OpenRaiser/Intern-Atlas huggingface dataset:
Comprehensive Metapath-based Heterogeneous Graph Transformer for Gene-Disease Association Prediction
Venue: arXiv cs.AI 2025
Year: 2025

Discovering gene-disease associations is crucial for understanding disease mechanisms, yet identifying these associations remains challenging due to the time and cost of biological experiments. Computational methods are increasingly vital for efficient and scalable gene-disease association prediction. Graph-based learning models, which leverage node features and network relationships, are commonly employed for biomolecular predictions. However, existing methods often struggle to effectively integrate node features, heterogeneous structures, and semantic information. To address these challenges, we propose COmprehensive MEtapath-based heterogeneous graph Transformer(COMET) for predicting gene-disease associations. COMET integrates diverse datasets to construct comprehensive heterogeneous networks, initializing node features with BioGPT. We define seven Metapaths and utilize a transformer framework to aggregate Metapath instances, capturing global contexts and long-distance dependencies. Through intra- and inter-metapath aggregation using attention mechanisms, COMET fuses latent vectors from multiple Metapaths to enhance GDA prediction accuracy. Our method demonstrates superior robustness compared to state-of-the-art approaches. Ablation studies and visualizations validate COMET's effectiveness, providing valuable insights for advancing human health research.
CHEQ-ing the Box: Safe Variable Impedance Learning for Robotic Polishing
Venue: arXiv cs.RO 2025
Year: 2025

Robotic systems are increasingly employed for industrial automation, with contact-rich tasks like polishing requiring dexterity and compliant behaviour. These tasks are difficult to model, making classical control challenging. Deep reinforcement learning (RL) offers a promising solution by enabling the learning of models and control policies directly from data. However, its application to real-world problems is limited by data inefficiency and unsafe exploration. Adaptive hybrid RL methods blend classical control and RL adaptively, combining the strengths of both: structure from control and learning from RL. This has led to improvements in data efficiency and exploration safety. However, their potential for hardware applications remains underexplored, with no evaluations on physical systems to date. Such evaluations are critical to fully assess the practicality and effectiveness of these methods in real-world settings. This work presents an experimental demonstration of the hybrid RL algorithm CHEQ for robotic polishing with variable impedance, a task requiring precise force and velocity tracking. In simulation, we show that variable impedance enhances polishing performance. We compare standalone RL with adaptive hybrid RL, demonstrating that CHEQ achieves effective learning while adhering to safety constraints. On hardware, CHEQ achieves effective polishing behaviour, requiring only eight hours of training and incurring just five failures. These results highlight the potential of adaptive hybrid RL for real-world, contact-rich tasks trained directly on hardware.
Maximizing Uncertainty for Federated learning via Bayesian Optimisation-based Model Poisoning
Venue: arXiv cs.LG 2025
Year: 2025

As we transition from Narrow Artificial Intelligence towards Artificial Super Intelligence, users are increasingly concerned about their privacy and the trustworthiness of machine learning (ML) technology. A common denominator for the metrics of trustworthiness is the quantification of uncertainty inherent in DL algorithms, and specifically in the model parameters, input data, and model predictions. One of the common approaches to address privacy-related issues in DL is to adopt distributed learning such as federated learning (FL), where private raw data is not shared among users. Despite the privacy-preserving mechanisms in FL, it still faces challenges in trustworthiness. Specifically, the malicious users, during training, can systematically create malicious model parameters to compromise the models predictive and generative capabilities, resulting in high uncertainty about their reliability. To demonstrate malicious behaviour, we propose a novel model poisoning attack method named Delphi which aims to maximise the uncertainty of the global model output. We achieve this by taking advantage of the relationship between the uncertainty and the model parameters of the first hidden layer of the local model. Delphi employs two types of optimisation , Bayesian Optimisation and Least Squares Trust Region, to search for the optimal poisoned model parameters, named as Delphi-BO and Delphi-LSTR. We quantify the uncertainty using the KL Divergence to minimise the distance of the predictive probability distribution towards an uncertain distribution of model output. Furthermore, we establish a mathematical proof for the attack effectiveness demonstrated in FL. Numerical results demonstrate that Delphi-BO induces a higher amount of uncertainty than Delphi-LSTR highlighting vulnerability of FL systems to model poisoning attacks.
Convergence Analysis of Real-time Recurrent Learning (RTRL) for a class of Recurrent Neural Networks
Venue: arXiv cs.LG 2025
Year: 2025

