OpenRaiser/Intern-Atlas huggingface dataset:
Boltzmann Graph Ensemble Embeddings for Aptamer Libraries
Venue: arXiv cs.LG 2025
Year: 2025

Machine-learning methods in biochemistry commonly represent molecules as graphs of pairwise intermolecular interactions for property and structure predictions. Most methods operate on a single graph, typically the minimal free energy (MFE) structure, for low-energy ensembles (conformations) representative of structures at thermodynamic equilibrium. We introduce a thermodynamically parameterized exponential-family random graph (ERGM) embedding that models molecules as Boltzmann-weighted ensembles of interaction graphs. We evaluate this embedding on SELEX datasets, where experimental biases (e.g., PCR amplification or sequencing noise) can obscure true aptamer-ligand affinity, producing anomalous candidates whose observed abundance diverges from their actual binding strength. We show that the proposed embedding enables robust community detection and subgraph-level explanations for aptamer ligand affinity, even in the presence of biased observations. This approach may be used to identify low-abundance aptamer candidates for further experimental evaluation.
Uncovering the Persuasive Fingerprint of LLMs in Jailbreaking Attacks
Venue: arXiv cs.CL 2025
Year: 2025

Despite recent advances, Large Language Models remain vulnerable to jailbreak attacks that bypass alignment safeguards and elicit harmful outputs. While prior research has proposed various attack strategies differing in human readability and transferability, little attention has been paid to the linguistic and psychological mechanisms that may influence a model's susceptibility to such attacks. In this paper, we examine an interdisciplinary line of research that leverages foundational theories of persuasion from the social sciences to craft adversarial prompts capable of circumventing alignment constraints in LLMs. Drawing on well-established persuasive strategies, we hypothesize that LLMs, having been trained on large-scale human-generated text, may respond more compliantly to prompts with persuasive structures. Furthermore, we investigate whether LLMs themselves exhibit distinct persuasive fingerprints that emerge in their jailbreak responses. Empirical evaluations across multiple aligned LLMs reveal that persuasion-aware prompts significantly bypass safeguards, demonstrating their potential to induce jailbreak behaviors. This work underscores the importance of cross-disciplinary insight in addressing the evolving challenges of LLM safety. The code and data are available.
AI-Mediated Communication Reshapes Social Structure in Opinion-Diverse Groups
Venue: arXiv cs.SI 2025
Year: 2025

Group segregation or cohesion can emerge from micro-level communication, and AI-assisted messaging may shape this process. Here, we report a preregistered online experiment (N = 557 across 60 sessions) in which participants discussed controversial political topics over multiple rounds and could freely change groups. Some participants received real-time message suggestions from a large language model (LLM), either personalized to their stance (individual assistance) or incorporating their group members' perspectives (relational assistance). We find that small variations in AI-mediated communication cascade into macro-level differences in group composition. Participants with individual assistance send more messages and show greater stance-based clustering, whereas those with relational assistance use more receptive language and form more heterogeneous ties. Hybrid expressive processes-jointly produced by humans and AI-can reshape collective organization. The patterns of structural division and cohesion depend on how AI incorporates users' interaction context.
Cost-Sensitive Evaluation for Binary Classifiers
Venue: arXiv cs.LG 2025
Year: 2025

