arXiv subjects

Aleksandar Vakanski

Publications and source records attributed to Aleksandar Vakanski.

At least 19 recordsLinked to original sources

arXiv2026

Machine Learning-based Correlation of Charpy Impact Properties Between Sub-sized and Standard-sized Specimens for Nuclear Structural Materials

Reliable correlations of Charpy impact test results between sub-sized and full-sized specimens are essential for structural integrity assessments, particularly in nuclear applications, where spatial constraints and limited material volume restrict specimen size. Although standards such as ASTM A370 and BS 7910 provide guidance on conversion methodologies, and numerous analytical correlation methods have been proposed in prior studies, these approaches generally have limited accuracy and their applicability is often constrained to specific materials, treatment conditions, and specimen geometries. In this study, a Machine Learning (ML)-based framework is proposed for correlating Charpy impact properties across specimen sizes. The proposed approach maps absorbed energy values across the full ductile-to-brittle transition region by applying a temperature shift combined with scaled residual projection, to align sub-sized test data with full-sized response. From the resulting temperature-energy profiles, the correlated values for upper shelf energy (USE) and ductile-to-brittle transition temperature (DBTT) are extracted by fitting data with a hyperbolic tangent model. The framework is validated using a dataset comprising 389 matched sub-sized and full-sized Charpy impact tests on SA533B steel. This ML-based approach demonstrates an improved correlation performance relative to conventional analytical methods, achieving R2 values of 0.942 for USE and 0.892 for DBTT. The trained ML models do not require access to full-sized Charpy data during inference, making this approach suitable for material surveillance programs, accelerated irradiation testing, and other applications involving small-size Charpy impact testing.

cs.LG↗

arXiv2026

Interpretable Graph Kolmogorov-Arnold Networks for Multi-Cancer Classification and Biomarker Identification using Multi-Omics Data

The integration of heterogeneous multi-omics datasets at a systems level remains a central challenge for developing analytical and computational models in precision cancer diagnostics. This paper introduces Multi-Omics Graph Kolmogorov-Arnold Network (MOGKAN), a deep learning framework that utilizes messenger-RNA, micro-RNA sequences, and DNA methylation samples together with Protein-Protein Interaction (PPI) networks for cancer classification across 31 different cancer types. The proposed approach combines differential gene expression with DESeq2, Linear Models for Microarray (LIMMA), and Least Absolute Shrinkage and Selection Operator (LASSO) regression to reduce multi-omics data dimensionality while preserving relevant biological features. The model architecture is based on the Kolmogorov-Arnold theorem principle and uses trainable univariate functions to enhance interpretability and feature analysis. MOGKAN achieves classification accuracy of 96.28 percent and exhibits low experimental variability in comparison to related deep learning-based models. The biomarkers identified by MOGKAN were validated as cancer-related markers through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. By integrating multi-omics data with graph-based deep learning, our proposed approach demonstrates robust predictive performance and interpretability with potential to enhance the translation of complex multi-omics data into clinically actionable cancer diagnostics.

cs.LG↗

arXiv2026

Post-Hoc Understanding of Metaphor Processing in Decoder-Only Language Models via Conditional Scale Entropy

Metaphor requires a language model to resolve a token whose contextual meaning diverges from its basic literal sense. Understanding how transformer models organize this reinterpretation across depth remains an open problem in mechanistic interpretability. We introduce conditional scale entropy (CSE), a wavelet-derived measure of how broadly transformer computation engages across frequency scales at each layer position. Two theorems establish that CSE is invariant to update magnitude, isolating the structural pattern of updates from their intensity. Using CSE, we find that metaphorical tokens produce significantly higher spectral breadth than literal tokens at contiguous layer positions on every decoder-only architecture tested, from 124M to 20B parameters (GPT-2 family, LLaMA-2 7B, GPT-oss 20B). The effect survives cluster-based permutation correction, recurs in the early-to-mid relative depth range across models, and converges with an independent analysis of 200 naturalistic VUA pairs. Specificity controls further show that the effect is not explained by semantic complexity or by matched propositional content. These results identify multi-scale coordination as a consistent signature of metaphorical language processing in the decoder-only architectures examined, and establish CSE as a principled tool for characterizing cross-depth structure in transformers.

cs.CL↗

arXiv2025

Decentralized Distributed Proximal Policy Optimization (DD-PPO) for High Performance Computing Scheduling on Multi-User Systems