Recurrent neural networks (RNNs) are commonly trained with the truncated backpropagation-through-time (TBPTT) algorithm. For the purposes of computational tractability, the TBPTT algorithm truncates the chain rule and calculates the gradient on a finite block of the overall data sequence. Such approximation could lead to significant inaccuracies, as the block length for the truncated backpropagation is typically limited to be much smaller than the overall sequence length. In contrast, Real-time recurrent learning (RTRL) is an online optimization algorithm which asymptotically follows the true gradient of the loss on the data sequence as the number of sequence time steps $t \rightarrow \infty$. RTRL forward propagates the derivatives of the RNN hidden/memory units with respect to the parameters and, using the forward derivatives, performs online updates of the parameters at each time step in the data sequence. RTRL's online forward propagation allows for exact optimization over extremely long data sequences, although it can be computationally costly for models with large numbers of parameters. We prove convergence of the RTRL algorithm for a class of RNNs. The convergence analysis establishes a fixed point for the joint distribution of the data sequence, RNN hidden layer, and the RNN hidden layer forward derivatives as the number of data samples from the sequence and the number of training steps tend to infinity. We prove convergence of the RTRL algorithm to a stationary point of the loss. Numerical studies illustrate our theoretical results. One potential application area for RTRL is the analysis of financial data, which typically involve long time series and models with small to medium numbers of parameters. This makes RTRL computationally tractable and a potentially appealing optimization method for training models. Thus, we include an example of RTRL applied to limit order book data.
PolyLUT: Ultra-low Latency Polynomial Inference with Hardware-Aware Structured Pruning
Venue: arXiv cs.LG 2025
Year: 2025

Standard deep neural network inference involves the computation of interleaved linear maps and nonlinear activation functions. Prior work for ultra-low latency implementations has hardcoded these operations inside FPGA lookup tables (LUTs). However, FPGA LUTs can implement a much greater variety of functions. In this paper, we propose a novel approach to training DNNs for FPGA deployment using multivariate polynomials as the basic building block. Our method takes advantage of the flexibility offered by the soft logic, hiding the polynomial evaluation inside the LUTs with minimal overhead. By using polynomial building blocks, we achieve the same accuracy using considerably fewer layers of soft logic than by using linear functions, leading to significant latency and area improvements. LUT-based implementations also face a significant challenge: the LUT size grows exponentially with the number of inputs. Prior work relies on a priori fixed sparsity, with results heavily dependent on seed selection. To address this, we propose a structured pruning strategy using a bespoke hardware-aware group regularizer that encourages a particular sparsity pattern that leads to a small number of inputs per neuron. We demonstrate the effectiveness of PolyLUT on three tasks: network intrusion detection, jet identification at the CERN Large Hadron Collider, and MNIST.
Exploring Narrative Clustering in Large Language Models: A Layerwise Analysis of BERT
Venue: arXiv cs.CL 2025
Year: 2025

This study investigates the internal mechanisms of BERT, a transformer-based large language model, with a focus on its ability to cluster narrative content and authorial style across its layers. Using a dataset of narratives developed via GPT-4, featuring diverse semantic content and stylistic variations, we analyze BERT's layerwise activations to uncover patterns of localized neural processing. Through dimensionality reduction techniques such as Principal Component Analysis (PCA) and Multidimensional Scaling (MDS), we reveal that BERT exhibits strong clustering based on narrative content in its later layers, with progressively compact and distinct clusters. While strong stylistic clustering might occur when narratives are rephrased into different text types (e.g., fables, sci-fi, kids' stories), minimal clustering is observed for authorial style specific to individual writers. These findings highlight BERT's prioritization of semantic content over stylistic features, offering insights into its representational capabilities and processing hierarchy. This study contributes to understanding how transformer models like BERT encode linguistic information, paving the way for future interdisciplinary research in artificial intelligence and cognitive neuroscience.
Logics and Algorithms for Hyperproperties
Venue: arXiv cs.LO 2025
Year: 2025

