pwc-archive/papers-with-abstracts huggingface dataset:
A multi-locus predictiveness curve and its summary assessment for genetic risk prediction
Authors: Changshuai Wei, Ming Li, Yalu Wen, Chengyin Ye, Qing Lu
Date: 2025-03-28 00:00:00
Tasks: Disease Prediction, Genetic Risk Prediction, Prediction

With the advance of high-throughput genotyping and sequencing technologies, it becomes feasible to comprehensive evaluate the role of massive genetic predictors in disease prediction. There exists, therefore, a critical need for developing appropriate statistical measurements to access the combined effects of these genetic variants in disease prediction. Predictiveness curve is commonly used as a graphical tool to measure the predictive ability of a risk prediction model on a single continuous biomarker. Yet, for most complex diseases, risk prediciton models are formed on multiple genetic variants. We therefore propose a multi-marker predictiveness curve and provide a non-parametric method to construct the curve for case-control studies. We further introduce a global predictiveness U and a partial predictiveness U to summarize prediction curve across the whole population and sub-population of clinical interest, respectively. We also demonstrate the connections of predictiveness curve with ROC curve and Lorenz curve. Through simulation, we compared the performance of the predictiveness U to other three summary indices: R square, Total Gain, and Average Entropy, and showed that Predictiveness U outperformed the other three indexes in terms of unbiasedness and robustness. Moreover, we simulated a series of rare-variants disease model, found partial predictiveness U performed better than global predictiveness U. Finally, we conducted a real data analysis, using predictiveness curve and predictiveness U to evaluate a risk prediction model for Nicotine Dependence.
Online Fault Detection and Classification of Chemical Process Systems Leveraging Statistical Process Control and Riemannian Geometric Analysis
Authors: Alireza Miraliakbar, Fangyuan Ma, Zheyu Jiang
Date: 2025-04-02 00:00:00
Tasks: Chemical Process, Fault Detection

In this work, we study an integrated fault detection and classification framework called FARM for fast, accurate, and robust online chemical process monitoring. The FARM framework integrates the latest advancements in statistical process control (SPC) for monitoring nonparametric and heterogeneous data streams with novel data analysis approaches based on Riemannian geometry together in a hierarchical framework for online process monitoring. We conduct a systematic evaluation of the FARM monitoring framework using the Tennessee Eastman Process (TEP) dataset. Results show that FARM performs competitively against state-of-the-art process monitoring algorithms by achieving a good balance among fault detection rate (FDR), fault detection speed (FDS), and false alarm rate (FAR). Specifically, FARM achieved an average FDR of 96.97% while also outperforming benchmark methods in successfully detecting hard-to-detect faults that are previously known, including Faults 3, 9 and 15, with FDRs being 97.08%, 96.30% and 95.99%, respectively. In terms of FAR, our FARM framework allows practitioners to customize their choice of FAR, thereby offering great flexibility. Moreover, we report a significant improvement in average fault classification accuracy during online monitoring from 61% to 82% when leveraging Riemannian geometric analysis, and further to 84.5% when incorporating additional features from SPC. This illustrates the synergistic effect of integrating fault detection and classification in a holistic, hierarchical monitoring framework.
ffstruc2vec: Flat, Flexible and Scalable Learning of Node Representations from Structural Identities
Authors: Mario Heidrich, Jeffrey Heidemann, Rüdiger Buchkremer, Gonzalo Wandosell Fernández de Bobadilla
Date: 2025-04-01 00:00:00

Node embedding refers to techniques that generate low-dimensional vector representations of nodes in a graph while preserving specific properties of the nodes. A key challenge in the field is developing scalable methods that can preserve structural properties suitable for the required types of structural patterns of a given downstream application task. While most existing methods focus on preserving node proximity, those that do preserve structural properties often lack the flexibility to preserve various types of structural patterns required by downstream application tasks. This paper introduces ffstruc2vec, a scalable deep-learning framework for learning node embedding vectors that preserve structural identities. Its flat, efficient architecture allows high flexibility in capturing diverse types of structural patterns, enabling broad adaptability to various downstream application tasks. The proposed framework significantly outperforms existing approaches across diverse unsupervised and supervised tasks in practical applications. Moreover, ffstruc2vec enables explainability by quantifying how individual structural patterns influence task outcomes, providing actionable interpretation. To our knowledge, no existing framework combines this level of flexibility, scalability, and structural interpretability, underscoring its unique capabilities.
Performative Drift Resistant Classification Using Generative Domain Adversarial Networks
Authors: Maciej Makowski, Brandon Gower-Winter, Georg Krempl
Date: 2025-04-01 00:00:00