Resource allocation in High Performance Computing (HPC) environments presents a complex and multifaceted challenge for job scheduling algorithms. Beyond the efficient allocation of system resources, schedulers must account for and optimize multiple performance metrics, including job wait time and system utilization. While traditional rule-based scheduling algorithms dominate the current deployments of HPC systems, the increasing heterogeneity and scale of those systems is expected to challenge the efficiency and flexibility of those algorithms in minimizing job wait time and maximizing utilization. Recent research efforts have focused on leveraging advancements in Reinforcement Learning (RL) to develop more adaptable and intelligent scheduling strategies. Recent RL-based scheduling approaches have explored a range of algorithms, from Deep Q-Networks (DQN) to Proximal Policy Optimization (PPO), and more recently, hybrid methods that integrate Graph Neural Networks with RL techniques. However, a common limitation across these methods is their reliance on relatively small datasets, and these methods face scalability issues when using large datasets. This study introduces a novel RL-based scheduler utilizing the Decentralized Distributed Proximal Policy Optimization (DD-PPO) algorithm, which supports large-scale distributed training across multiple workers without requiring parameter synchronization at every step. By eliminating reliance on centralized updates to a shared policy, the DD-PPO scheduler enhances scalability, training efficiency, and sample utilization. The validation dataset leveraged over 11.5 million real HPC job traces for comparing DD-PPO performance between traditional and advanced scheduling approaches, and the experimental results demonstrate improved scheduling performance in comparison to both rule-based schedulers and existing RL-based scheduling algorithms.

cs.DC↗

arXiv2025

GCSAM: Gradient Centralized Sharpness Aware Minimization

The generalization performance of deep neural networks (DNNs) is a critical factor in achieving robust model behavior on unseen data. Recent studies have highlighted the importance of sharpness-based measures in promoting generalization by encouraging convergence to flatter minima. Among these approaches, Sharpness-Aware Minimization (SAM) has emerged as an effective optimization technique for reducing the sharpness of the loss landscape, thereby improving generalization. However, SAM's computational overhead and sensitivity to noisy gradients limit its scalability and efficiency. To address these challenges, we propose Gradient-Centralized Sharpness-Aware Minimization (GCSAM), which incorporates Gradient Centralization (GC) to stabilize gradients and accelerate convergence. GCSAM normalizes gradients before the ascent step, reducing noise and variance, and improving stability during training. Our evaluations indicate that GCSAM consistently outperforms SAM and the Adam optimizer in terms of generalization and computational efficiency. These findings demonstrate GCSAM's effectiveness across diverse domains, including general and medical imaging tasks.

cs.LG↗

arXiv2025

Predictive Modeling and Uncertainty Quantification of Fatigue Life in Metal Alloys using Machine Learning

Recent advancements in machine learning-based methods have demonstrated great potential for improved property prediction in material science. However, reliable estimation of the confidence intervals for the predicted values remains a challenge, due to the inherent complexities in material modeling. This study introduces a novel approach for uncertainty quantification in fatigue life prediction of metal materials based on integrating knowledge from physics-based fatigue life models and machine learning models. The proposed approach employs physics-based input features estimated using the Basquin fatigue model to augment the experimentally collected data of fatigue life. Furthermore, a physics-informed loss function that enforces boundary constraints for the estimated fatigue life of considered materials is introduced for the neural network models. Experimental validation on datasets comprising collected data from fatigue life tests for Titanium alloys and Carbon steel alloys demonstrates the effectiveness of the proposed approach. The synergy between physics-based models and data-driven models enhances the consistency in predicted values and improves uncertainty interval estimates.

cs.LG↗

arXiv2024

Dataset of Tensile Properties for Sub-sized Specimens of Nuclear Structural Materials

Mechanical testing with sub-sized specimens plays an important role in the nuclear industry, facilitating tests in confined experimental spaces with lower irradiation levels and accelerating the qualification of new materials. The reduced size of specimens results in different material behavior at the microscale, mesoscale, and macroscale, in comparison to standard-sized specimens, which is referred to as the specimen size effect. Although analytical models have been proposed to correlate the properties of sub-sized specimens to standard-sized specimens, these models lack broad applicability across different materials and testing conditions. The objective of this study is to create the first large public dataset of tensile properties for sub-sized specimens used in nuclear structural materials. We performed an extensive literature review of relevant publications and extracted over 1,000 tensile testing records comprising 54 parameters including material type and composition, manufacturing information, irradiation conditions, specimen dimensions, and tensile properties. The dataset can serve as a valuable resource to investigate the specimen size effect and develop computational methods to correlate the tensile properties of sub-sized specimens.