Selecting an appropriate evaluation metric for classifiers is crucial for model comparison and parameter optimization, yet there is not consensus on a universally accepted metric that serves as a definitive standard. Moreover, there is often a misconception about the perceived need to mitigate imbalance in datasets used to train classification models. Since the final goal in classifier optimization is typically maximizing the return of investment or, equivalently, minimizing the Total Classification Cost (TCC), we define Weighted Accuracy (WA), an evaluation metric for binary classifiers with a straightforward interpretation as a weighted version of the well-known accuracy metric, coherent with the need of minimizing TCC. We clarify the conceptual framework for handling class imbalance in cost-sensitive scenarios, providing an alternative to rebalancing techniques. This framework can be applied to any metric that, like WA, can be expressed as a linear combination of example-dependent quantities and allows for comparing the results obtained in different datasets and for addressing discrepancies between the development dataset, used to train and validate the model, and the target dataset, where the model will be deployed. It also specifies in which scenarios using UCCs-unaware class rebalancing techniques or rebalancing metrics aligns with TCC minimization and when it is instead counterproductive. Finally, we propose a procedure to estimate the WA weight parameter in the absence of fully specified UCCs and demonstrate the robustness of WA by analyzing its correlation with TCC in example-dependent scenarios.
K-DAREK: Distance Aware Error for Kurkova Kolmogorov Networks
Venue: arXiv cs.LG 2025
Year: 2025

Neural networks are powerful parametric function approximators, while Gaussian processes (GPs) are nonparametric probabilistic models that place distributions over functions via kernel-defined correlations but become computationally expensive for large-scale problems. Kolmogorov-Arnold networks (KANs), semi-parametric neural architectures, model complex functions efficiently using spline layers. Kurkova Kolmogorov-Arnold networks (KKANs) extend KANs by replacing the early spline layers with multi-layer perceptrons that map inputs into higher-dimensional spaces before applying spline-based transformations, which yield more stable training and provide robust architectures for system modeling. By enhancing the KKAN architecture, we develop a novel learning algorithm, distance-aware error for Kurkova-Kolmogorov networks (K-DAREK), for efficient and interpretable function approximation with uncertainty quantification. Our approach establishes robust error bounds that are distance-aware; this means they reflect the proximity of a test point to its nearest training points. In safe control case studies, we demonstrate that K-DAREK is about four times faster and ten times more computationally efficient than Ensemble of KANs, 8.6 times more scalable than GP as data size increases, and 7.2% safer than our previous work distance-aware error for Kolmogorov networks (DAREK). Moreover, on real data (e.g., Real Estate Valuation), K-DAREK's error bound achieves zero coverage violations.
Energy-Efficient Domain-Specific Artificial Intelligence Models and Agents: Pathways and Paradigms
Venue: arXiv cs.AI 2025
Year: 2025

The field of artificial intelligence (AI) has taken a tight hold on broad aspects of society, industry, business, and governance in ways that dictate the prosperity and might of the world's economies. The AI market size is projected to grow from 189 billion USD in 2023 to 4.8 trillion USD by 2033. Currently, AI is dominated by large language models that exhibit linguistic and visual intelligence. However, training these models requires a massive amount of data scraped from the web as well as large amounts of energy (50--60 GWh to train GPT-4). Despite these costs, these models often hallucinate, a characteristic that prevents them from being deployed in critical application domains. In contrast, the human brain consumes only 20~W of power. What is needed is the next level of AI evolution in which lightweight domain-specific multimodal models with higher levels of intelligence can reason, plan, and make decisions in dynamic environments with real-time data and prior knowledge, while learning continuously and evolving in ways that enhance future decision-making capability. This will define the next wave of AI, progressing from today's large models, trained with vast amounts of data, to nimble energy-efficient domain-specific agents that can reason and think in a world full of uncertainty. To support such agents, hardware will need to be reimagined to allow energy efficiencies greater than 1000x over the state of the art. Such a vision of future AI systems is developed in this work.
Capturing Gaze Shifts for Guidance: Cross-Modal Fusion Enhancement for VLM Hallucination Mitigation
Venue: arXiv cs.CV 2025
Year: 2025

