OpenRaiser/Intern-Atlas huggingface dataset:
Predicting effect of novel treatments using molecular pathways and real-world data
Venue: arXiv cs.LG 2025
Year: 2025

In pharmaceutical R&D, predicting the efficacy of a pharmaceutical in treating a particular disease prior to clinical testing or any real-world use has been challenging. In this paper, we propose a flexible and modular machine learning-based approach for predicting the efficacy of an untested pharmaceutical for treating a disease. We train a machine learning model using sets of pharmaceutical-pathway weight impact scores and patient data, which can include patient characteristics and observed clinical outcomes. The resulting model then analyses weighted impact scores of an untested pharmaceutical across human biological molecule-protein pathways to generate a predicted efficacy value. We demonstrate how the method works on a real-world dataset with patient treatments and outcomes, with two different weight impact score algorithms We include methods for evaluating the generalisation performance on unseen treatments, and to characterise conditions under which the approach can be expected to be most predictive. We discuss specific ways in which our approach can be iterated on, making it an initial framework to support future work on predicting the effect of untested drugs, leveraging RWD clinical data and drug embeddings.
Quantum Machine Learning and Grover's Algorithm for Quantum Optimization of Robotic Manipulators
Venue: arXiv cs.RO 2025
Year: 2025

Optimizing high-degree of freedom robotic manipulators requires searching complex, high-dimensional configuration spaces, a task that is computationally challenging for classical methods. This paper introduces a quantum native framework that integrates quantum machine learning with Grover's algorithm to solve kinematic optimization problems efficiently. A parameterized quantum circuit is trained to approximate the forward kinematics model, which then constructs an oracle to identify optimal configurations. Grover's algorithm leverages this oracle to provide a quadratic reduction in search complexity. Demonstrated on simulated 1-DoF, 2-DoF, and dual-arm manipulator tasks, the method achieves significant speedups-up to 93x over classical optimizers like Nelder Mead as problem dimensionality increases. This work establishes a foundational, quantum-native framework for robot kinematic optimization, effectively bridging quantum computing and robotics problems.
Explaining How Quantization Disparately Skews a Model
Venue: arXiv cs.LG 2025
Year: 2025

Post Training Quantization (PTQ) is widely adopted due to its high compression capacity and speed with minimal impact on accuracy. However, we observed that disparate impacts are exacerbated by quantization, especially for minority groups. Our analysis explains that in the course of quantization there is a chain of factors attributed to a disparate impact across groups during forward and backward passes. We explore how the changes in weights and activations induced by quantization cause cascaded impacts in the network, resulting in logits with lower variance, increased loss, and compromised group accuracies. We extend our study to verify the influence of these impacts on group gradient norms and eigenvalues of the Hessian matrix, providing insights into the state of the network from an optimization point of view. To mitigate these effects, we propose integrating mixed precision Quantization Aware Training (QAT) with dataset sampling methods and weighted loss functions, therefore providing fair deployment of quantized neural networks.
Datasets for Navigating Sensitive Topics in Recommendation Systems
Venue: arXiv cs.IR 2025
Year: 2025

Personalized AI systems, from recommendation systems to chatbots, are a prevalent method for distributing content to users based on their learned preferences. However, there is growing concern about the adverse effects of these systems, including their potential tendency to expose users to sensitive or harmful material, negatively impacting overall well-being. To address this concern quantitatively, it is necessary to create datasets with relevant sensitivity labels for content, enabling researchers to evaluate personalized systems beyond mere engagement metrics. To this end, we introduce two novel datasets that include a taxonomy of sensitivity labels alongside user-content ratings: one that integrates MovieLens rating data with content warnings from the Does the Dog Die? community ratings website, and another that combines fan-fiction interaction data and user-generated warnings from Archive of Our Own.
A Unified Data-Driven Framework for Efficient Scientific Discovery
Venue: arXiv cs.CE 2025
Year: 2025

Scientific discovery drives progress across disciplines, from fundamental physics to industrial applications. However, identifying physical laws automatically from gathered datasets requires identifying the structure and parameters of the formula underlying the data, which involves navigating a vast search space and consuming substantial computational resources. To address these issues, we build on the Buckingham $Π$ theorem and Taylor's theorem to create a unified representation of diverse formulas, which introduces latent variables to form a two-stage structure. To minimize the search space, we initially focus on determining the structure of the latent formula, including the relevant contributing inputs, the count of latent variables, and their interconnections. Following this, the process of parameter identification is expedited by enforcing dimensional constraints for physical relevance, favoring simplicity in the formulas, and employing strategic optimization techniques. Any overly complex outcomes are refined using symbolic regression for a compact form. These general strategic techniques drastically reduce search iterations from hundreds of millions to just tens, significantly enhancing the efficiency of data-driven formula discovery. We performed comprehensive validation to demonstrate FIND's effectiveness in discovering physical laws, dimensionless numbers, partial differential equations, and uniform critical system parameters across various fields, including astronomy, physics, chemistry, and electronics. The excellent performances across 11 distinct datasets position FIND as a powerful and versatile tool for advancing data-driven scientific discovery in multiple domains.
Free Elections in the Free State: Ensemble Analysis of Redistricting in New Hampshire
Venue: arXiv cs.SI 2025
Year: 2025