physics.ins-det↗

arXiv2024

Comparative Analysis of Multi-Omics Integration Using Advanced Graph Neural Networks for Cancer Classification

Multi-omics data is increasingly being utilized to advance computational methods for cancer classification. However, multi-omics data integration poses significant challenges due to the high dimensionality, data complexity, and distinct characteristics of various omics types. This study addresses these challenges and evaluates three graph neural network architectures for multi-omics (MO) integration based on graph-convolutional networks (GCN), graph-attention networks (GAT), and graph-transformer networks (GTN) for classifying 31 cancer types and normal tissues. To address the high-dimensionality of multi-omics data, we employed LASSO (Least Absolute Shrinkage and Selection Operator) regression for feature selection, leading to the creation of LASSO-MOGCN, LASSO-MOGAT, and LASSO-MOTGN models. Graph structures for the networks were constructed using gene correlation matrices and protein-protein interaction networks for multi-omics integration of messenger-RNA, micro-RNA, and DNA methylation data. Such data integration enables the networks to dynamically focus on important relationships between biological entities, improving both model performance and interpretability. Among the models, LASSO-MOGAT with a correlation-based graph structure achieved state-of-the-art accuracy (95.9%) and outperformed the LASSO-MOGCN and LASSO-MOTGN models in terms of precision, recall, and F1-score. Our findings demonstrate that integrating multi-omics data in graph-based architectures enhances cancer classification performance by uncovering distinct molecular patterns that contribute to a better understanding of cancer biology and potential biomarkers for disease progression.

q-bio.GN↗

arXiv2024

LASSO-MOGAT: A Multi-Omics Graph Attention Framework for Cancer Classification

The application of machine learning methods to analyze changes in gene expression patterns has recently emerged as a powerful approach in cancer research, enhancing our understanding of the molecular mechanisms underpinning cancer development and progression. Combining gene expression data with other types of omics data has been reported by numerous works to improve cancer classification outcomes. Despite these advances, effectively integrating high-dimensional multi-omics data and capturing the complex relationships across different biological layers remains challenging. This paper introduces LASSO-MOGAT (LASSO-Multi-Omics Gated ATtention), a novel graph-based deep learning framework that integrates messenger RNA, microRNA, and DNA methylation data to classify 31 cancer types. Utilizing differential expression analysis with LIMMA and LASSO regression for feature selection, and leveraging Graph Attention Networks (GATs) to incorporate protein-protein interaction (PPI) networks, LASSO-MOGAT effectively captures intricate relationships within multi-omics data. Experimental validation using five-fold cross-validation demonstrates the method's precision, reliability, and capacity for providing comprehensive insights into cancer molecular mechanisms. The computation of attention coefficients for the edges in the graph by the proposed graph-attention architecture based on protein-protein interactions proved beneficial for identifying synergies in multi-omics data for cancer classification.

cs.LG↗

arXiv2024

Do Sharpness-based Optimizers Improve Generalization in Medical Image Analysis?

Effective clinical deployment of deep learning models in healthcare demands high generalization performance to ensure accurate diagnosis and treatment planning. In recent years, significant research has focused on improving the generalization of deep learning models by regularizing the sharpness of the loss landscape. Among the optimization approaches that explicitly minimize sharpness, Sharpness-Aware Minimization (SAM) has shown potential in enhancing generalization performance on general domain image datasets. This success has led to the development of several advanced sharpness-based algorithms aimed at addressing the limitations of SAM, such as Adaptive SAM, surrogate-Gap SAM, Weighted SAM, and Curvature Regularized SAM. These sharpness-based optimizers have shown improvements in model generalization compared to conventional stochastic gradient descent optimizers and their variants on general domain image datasets, but they have not been thoroughly evaluated on medical images. This work provides a review of recent sharpness-based methods for improving the generalization of deep learning networks and evaluates the methods performance on medical breast ultrasound images. Our findings indicate that the initial SAM method successfully enhances the generalization of various deep learning models. While Adaptive SAM improves generalization of convolutional neural networks, it fails to do so for vision transformers. Other sharpness-based optimizers, however, do not demonstrate consistent results. The results reveal that, contrary to findings in the non-medical domain, SAM is the only recommended sharpness-based optimizer that consistently improves generalization in medical image analysis, and further research is necessary to refine the variants of SAM to enhance generalization performance in this field

eess.IV↗

arXiv2024

Review of Machine Learning Methods for Additive Manufacturing of Functionally Graded Materials