Vision language models (VLMs) often generate hallucination, i.e., content that cannot be substantiated by either textual or visual inputs. Prior work primarily attributes this to over-reliance on linguistic prior knowledge rather than visual inputs. Some methods attempt to mitigate hallucination by amplifying visual token attention proportionally to their attention scores. However, these methods overlook the visual attention sink problem, where attention is frequently misallocated to task-irrelevant visual regions, and neglect cross-modal fusion balance by enhancing only visual attention without adjusting attention to the user query. This can result in amplifying incorrect areas while failing to properly interpret the user query. To address these challenges, we propose a simple yet effective method called Gaze Shift-Guided Cross-modal Fusion Enhancement (GIFT). GIFT pre-computes a holistic visual saliency map by tracking positive changes in visual attention, or "gaze shifts", during user query comprehension, and leverages this map to amplify attention to both salient visual information and the user query at each decoding step. This reduces the impact of visual attention sink, as irrelevant tokens exhibit minimal shifts, while ensuring balanced cross-modal fusion for well-integrated representation. Extensive experiments show that GIFT effectively mitigates hallucination in VLMs across both generative and classification tasks, achieving up to 20.7% improvement over greedy decoding, while maintaining general vision-language performance with low computational overhead.
Scanner-Agnostic MRI Harmonization via SSIM-Guided Disentanglement
Venue: arXiv cs.CV 2025
Year: 2025

The variability introduced by differences in MRI scanner models, acquisition protocols, and imaging sites hinders consistent analysis and generalizability across multicenter studies. We present a novel image-based harmonization framework for 3D T1-weighted brain MRI, which disentangles anatomical content from scanner- and site-specific variations. The model incorporates a differentiable loss based on the Structural Similarity Index (SSIM) to preserve biologically meaningful features while reducing inter-site variability. This loss enables separate evaluation of image luminance, contrast, and structural components. Training and validation were performed on multiple publicly available datasets spanning diverse scanners and sites, with testing on both healthy and clinical populations. Harmonization using multiple style targets, including style-agnostic references, produced consistent and high-quality outputs. Visual comparisons, voxel intensity distributions, and SSIM-based metrics demonstrated that harmonized images achieved strong alignment across acquisition settings while maintaining anatomical fidelity. Following harmonization, structural SSIM reached 0.97, luminance SSIM ranged from 0.98 to 0.99, and Wasserstein distances between mean voxel intensity distributions decreased substantially. Downstream tasks showed substantial improvements: mean absolute error for brain age prediction decreased from 5.36 to 3.30 years, and Alzheimer's disease classification AUC increased from 0.78 to 0.85. Overall, our framework enhances cross-site image consistency, preserves anatomical fidelity, and improves downstream model performance, providing a robust and generalizable solution for large-scale multicenter neuroimaging studies.
QuArch: A Benchmark for Evaluating LLM Reasoning in Computer Architecture
Venue: arXiv cs.AR 2025
Year: 2025

The field of computer architecture, which bridges high-level software abstractions and low-level hardware implementations, remains absent from current large language model (LLM) evaluations. To this end, we present QuArch (pronounced 'quark'), the first benchmark designed to facilitate the development and evaluation of LLM knowledge and reasoning capabilities specifically in computer architecture. QuArch provides a comprehensive collection of 2,671 expert-validated question-answer (QA) pairs covering various aspects of computer architecture, including processor design, memory systems, and interconnection networks. Our evaluation reveals that while frontier models possess domain-specific knowledge, they struggle with skills that require higher-order thinking in computer architecture. Frontier model accuracies vary widely (from 34% to 72%) on these advanced questions, highlighting persistent gaps in architectural reasoning across analysis, design, and implementation QAs. By holistically assessing fundamental skills, QuArch provides a foundation for building and measuring LLM capabilities that can accelerate innovation in computing systems. With over 140 contributors from 40 institutions, this benchmark represents a community effort to set the standard for architectural reasoning in LLM evaluation.
Scaling Up Efficient Small Language Models Serving and Deployment for Semantic Job Search
Venue: arXiv cs.IR 2025
Year: 2025