The process of legislative redistricting in New Hampshire, along with many other states across the country, was particularly contentious during the 2020 census cycle. In this paper we present an ensemble analysis of the enacted districts to provide mathematical context for claims made about these maps in litigation. Operationalizing the New Hampshire redistricting rules and algorithmically generating a large collection of districting plans allows us to construct a baseline for expected behavior of districting plans in the state and evaluate non-partisan justifications and geographic tradeoffs between districting criteria and partisan outcomes. In addition, our results demonstrate the impact of selection and aggregation of election data for analyzing partisan symmetry measures.
SBS: Enhancing Parameter-Efficiency of Neural Representations for Neural Networks via Spectral Bias Suppression
Venue: arXiv cs.LG 2025
Year: 2025

Implicit neural representations have recently been extended to represent convolutional neural network weights via neural representation for neural networks, offering promising parameter compression benefits. However, standard multi-layer perceptrons used in neural representation for neural networks exhibit a pronounced spectral bias, hampering their ability to reconstruct high-frequency details effectively. In this paper, we propose SBS, a parameter-efficient enhancement to neural representation for neural networks that suppresses spectral bias using two techniques: (1) a unidirectional ordering-based smoothing that improves kernel smoothness in the output space, and (2) unidirectional ordering-based smoothing aware random fourier features that adaptively modulate the frequency bandwidth of input encodings based on layer-wise parameter count. Extensive evaluations on various ResNet models with datasets CIFAR-10, CIFAR-100, and ImageNet, demonstrate that SBS achieves significantly better reconstruction accuracy with less parameters compared to SOTA.
In the Eye of MLLM: Benchmarking Egocentric Video Intent Understanding with Gaze-Guided Prompting
Venue: arXiv cs.CV 2025
Year: 2025

The emergence of advanced multimodal large language models (MLLMs) has significantly enhanced AI assistants' ability to process complex information across modalities. Recently, egocentric videos, by directly capturing user focus, actions, and context in an unified coordinate, offer an exciting opportunity to enable proactive and personalized AI user experiences with MLLMs. However, existing benchmarks overlook the crucial role of gaze as an indicator of user intent. To address this gap, we introduce EgoGazeVQA, an egocentric gaze-guided video question answering benchmark that leverages gaze information to improve the understanding of longer daily-life videos. EgoGazeVQA consists of gaze-based QA pairs generated by MLLMs and refined by human annotators. Our experiments reveal that existing MLLMs struggle to accurately interpret user intentions. In contrast, our gaze-guided intent prompting methods significantly enhance performance by integrating spatial, temporal, and intent-related cues. We further conduct experiments on gaze-related fine-tuning and analyze how gaze estimation accuracy impacts prompting effectiveness. These results underscore the value of gaze for more personalized and effective AI assistants in egocentric settings. Project page: https://taiyi98.github.io/projects/EgoGazeVQA
Aspect-Oriented Programming in Secure Software Development: A Case Study of Security Aspects in Web Applications
Venue: arXiv cs.SE 2025
Year: 2025

Security remains a critical challenge in modern web applications, where threats such as unauthorized access, data breaches, and injection attacks continue to undermine trust and reliability. Traditional Object-Oriented Programming (OOP) often intertwines security logic with business functionality, leading to code tangling, scattering, and reduced maintainability. This study investigates the role of Aspect-Oriented Programming (AOP) in enhancing secure software development by modularizing cross-cutting security concerns. Using a case study approach, we compare AOP-based implementations of security features including authentication, authorization, input validation, encryption, logging, and session management with conventional OOP or middleware-based approaches. Data collection involves analyzing code quality metrics (e.g., lines of code, coupling, cohesion, modularity index, reusability), performance metrics (response time, throughput, memory usage), and maintainability indicators. Developer feedback is also incorporated to assess integration and debugging experiences. Statistical methods, guided by the ISO/IEC 25010 software quality model, are applied to evaluate differences across implementations. The findings demonstrate that AOP enhances modularity, reusability, and maintainability of security mechanisms, while introducing only minimal performance overhead. The study contributes practical insights for software engineers and researchers seeking to balance security with software quality in web application development.
Accurate and Complete Surface Reconstruction from 3D Gaussians via Direct SDF Learning
Venue: arXiv cs.CV 2025
Year: 2025