System requirements related to concepts like information flow, knowledge, and robustness cannot be judged in terms of individual system executions, but rather require an analysis of the relationship between multiple executions. Such requirements belong to the class of hyperproperties, which generalize classic trace properties to properties of sets of traces. During the past decade, a range of new specification logics has been introduced with the goal of providing a unified theory for reasoning about hyperproperties. This paper gives an overview on the current landscape of logics for the specification of hyperproperties and on algorithms for satisfiability checking, model checking, monitoring, and synthesis.
A Roadmap to Guide the Integration of LLMs in Hierarchical Planning
Venue: arXiv cs.AI 2025
Year: 2025

Recent advances in Large Language Models (LLMs) are fostering their integration into several reasoning-related fields, including Automated Planning (AP). However, their integration into Hierarchical Planning (HP), a subfield of AP that leverages hierarchical knowledge to enhance planning performance, remains largely unexplored. In this preliminary work, we propose a roadmap to address this gap and harness the potential of LLMs for HP. To this end, we present a taxonomy of integration methods, exploring how LLMs can be utilized within the HP life cycle. Additionally, we provide a benchmark with a standardized dataset for evaluating the performance of future LLM-based HP approaches, and present initial results for a state-of-the-art HP planner and LLM planner. As expected, the latter exhibits limited performance (3\% correct plans, and none with a correct hierarchical decomposition) but serves as a valuable baseline for future approaches.
AgentPose: Progressive Distribution Alignment via Feature Agent for Human Pose Distillation
Venue: arXiv cs.CV 2025
Year: 2025

Pose distillation is widely adopted to reduce model size in human pose estimation. However, existing methods primarily emphasize the transfer of teacher knowledge while often neglecting the performance degradation resulted from the curse of capacity gap between teacher and student. To address this issue, we propose AgentPose, a novel pose distillation method that integrates a feature agent to model the distribution of teacher features and progressively aligns the distribution of student features with that of the teacher feature, effectively overcoming the capacity gap and enhancing the ability of knowledge transfer. Our comprehensive experiments conducted on the COCO dataset substantiate the effectiveness of our method in knowledge transfer, particularly in scenarios with a high capacity gap.
Guiding the classification of hepatocellular carcinoma on 3D CT-scans using deep and handcrafted radiological features
Venue: arXiv cs.CV 2025
Year: 2025

Hepatocellular carcinoma is the most spread primary liver cancer across the world ($\sim$80\% of the liver tumors). The gold standard for HCC diagnosis is liver biopsy. However, in the clinical routine, expert radiologists provide a visual diagnosis by interpreting hepatic CT-scans according to a standardized protocol, the LI-RADS, which uses five radiological criteria with an associated decision tree. In this paper, we propose an automatic approach to predict histology-proven HCC from CT images in order to reduce radiologists' inter-variability. We first show that standard deep learning methods fail to accurately predict HCC from CT-scans on a challenging database, and propose a two-step approach inspired by the LI-RADS system to improve the performance. We achieve improvements from 6 to 18 points of AUC with respect to deep learning baselines trained with different architectures. We also provide clinical validation of our method, achieving results that outperform non-expert radiologists and are on par with expert ones.
Data-driven inventory management for new products: An adjusted Dyna-$Q$ approach with transfer learning
Venue: arXiv cs.LG 2025
Year: 2025