Large Language Models (LLMs) have demonstrated impressive quality when applied to predictive tasks such as relevance ranking and semantic search. However, deployment of such LLMs remains prohibitively expensive for industry applications with strict latency and throughput requirements. In this work, we present lessons and efficiency insights from developing a purely text-based decoder-only Small Language Model (SLM) for a semantic search application at LinkedIn. Particularly, we discuss model compression techniques such as pruning that allow us to reduce the model size by up to $40\%$ while maintaining the accuracy. Additionally, we present context compression techniques that allow us to reduce the input context length by up to $10$x with minimal loss of accuracy. Finally, we present practical lessons from optimizing the serving infrastructure for deploying such a system on GPUs at scale, serving millions of requests per second. Taken together, this allows us to increase our system's throughput by $10$x in a real-world deployment, while meeting our quality bar.
What Exactly is a Deepfake?
Venue: arXiv cs.CY 2025
Year: 2025

Deepfake technologies are often associated with deception, misinformation, and identity fraud, raising legitimate societal concerns. Yet such narratives may obscure a key insight: deepfakes embody sophisticated capabilities for sensory manipulation that can alter human perception, potentially enabling beneficial applications in domains such as healthcare and education. Realizing this potential, however, requires understanding how the technology is conceptualized across disciplines. This paper analyzes 826 peer-reviewed publications from 2017 to 2025 to examine how deepfakes are defined and understood in the literature. Using large language models for content analysis, we categorize deepfake conceptualizations along three dimensions: Identity Source (the relationship between original and generated content), Intent (deceptive versus non-deceptive purposes), and Manipulation Granularity (holistic versus targeted modifications). Results reveal substantial heterogeneity that challenges simplified public narratives. Notably, a subset of studies discuss non-deceptive applications, highlighting an underexplored potential for social good. Temporal analysis shows an evolution from predominantly threat-focused views (2017 to 2019) toward recognition of beneficial applications (2022 to 2025). This study provides an empirical foundation for developing nuanced governance and research frameworks that distinguish applications warranting prohibition from those deserving support, showing that, with safeguards, deepfakes' realism can serve important social purposes beyond deception.
HandPass: A Wi-Fi CSI Palm Authentication Approach for Access Control
Venue: arXiv cs.NI 2025
Year: 2025

Wi-Fi Channel State Information (CSI) has been extensively studied for sensing activities. However, its practical application in user authentication still needs to be explored. This study presents a novel approach to biometric authentication using Wi-Fi Channel State Information (CSI) data for palm recognition. The research delves into utilizing a Raspberry Pi encased in a custom-built box with antenna power reduced to 1dBm, which was used to capture CSI data from the right hands of 20 participants (10 men and 10 women). The dataset was normalized using MinMax scaling to ensure uniformity and accuracy. By focusing on biophysical aspects such as hand size, shape, angular spread between fingers, and finger phalanx lengths, among other characteristics, the study explores how these features affect electromagnetic signals, which are then reflected in Wi-Fi CSI, allowing for precise user identification. Five classification algorithms were evaluated, with the Random Forest classifier achieving an average F1-Score of 99.82\% using 10-fold cross-validation. Amplitude and Phase data were used, with each capture session recording approximately 1000 packets per second in five 5-second intervals for each User. This high accuracy highlights the potential of Wi-Fi CSI in developing robust and reliable user authentication systems based on palm biometric data.
Tractable Shapley Values and Interactions via Tensor Networks
Venue: arXiv cs.LG 2025
Year: 2025

We show how to replace the O(2^n) coalition enumeration over n features behind Shapley values and Shapley-style interaction indices with a few-evaluation scheme on a tensor-network (TN) surrogate: TN-SHAP. The key idea is to represent a predictor's local behavior as a factorized multilinear map, so that coalitional quantities become linear probes of a coefficient tensor. TN-SHAP replaces exhaustive coalition sweeps with just a small number of targeted evaluations to extract order-k Shapley interactions. In particular, both order-1 (single-feature) and order-2 (pairwise) computations have cost O(n*poly(chi) + n^2), where chi is the TN's maximal cut rank. We provide theoretical guarantees on the approximation error and tractability of TN-SHAP. On UCI datasets, our method matches enumeration on the fitted surrogate while reducing evaluation by orders of magnitude and achieves 25-1000x wall-clock speedups over KernelSHAP-IQ at comparable accuracy, while amortizing training across local cohorts.
HARMONY: Hidden Activation Representations and Model Output-Aware Uncertainty Estimation for Vision-Language Models
Venue: arXiv cs.CV 2025
Year: 2025