3D Gaussian Splatting (3DGS) has recently emerged as a powerful paradigm for photorealistic view synthesis, representing scenes with spatially distributed Gaussian primitives. While highly effective for rendering, achieving accurate and complete surface reconstruction remains challenging due to the unstructured nature of the representation and the absence of explicit geometric supervision. In this work, we propose DiGS, a unified framework that embeds Signed Distance Field (SDF) learning directly into the 3DGS pipeline, thereby enforcing strong and interpretable surface priors. By associating each Gaussian with a learnable SDF value, DiGS explicitly aligns primitives with underlying geometry and improves cross-view consistency. To further ensure dense and coherent coverage, we design a geometry-guided grid growth strategy that adaptively distributes Gaussians along geometry-consistent regions under a multi-scale hierarchy. Extensive experiments on standard benchmarks, including DTU, Mip-NeRF 360, and Tanks& Temples, demonstrate that DiGS consistently improves reconstruction accuracy and completeness while retaining high rendering fidelity.
Generating Transferrable Adversarial Examples via Local Mixing and Logits Optimization for Remote Sensing Object Recognition
Venue: arXiv cs.CV 2025
Year: 2025

Deep Neural Networks (DNNs) are vulnerable to adversarial attacks, posing significant security threats to their deployment in remote sensing applications. Research on adversarial attacks not only reveals model vulnerabilities but also provides critical insights for enhancing robustness. Although current mixing-based strategies have been proposed to increase the transferability of adversarial examples, they either perform global blending or directly exchange a region in the images, which may destroy global semantic features and mislead the optimization of adversarial examples. Furthermore, their reliance on cross-entropy loss for perturbation optimization leads to gradient diminishing during iterative updates, compromising adversarial example quality. To address these limitations, we focus on non-targeted attacks and propose a novel framework via local mixing and logits optimization. First, we present a local mixing strategy to generate diverse yet semantically consistent inputs. Different from MixUp, which globally blends two images, and MixCut, which stitches images together, our method merely blends local regions to preserve global semantic information. Second, we adapt the logit loss from targeted attacks to non-targeted scenarios, mitigating the gradient vanishing problem of cross-entropy loss. Third, a perturbation smoothing loss is applied to suppress high-frequency noise and enhance transferability. Extensive experiments on FGSCR-42 and MTARSI datasets demonstrate superior performance over 12 state-of-the-art methods across 6 surrogate models. Notably, with ResNet as the surrogate on MTARSI, our method achieves a 17.28% average improvement in black-box attack success rate.
Astra: A Multi-Agent System for GPU Kernel Performance Optimization
Venue: arXiv cs.DC 2025
Year: 2025

GPU kernel optimization has long been a central challenge at the intersection of high-performance computing and machine learning. Efficient kernels are crucial for accelerating large language model (LLM) training and serving, yet attaining high performance typically requires extensive manual tuning. Compiler-based systems reduce some of this burden, but still demand substantial manual design and engineering effort. Recently, researchers have explored using LLMs for GPU kernel generation, though prior work has largely focused on translating high-level PyTorch modules into CUDA code. In this work, we introduce Astra, the first LLM-based multi-agent system for GPU kernel optimization. Unlike previous approaches, Astra starts from existing CUDA implementations extracted from SGLang, a widely deployed framework for serving LLMs, rather than treating PyTorch modules as the specification. Within Astra, specialized LLM agents collaborate through iterative code generation, testing, profiling, and planning to produce kernels that are both correct and high-performance. On kernels from SGLang, Astra achieves an average speedup of 1.32x using zero-shot prompting with OpenAI o4-mini. A detailed case study further demonstrates that LLMs can autonomously apply loop transformations, optimize memory access patterns, exploit CUDA intrinsics, and leverage fast math operations to yield substantial performance gains. Our work highlights multi-agent LLM systems as a promising new paradigm for GPU kernel optimization. Our code is publicly available at https://github.com/Anjiang-Wei/Astra.
Avoiding Knowledge Edit Skipping in Multi-hop Question Answering with Guided Decomposition
Venue: arXiv cs.CL 2025
Year: 2025

In a rapidly evolving world where information updates swiftly, knowledge in large language models (LLMs) becomes outdated quickly. Retraining LLMs is not a cost-effective option, making knowledge editing (KE) without modifying parameters particularly necessary. We find that although existing retrieval-augmented generation (RAG)-based KE methods excel at editing simple knowledge, they struggle with KE in multi-hop question answering due to the issue of "edit skipping", which refers to skipping the relevant edited fact in inference. In addition to the diversity of natural language expressions of knowledge, edit skipping also arises from the mismatch between the granularity of LLMs in problem-solving and the facts in the edited memory. To address this issue, we propose a novel Iterative Retrieval-Augmented Knowledge Editing method with guided decomposition (IRAKE) through the guidance from single edited facts and entire edited cases. Experimental results demonstrate that IRAKE mitigates the failure of editing caused by edit skipping and outperforms state-of-the-art methods for KE in multi-hop question answering.
Bio-inspired decision making in swarms under biases from stubborn robots, corrupted communication, and independent discovery
Venue: arXiv cs.MA 2025
Year: 2025