Performative Drift is a special type of Concept Drift that occurs when a model's predictions influence the future instances the model will encounter. In these settings, retraining is not always feasible. In this work, we instead focus on drift understanding as a method for creating drift-resistant classifiers. To achieve this, we introduce the Generative Domain Adversarial Network (GDAN) which combines both Domain and Generative Adversarial Networks. Using GDAN, domain-invariant representations of incoming data are created and a generative network is used to reverse the effects of performative drift. Using semi-real and synthetic data generators, we empirically evaluate GDAN's ability to provide drift-resistant classification. Initial results are promising with GDAN limiting performance degradation over several timesteps. Additionally, GDAN's generative network can be used in tandem with other models to limit their performance degradation in the presence of performative drift. Lastly, we highlight the relationship between model retraining and the unpredictability of performative drift, providing deeper insights into the challenges faced when using traditional Concept Drift mitigation strategies in the performative setting.
Efficient n-body simulations using physics informed graph neural networks
Authors: Víctor Ramos-Osuna, Alberto Díaz-Álvarez, Raúl Lara-Cabrera
Date: 2025-04-01 00:00:00
Tasks: Computational Efficiency

This paper presents a novel approach for accelerating n-body simulations by integrating a physics-informed graph neural networks (GNN) with traditional numerical methods. Our method implements a leapfrog-based simulation engine to generate datasets from diverse astrophysical scenarios which are then transformed into graph representations. A custom-designed GNN is trained to predict particle accelerations with high precision. Experiments, conducted on 60 training and 6 testing simulations spanning from 3 to 500 bodies over 1000 time steps, demonstrate that the proposed model achieves extremely low prediction errors-loss values while maintaining robust long-term stability, with accumulated errors in position, velocity, and acceleration remaining insignificant. Furthermore, our method yields a modest speedup of approximately 17% over conventional simulation techniques. These results indicate that the integration of deep learning with traditional physical simulation methods offers a promising pathway to significantly enhance computational efficiency without compromising accuracy.
Neural Approaches to SAT Solving: Design Choices and Interpretability
Authors: David Mojžíšek, Jan Hůla, Ziwei Li, Ziyu Zhou, Mikoláš Janota
Date: 2025-04-01 00:00:00
Tasks: Graph Neural Network

In this contribution, we provide a comprehensive evaluation of graph neural networks applied to Boolean satisfiability problems, accompanied by an intuitive explanation of the mechanisms enabling the model to generalize to different instances. We introduce several training improvements, particularly a novel closest assignment supervision method that dynamically adapts to the model's current state, significantly enhancing performance on problems with larger solution spaces. Our experiments demonstrate the suitability of variable-clause graph representations with recurrent neural network updates, which achieve good accuracy on SAT assignment prediction while reducing computational demands. We extend the base graph neural network into a diffusion model that facilitates incremental sampling and can be effectively combined with classical techniques like unit propagation. Through analysis of embedding space patterns and optimization trajectories, we show how these networks implicitly perform a process very similar to continuous relaxations of MaxSAT, offering an interpretable view of their reasoning process. This understanding guides our design choices and explains the ability of recurrent architectures to scale effectively at inference time beyond their training distribution, which we demonstrate with test-time scaling experiments.
Global explainability of a deep abstaining classifier
Authors: Sayera Dhaubhadel, Jamaludin Mohd-Yusof, Benjamin H. McMahon, Trilce Estrada, Kumkum Ganguly, Adam Spannaus, John P. Gounley, Xiao-Cheng Wu, Eric B. Durbin, Heidi A. Hanson, Tanmoy Bhattacharya
Date: 2025-04-01 00:00:00
Tasks: Dimensionality Reduction

