuracy in model tool calls, increasing the performance of GPT-4o from 41.1% to 96.3%, and Qwen3-14B from 32.6% to 83.3%. We further constructed a Routine-following training dataset and fine-tuned Qwen3-14B, resulting in an accuracy increase to 88.2% on scenario-specific evaluations, indicating improved adherence to execution plans. In addition, we employed Routine-based distillation to create a scenario-specific, multi-step tool-calling dataset. Fine-tuning on this distilled dataset raised the model's accuracy to 95.5%, approaching GPT-4o's performance. These results highlight Routine's effectiveness in distilling domain-specific tool-usage patterns and enhancing model adaptability to new scenarios. Our experimental results demonstrate that Routine provides a practical and accessible approach to building stable agent workflows, accelerating the deployment and adoption of agent systems in enterprise environments, and advancing the technical vision of AI for Process.
BioGraphFusion: Graph Knowledge Embedding for Biological Completion and Reasoning
Venue: arXiv cs.AI 2025
Year: 2025

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.
Conch: Competitive Debate Analysis via Visualizing Clash Points and Hierarchical Strategies
Venue: arXiv cs.HC 2025
Year: 2025

In-depth analysis of competitive debates is essential for participants to develop argumentative skills and refine strategies, and further improve their debating performance. However, manual analysis of unstructured and unlabeled textual records of debating is time-consuming and ineffective, as it is challenging to reconstruct contextual semantics and track logical connections from raw data. To address this, we propose Conch, an interactive visualization system that systematically analyzes both what is debated and how it is debated. In particular, we propose a novel parallel spiral visualization that compactly traces the multidimensional evolution of clash points and participant interactions throughout debate process. In addition, we leverage large language models with well-designed prompts to automatically identify critical debate elements such as clash points, disagreements, viewpoints, and strategies, enabling participants to understand the debate context comprehensively. Finally, through two case studies on real-world debates and a carefully-designed user study, we demonstrate Conch's effectiveness and usability for competitive debate analysis.