Minimalistic robot swarms offer a scalable, robust, and cost-effective approach to performing complex tasks with the potential to transform applications in healthcare, disaster response, and environmental monitoring. However, coordinating such decentralised systems remains a fundamental challenge, particularly when robots are constrained in communication, computation, and memory. In our study, individual robots frequently make errors when sensing the environment, yet the swarm can rapidly and reliably reach consensus on the best among $n$ discrete options. We compare two canonical mechanisms of opinion dynamics -- direct-switch and cross-inhibition -- which are simple yet effective rules for collective information processing observed in biological systems across scales, from neural populations to insect colonies. We generalise the existing mean-field models by considering asocial biases influencing the opinion dynamics. While swarms using direct-switch reliably select the best option in absence of asocial dynamics, their performance deteriorates once such biases are introduced, often resulting in decision deadlocks. In contrast, bio-inspired cross-inhibition enables faster, more cohesive, accurate, robust, and scalable decisions across a wide range of biased conditions. Our findings provide theoretical and practical insights into the coordination of minimal swarms and offer insights that extend to a broad class of decentralised decision-making systems in biology and engineering.
Self-Supervised Cross-Encoder for Neurodegenerative Disease Diagnosis
Venue: arXiv cs.CV 2025
Year: 2025

Deep learning has shown significant potential in diagnosing neurodegenerative diseases from MRI data. However, most existing methods rely heavily on large volumes of labeled data and often yield representations that lack interpretability. To address both challenges, we propose a novel self-supervised cross-encoder framework that leverages the temporal continuity in longitudinal MRI scans for supervision. This framework disentangles learned representations into two components: a static representation, constrained by contrastive learning, which captures stable anatomical features; and a dynamic representation, guided by input-gradient regularization, which reflects temporal changes and can be effectively fine-tuned for downstream classification tasks. Experimental results on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset demonstrate that our method achieves superior classification accuracy and improved interpretability. Furthermore, the learned representations exhibit strong zero-shot generalization on the Open Access Series of Imaging Studies (OASIS) dataset and cross-task generalization on the Parkinson Progression Marker Initiative (PPMI) dataset. The code for the proposed method will be made publicly available.
Influence Maximization Considering Influence, Cost and Time
Venue: arXiv cs.SI 2025
Year: 2025

Influence maximization has been studied for social network analysis, such as viral marketing (advertising), rumor prevention, and opinion leader identification. However, most studies neglect the interplay between influence spread, cost efficiency, and temporal urgency. In practical scenarios such as viral marketing and information campaigns, jointly optimizing Influence, Cost, and Time is essential, yet remaining largely unaddressed in current literature. To bridge the gap, this paper proposes a new multi-objective influence maximization problem that simultaneously optimizes influence, cost, and time. We show the intuitive and empirical evidence to prove the feasibility and necessity of this multi-objective problem. We also develop an evolutionary variable-length search algorithm that can effectively search for optimal node combinations. The proposed EVEA algorithm outperforms all baselines, achieving up to 19.3% higher hypervolume and 25 to 40% faster convergence across four real-world networks, while maintaining a diverse and balanced Pareto front among influence, cost, and time objectives.
DeepGraphLog for Layered Neurosymbolic AI
Venue: arXiv cs.AI 2025
Year: 2025

Neurosymbolic AI (NeSy) aims to integrate the statistical strengths of neural networks with the interpretability and structure of symbolic reasoning. However, current NeSy frameworks like DeepProbLog enforce a fixed flow where symbolic reasoning always follows neural processing. This restricts their ability to model complex dependencies, especially in irregular data structures such as graphs. In this work, we introduce DeepGraphLog, a novel NeSy framework that extends ProbLog with Graph Neural Predicates. DeepGraphLog enables multi-layer neural-symbolic reasoning, allowing neural and symbolic components to be layered in arbitrary order. In contrast to DeepProbLog, which cannot handle symbolic reasoning via neural methods, DeepGraphLog treats symbolic representations as graphs, enabling them to be processed by Graph Neural Networks (GNNs). We showcase the capabilities of DeepGraphLog on tasks in planning, knowledge graph completion with distant supervision, and GNN expressivity. Our results demonstrate that DeepGraphLog effectively captures complex relational dependencies, overcoming key limitations of existing NeSy systems. By broadening the applicability of neurosymbolic AI to graph-structured domains, DeepGraphLog offers a more expressive and flexible framework for neural-symbolic integration.