In this paper, we propose a novel reinforcement learning algorithm for inventory management of newly launched products with no historical demand information. The algorithm follows the classic Dyna-$Q$ structure, balancing the model-free and model-based approaches, while accelerating the training process of Dyna-$Q$ and mitigating the model discrepancy generated by the model-based feedback. Based on the idea of transfer learning, warm-start information from the demand data of existing similar products can be incorporated into the algorithm to further stabilize the early-stage training and reduce the variance of the estimated optimal policy. Our approach is validated through a case study of bakery inventory management with real data. The adjusted Dyna-$Q$ shows up to a 23.7\% reduction in average daily cost compared with $Q$-learning, and up to a 77.5\% reduction in training time within the same horizon compared with classic Dyna-$Q$. By using transfer learning, it can be found that the adjusted Dyna-$Q$ has the lowest total cost, lowest variance in total cost, and relatively low shortage percentages among all the benchmarking algorithms under a 30-day testing.
RoHan: Robust Hand Detection in Operation Room
Venue: arXiv cs.CV 2025
Year: 2025

Hand-specific localization has garnered significant interest within the computer vision community. Although there are numerous datasets with hand annotations from various angles and settings, domain transfer techniques frequently struggle in surgical environments. This is mainly due to the limited availability of gloved hand instances and the unique challenges of operating rooms (ORs). Thus, hand-detection models tailored to OR settings require extensive training and expensive annotation processes. To overcome these challenges, we present "RoHan" - a novel approach for robust hand detection in the OR, leveraging advanced semi-supervised domain adaptation techniques to tackle the challenges of varying recording conditions, diverse glove colors, and occlusions common in surgical settings. Our methodology encompasses two main stages: (1) data augmentation strategy that utilizes "Artificial Gloves," a method for augmenting publicly available hand datasets with synthetic images of hands-wearing gloves; (2) semi-supervised domain adaptation pipeline that improves detection performance in real-world OR settings through iterative prediction refinement and efficient frame filtering. We evaluate our method using two datasets: simulated enterotomy repair and saphenous vein graft harvesting. "RoHan" substantially reduces the need for extensive labeling and model training, paving the way for the practical implementation of hand detection technologies in medical settings.
In-situ graph reasoning and knowledge expansion using Graph-PReFLexOR
Venue: arXiv cs.AI 2025
Year: 2025

The pursuit of automated scientific discovery has fueled progress from symbolic logic to modern AI, forging new frontiers in reasoning and pattern recognition. Transformers function as potential systems, where every possible relationship remains latent potentiality until tasks impose constraints, akin to measurement. Yet, refining their sampling requires more than probabilistic selection: solutions must conform to specific structures or rules, ensuring consistency and the invocation of general principles. We present Graph-PReFLexOR (Graph-based Preference-based Recursive Language Modeling for Exploratory Optimization of Reasoning), a framework that combines graph reasoning with symbolic abstraction to dynamically expand domain knowledge. Inspired by reinforcement learning, Graph-PReFLexOR defines reasoning as a structured mapping, where tasks yield knowledge graphs, abstract patterns, and ultimately, final answers. Inspired by category theory, it encodes concepts as nodes and their relationships as edges, supporting hierarchical inference and adaptive learning through isomorphic representations. Demonstrations include hypothesis generation, materials design, and creative reasoning, such as discovering relationships between mythological concepts like 'thin places' with materials science. We propose a 'knowledge garden growth' strategy that integrates insights across domains, promoting interdisciplinary connections. Results with a 3-billion-parameter Graph-PReFLexOR model show superior reasoning depth and adaptability, underscoring the potential for transparent, multidisciplinary AI-driven discovery. It lays the groundwork for general autonomous reasoning solutions.
Evaluating Policy Effects through Opinion Dynamics and Network Sampling
Venue: arXiv cs.SI 2025
Year: 2025