We present a global explainability method to characterize sources of errors in the histology prediction task of our real-world multitask convolutional neural network (MTCNN)-based deep abstaining classifier (DAC), for automated annotation of cancer pathology reports from NCI-SEER registries. Our classifier was trained and evaluated on 1.04 million hand-annotated samples and makes simultaneous predictions of cancer site, subsite, histology, laterality, and behavior for each report. The DAC framework enables the model to abstain on ambiguous reports and/or confusing classes to achieve a target accuracy on the retained (non-abstained) samples, but at the cost of decreased coverage. Requiring 97% accuracy on the histology task caused our model to retain only 22% of all samples, mostly the less ambiguous and common classes. Local explainability with the GradInp technique provided a computationally efficient way of obtaining contextual reasoning for thousands of individual predictions. Our method, involving dimensionality reduction of approximately 13000 aggregated local explanations, enabled global identification of sources of errors as hierarchical complexity among classes, label noise, insufficient information, and conflicting evidence. This suggests several strategies such as exclusion criteria, focused annotation, and reduced penalties for errors involving hierarchically related classes to iteratively improve our DAC in this complex real-world implementation.
Prompting Forgetting: Unlearning in GANs via Textual Guidance
Authors: Piyush Nagasubramaniam, Neeraj Karamchandani, Chen Wu, Sencun Zhu
Date: 2025-04-01 00:00:00
Tasks: Attribute, Image Generation, Machine Unlearning

State-of-the-art generative models exhibit powerful image-generation capabilities, introducing various ethical and legal challenges to service providers hosting these models. Consequently, Content Removal Techniques (CRTs) have emerged as a growing area of research to control outputs without full-scale retraining. Recent work has explored the use of Machine Unlearning in generative models to address content removal. However, the focus of such research has been on diffusion models, and unlearning in Generative Adversarial Networks (GANs) has remained largely unexplored. We address this gap by proposing Text-to-Unlearn, a novel framework that selectively unlearns concepts from pre-trained GANs using only text prompts, enabling feature unlearning, identity unlearning, and fine-grained tasks like expression and multi-attribute removal in models trained on human faces. Leveraging natural language descriptions, our approach guides the unlearning process without requiring additional datasets or supervised fine-tuning, offering a scalable and efficient solution. To evaluate its effectiveness, we introduce an automatic unlearning assessment method adapted from state-of-the-art image-text alignment metrics, providing a comprehensive analysis of the unlearning methodology. To our knowledge, Text-to-Unlearn is the first cross-modal unlearning framework for GANs, representing a flexible and efficient advancement in managing generative model behavior.
Gradient-free Continual Learning
Authors: Grzegorz Rypeść
Date: 2025-04-01 00:00:00
Tasks: Continual Learning

Continual learning (CL) presents a fundamental challenge in training neural networks on sequential tasks without experiencing catastrophic forgetting. Traditionally, the dominant approach in CL has been gradient-based optimization, where updates to the network parameters are performed using stochastic gradient descent (SGD) or its variants. However, a major limitation arises when previous data is no longer accessible, as is often assumed in CL settings. In such cases, there is no gradient information available for past data, leading to uncontrolled parameter changes and consequently severe forgetting of previously learned tasks. By shifting focus from data availability to gradient availability, this work opens up new avenues for addressing forgetting in CL. We explore the hypothesis that gradient-free optimization methods can provide a robust alternative to conventional gradient-based continual learning approaches. We discuss the theoretical underpinnings of such method, analyze their potential advantages and limitations, and present empirical evidence supporting their effectiveness. By reconsidering the fundamental cause of forgetting, this work aims to contribute a fresh perspective to the field of continual learning and inspire novel research directions.
AutoML Benchmark with shorter time constraints and early stopping
Authors: Israel Campero Jurado, Pieter Gijsbers, Joaquin Vanschoren
Date: 2025-04-01 00:00:00
Tasks: AutoML