Uncertainty Estimation (UE) plays a central role in quantifying the reliability of model outputs and reducing unsafe generations via selective prediction. In this regard, most existing probability-based UE approaches rely on predefined functions, aggregating token probabilities into a single UE score using heuristics such as length-normalization. However, these methods often fail to capture the complex relationships between generated tokens and struggle to identify biased probabilities often influenced by \textbf{language priors}. Another line of research uses hidden representations of the model and trains simple MLP architectures to predict uncertainty. However, such functions often lose the intricate \textbf{ inter-token dependencies}. While prior works show that hidden representations encode multimodal alignment signals, our work demonstrates that how these signals are processed has a significant impact on the UE performance. To effectively leverage these signals to identify inter-token dependencies, and vision-text alignment, we propose \textbf{HARMONY} (Hidden Activation Representations and Model Output-Aware Uncertainty Estimation for Vision-Language Models), a novel UE framework that integrates generated tokens ('text'), model's uncertainty score at the output ('MaxProb'), and its internal belief on the visual understanding of the image and the generated token (captured by 'hidden representations') at token level via appropriate input mapping design and suitable architecture choice. Our experimental experiments across two open-ended VQA benchmarks (A-OKVQA, and VizWiz) and four state-of-the-art VLMs (LLaVA-7B, LLaVA-13B, InstructBLIP, and Qwen-VL) show that HARMONY consistently matches or surpasses existing approaches, achieving up to 5\% improvement in AUROC and 9\% in PRR.
Estimating the Error of Large Language Models at Pairwise Text Comparison
Venue: arXiv cs.CL 2025
Year: 2025

We measure LLMs' output error at pairwise text comparison, noting the probability of error in their preferences. Our method does not rely on the ground truth and supports two scenarios: (i) uniform error rate regardless of the order of comparison, estimated with two comparisons for each text pair with either text placed first; (ii) binary positional bias assuming distinct error rates for the two orders of comparison, estimated with repeated comparisons between the texts. The Copeland counting constructs a ranking over the compared texts from pairwise preferences; the ranking reveals the poor scalability of LLM-based pairwise comparison and helps yield the estimates for LLMs' error rates. We apply the method to six LLMs (ChatGPT, Claude, DeepSeek, Gemini, Grok, Qwen) with five types of text input and obtain consistent estimates of LLMs' error. In general, the measured two positional bias terms are similar, close to the uniform error. Considering both the error rates and the robustness to the variation of prompts, Claude obtained the most desirable performance in this experiment. Our model outperforms the biased Bradley-Terry model and the commutativity score in indicating LLMs' error at this task.
CreditXAI: A Multi-Agent System for Explainable Corporate Credit Rating
Venue: arXiv cs.MA 2025
Year: 2025

In the domain of corporate credit rating, traditional deep learning methods have improved predictive accuracy but still suffer from the inherent 'black-box' problem and limited interpretability. While incorporating non-financial information enriches the data and provides partial interpretability, the models still lack hierarchical reasoning mechanisms, limiting their comprehensive analytical capabilities. To address these challenges, we propose CreditXAI, a Multi-Agent System (MAS) framework that simulates the collaborative decision-making process of professional credit analysts. The framework focuses on business, financial, and governance risk dimensions to generate consistent and interpretable credit assessments. Experimental results demonstrate that multi-agent collaboration improves predictive accuracy by more than 7% over the best single-agent baseline, confirming its significant synergistic advantage in corporate credit risk evaluation. This study provides a new technical pathway to build intelligent and interpretable credit rating models.