In the process of enacting or introducing a new policy, policymakers frequently consider the population's responses. These considerations are critical for effective governance. There are numerous methods to gauge the ground sentiment from a subset of the population; examples include surveys or listening to various feedback channels. Many conventional approaches implicitly assume that opinions are static; however, in reality, the population will discuss and debate these new policies among themselves, and reform new opinions in the process. In this paper, we pose the following questions: Can we quantify the effect of these social dynamics on the broader opinion towards a new policy? Given some information about the relationship network that underlies the population, how does overall opinion change post-discussion? We investigate three different settings in which the policy is revealed: respondents who do not know each other, groups of respondents who all know each other, and respondents chosen randomly. By controlling who the policy is revealed to, we control the degree of discussion among the population. We quantify how these factors affect the changes in policy beliefs via the Wasserstein distance between the empirically observed data post-discussion and its distribution pre-discussion. We also provide several numerical analyses based on generated network and real-life network datasets. Our work aims to address the challenges associated with network topology and social interactions, and provide policymakers with a quantitative lens to assess policy effectiveness in the face of resource constraints and network complexities.
I Can Find You in Seconds! Leveraging Large Language Models for Code Authorship Attribution
Venue: arXiv cs.SE 2025
Year: 2025

Source code authorship attribution is important in software forensics, plagiarism detection, and protecting software patch integrity. Existing techniques often rely on supervised machine learning, which struggles with generalization across different programming languages and coding styles due to the need for large labeled datasets. Inspired by recent advances in natural language authorship analysis using large language models (LLMs), which have shown exceptional performance without task-specific tuning, this paper explores the use of LLMs for source code authorship attribution. We present a comprehensive study demonstrating that state-of-the-art LLMs can successfully attribute source code authorship across different languages. LLMs can determine whether two code snippets are written by the same author with zero-shot prompting, achieving a Matthews Correlation Coefficient (MCC) of 0.78, and can attribute code authorship from a small set of reference code snippets via few-shot learning, achieving MCC of 0.77. Additionally, LLMs show some adversarial robustness against misattribution attacks. Despite these capabilities, we found that naive prompting of LLMs does not scale well with a large number of authors due to input token limitations. To address this, we propose a tournament-style approach for large-scale attribution. Evaluating this approach on datasets of C++ (500 authors, 26,355 samples) and Java (686 authors, 55,267 samples) code from GitHub, we achieve classification accuracy of up to 65% for C++ and 68.7% for Java using only one reference per author. These results open new possibilities for applying LLMs to code authorship attribution in cybersecurity and software engineering.
Potential and Perils of Large Language Models as Judges of Unstructured Textual Data
Venue: arXiv cs.CL 2025
Year: 2025

Rapid advancements in large language models have unlocked remarkable capabilities when it comes to processing and summarizing unstructured text data. This has implications for the analysis of rich, open-ended datasets, such as survey responses, where LLMs hold the promise of efficiently distilling key themes and sentiments. However, as organizations increasingly turn to these powerful AI systems to make sense of textual feedback, a critical question arises, can we trust LLMs to accurately represent the perspectives contained within these text based datasets? While LLMs excel at generating human-like summaries, there is a risk that their outputs may inadvertently diverge from the true substance of the original responses. Discrepancies between the LLM-generated outputs and the actual themes present in the data could lead to flawed decision-making, with far-reaching consequences for organizations. This research investigates the effectiveness of LLM-as-judge models to evaluate the thematic alignment of summaries generated by other LLMs. We utilized an Anthropic Claude model to generate thematic summaries from open-ended survey responses, with Amazon's Titan Express, Nova Pro, and Meta's Llama serving as judges. This LLM-as-judge approach was compared to human evaluations using Cohen's kappa, Spearman's rho, and Krippendorff's alpha, validating a scalable alternative to traditional human centric evaluation methods. Our findings reveal that while LLM-as-judge offer a scalable solution comparable to human raters, humans may still excel at detecting subtle, context-specific nuances. Our research contributes to the growing body of knowledge on AI assisted text analysis. Further, we provide recommendations for future research, emphasizing the need for careful consideration when generalizing LLM-as-judge models across various contexts and use cases.