Automated Machine Learning (AutoML) automatically builds machine learning (ML) models on data. The de facto standard for evaluating new AutoML frameworks for tabular data is the AutoML Benchmark (AMLB). AMLB proposed to evaluate AutoML frameworks using 1- and 4-hour time budgets across 104 tasks. We argue that shorter time constraints should be considered for the benchmark because of their practical value, such as when models need to be retrained with high frequency, and to make AMLB more accessible. This work considers two ways in which to reduce the overall computation used in the benchmark: smaller time constraints and the use of early stopping. We conduct evaluations of 11 AutoML frameworks on 104 tasks with different time constraints and find the relative ranking of AutoML frameworks is fairly consistent across time constraints, but that using early-stopping leads to a greater variety in model performance.
Dynamic Graph Structure Estimation for Learning Multivariate Point Process using Spiking Neural Networks
Authors: Biswadeep Chakraborty, Hemant Kumawat, Beomseok Kang, Saibal Mukhopadhyay
Date: 2025-04-01 00:00:00
Tasks: Computational Efficiency, Epidemiology, Point Processes

Modeling and predicting temporal point processes (TPPs) is critical in domains such as neuroscience, epidemiology, finance, and social sciences. We introduce the Spiking Dynamic Graph Network (SDGN), a novel framework that leverages the temporal processing capabilities of spiking neural networks (SNNs) and spike-timing-dependent plasticity (STDP) to dynamically estimate underlying spatio-temporal functional graphs. Unlike existing methods that rely on predefined or static graph structures, SDGN adapts to any dataset by learning dynamic spatio-temporal dependencies directly from the event data, enhancing generalizability and robustness. While SDGN offers significant improvements over prior methods, we acknowledge its limitations in handling dense graphs and certain non-Gaussian dependencies, providing opportunities for future refinement. Our evaluations, conducted on both synthetic and real-world datasets including NYC Taxi, 911, Reddit, and Stack Overflow, demonstrate that SDGN achieves superior predictive accuracy while maintaining computational efficiency. Furthermore, we include ablation studies to highlight the contributions of its core components.
FLAMES: A Hybrid Spiking-State Space Model for Adaptive Memory Retention in Event-Based Learning
Authors: Biswadeep Chakraborty, Saibal Mukhopadhyay
Date: 2025-04-02 00:00:00
Tasks: Computational Efficiency

We propose \textbf{FLAMES (Fast Long-range Adaptive Memory for Event-based Systems)}, a novel hybrid framework integrating structured state-space dynamics with event-driven computation. At its core, the \textit{Spike-Aware HiPPO (SA-HiPPO) mechanism} dynamically adjusts memory retention based on inter-spike intervals, preserving both short- and long-range dependencies. To maintain computational efficiency, we introduce a normal-plus-low-rank (NPLR) decomposition, reducing complexity from $\mathcal{O}(N^2)$ to $\mathcal{O}(Nr)$. FLAMES achieves state-of-the-art results on the Long Range Arena benchmark and event datasets like HAR-DVS and Celex-HAR. By bridging neuromorphic computing and structured sequence modeling, FLAMES enables scalable long-range reasoning in event-driven systems.
Scaling Test-Time Inference with Policy-Optimized, Dynamic Retrieval-Augmented Generation via KV Caching and Decoding
Authors: Sakhinana Sagar Srinivas, Akash Das, Shivam Gupta, Venkataramana Runkana
Date: 2025-04-02 00:00:00
Tasks: Question Answering, RAG, Retrieval, Retrieval-augmented Generation

We present a comprehensive framework for enhancing Retrieval-Augmented Generation (RAG) systems through dynamic retrieval strategies and reinforcement fine-tuning. This approach significantly improves large language models on knowledge-intensive tasks, including opendomain question answering and complex reasoning. Our framework integrates two complementary techniques: Policy-Optimized RetrievalAugmented Generation (PORAG), which optimizes the use of retrieved information, and Adaptive Token-Layer Attention Scoring (ATLAS), which dynamically determines retrieval timing and content based on contextual needs. Together, these techniques enhance both the utilization and relevance of retrieved content, improving factual accuracy and response quality. Designed as a lightweight solution compatible with any Transformer-based LLM without requiring additional training, our framework excels in knowledge-intensive tasks, boosting output accuracy in RAG settings. We further propose CRITIC, a novel method to selectively compress key-value caches by token importance, mitigating memory bottlenecks in long-context applications. The framework also incorporates test-time scaling techniques to dynamically balance reasoning depth and computational resources, alongside optimized decoding strategies for faster inference. Experiments on benchmark datasets show that our framework reduces hallucinations, strengthens domain-specific reasoning, and achieves significant efficiency and scalability gains over traditional RAG systems. This integrated approach advances the development of robust, efficient, and scalable RAG systems across diverse applications.
Flexible and Explainable Graph Analysis for EEG-based Alzheimer's Disease Classification
Authors: Jing Wang, Jun-En Ding, Feng Liu, Elisa Kallioniemi, Shuqiang Wang, Wen-Xiang Tsai, Albert C. Yang
Date: 2025-04-02 00:00:00
Tasks: EEG, Specificity

Alzheimer's Disease is a progressive neurological disorder that is one of the most common forms of dementia. It leads to a decline in memory, reasoning ability, and behavior, especially in older people. The cause of Alzheimer's Disease is still under exploration and there is no all-inclusive theory that can explain the pathologies in each individual patient. Nevertheless, early intervention has been found to be effective in managing symptoms and slowing down the disease's progression. Recent research has utilized electroencephalography (EEG) data to identify biomarkers that distinguish Alzheimer's Disease patients from healthy individuals. Prior studies have used various machine learning methods, including deep learning and graph neural networks, to examine electroencephalography-based signals for identifying Alzheimer's Disease patients. In our research, we proposed a Flexible and Explainable Gated Graph Convolutional Network (GGCN) with Multi-Objective Tree-Structured Parzen Estimator (MOTPE) hyperparameter tuning. This provides a flexible solution that efficiently identifies the optimal number of GGCN blocks to achieve the optimized precision, specificity, and recall outcomes, as well as the optimized area under the Receiver Operating Characteristic (AUC). Our findings demonstrated a high efficacy with an over 0.9 Receiver Operating Characteristic score, alongside precision, specificity, and recall scores in distinguishing health control with Alzheimer's Disease patients in Moderate to Severe Dementia using the power spectrum density (PSD) of electroencephalography signals across various frequency bands. Moreover, our research enhanced the interpretability of the embedded adjacency matrices, revealing connectivity differences in frontal and parietal brain regions between Alzheimer's patients and healthy individuals.
Advancing MoE Efficiency: A Collaboration-Constrained Routing (C2R) Strategy for Better Expert Parallelism Design
Authors: Mohan Zhang, Pingzhi Li, Jie Peng, Mufan Qiu, Tianlong Chen
Date: 2025-04-02 00:00:00
Tasks: Attribute, Mixture-of-Experts

Mixture-of-Experts (MoE) has successfully scaled up models while maintaining nearly constant computing costs. By employing a gating network to route input tokens, it selectively activates a subset of expert networks to process the corresponding token embeddings. However, in practice, the efficiency of MoE is challenging to achieve due to two key reasons: imbalanced expert activation, which leads to substantial idle time during model or expert parallelism, and insufficient capacity utilization; massive communication overhead, induced by numerous expert routing combinations in expert parallelism at the system level. Previous works typically formulate it as the load imbalance issue characterized by the gating network favoring certain experts over others or attribute it to static execution which fails to adapt to the dynamic expert workload at runtime. In this paper, we exploit it from a brand new perspective, a higher-order view and analysis of MoE routing policies: expert collaboration and specialization where some experts tend to activate broadly with others (collaborative), while others are more likely to activate only with a specific subset of experts (specialized). Our experiments reveal that most experts tend to be overly collaborative, leading to increased communication overhead from repeatedly sending tokens to different accelerators. To this end, we propose a novel collaboration-constrained routing (C2R) strategy to encourage more specialized expert groups, as well as to improve expert utilization, and present an efficient implementation of MoE that further leverages expert specialization. We achieve an average performance improvement of 0.51% and 0.33% on LLaMA-MoE and Qwen-MoE respectively across ten downstream NLP benchmarks, and reduce the all2all communication costs between GPUs, bringing an extra 20%-30% total running time savings on top of the existing SoTA, i.e. MegaBlocks.