Additive Manufacturing (AM) is a transformative manufacturing technology enabling direct fabrication of complex parts layer-be-layer from 3D modeling data. Among AM applications, the fabrication of Functionally Graded Materials (FGMs) has significant importance due to the potential to enhance component performance across several industries. FGMs are manufactured with a gradient composition transition between dissimilar materials, enabling the design of new materials with location-dependent mechanical and physical properties. This study presents a comprehensive review of published literature pertaining to the implementation of Machine Learning (ML) techniques in AM, with an emphasis on ML-based methods for optimizing FGMs fabrication processes. Through an extensive survey of the literature, this review article explores the role of ML in addressing the inherent challenges in FGMs fabrication and encompasses parameter optimization, defect detection, and real-time monitoring. The article also provides a discussion of future research directions and challenges in employing ML-based methods in AM fabrication of FGMs.

cs.LG↗

arXiv2024

Uncertainty Quantification in Multivariable Regression for Material Property Prediction with Bayesian Neural Networks

With the increased use of data-driven approaches and machine learning-based methods in material science, the importance of reliable uncertainty quantification (UQ) of the predicted variables for informed decision-making cannot be overstated. UQ in material property prediction poses unique challenges, including the multi-scale and multi-physics nature of advanced materials, intricate interactions between numerous factors, limited availability of large curated datasets for model training, etc. Recently, Bayesian Neural Networks (BNNs) have emerged as a promising approach for UQ, offering a probabilistic framework for capturing uncertainties within neural networks. In this work, we introduce an approach for UQ within physics-informed BNNs, which integrates knowledge from governing laws in material modeling to guide the models toward physically consistent predictions. To evaluate the effectiveness of this approach, we present case studies for predicting the creep rupture life of steel alloys. Experimental validation with three datasets of collected measurements from creep tests demonstrates the ability of BNNs to produce accurate point and uncertainty estimates that are competitive or exceed the performance of the conventional method of Gaussian Process Regression. Similarly, we evaluated the suitability of BNNs for UQ in an active learning application and reported competitive performance. The most promising framework for creep life prediction is BNNs based on Markov Chain Monte Carlo approximation of the posterior distribution of network parameters, as it provided more reliable results in comparison to BNNs based on variational inference approximation or related NNs with probabilistic outputs. The codes are available at: https://github.com/avakanski/Creep-uncertainty-quantification.

cs.LG↗

arXiv2024

A2DMN: Anatomy-Aware Dilated Multiscale Network for Breast Ultrasound Semantic Segmentation

In recent years, convolutional neural networks for semantic segmentation of breast ultrasound (BUS) images have shown great success; however, two major challenges still exist. 1) Most current approaches inherently lack the ability to utilize tissue anatomy, resulting in misclassified image regions. 2) They struggle to produce accurate boundaries due to the repeated down-sampling operations. To address these issues, we propose a novel breast anatomy-aware network for capturing fine image details and a new smoothness term that encodes breast anatomy. It incorporates context information across multiple spatial scales to generate more accurate semantic boundaries. Extensive experiments are conducted to compare the proposed method and eight state-of-the-art approaches using a BUS dataset with 325 images. The results demonstrate the proposed method significantly improves the segmentation of the muscle, mammary, and tumor classes and produces more accurate fine details of tissue boundaries.

eess.IV↗

arXiv2023

Post-Hoc Explainability of BI-RADS Descriptors in a Multi-task Framework for Breast Cancer Detection and Segmentation

Despite recent medical advancements, breast cancer remains one of the most prevalent and deadly diseases among women. Although machine learning-based Computer-Aided Diagnosis (CAD) systems have shown potential to assist radiologists in analyzing medical images, the opaque nature of the best-performing CAD systems has raised concerns about their trustworthiness and interpretability. This paper proposes MT-BI-RADS, a novel explainable deep learning approach for tumor detection in Breast Ultrasound (BUS) images. The approach offers three levels of explanations to enable radiologists to comprehend the decision-making process in predicting tumor malignancy. Firstly, the proposed model outputs the BI-RADS categories used for BUS image analysis by radiologists. Secondly, the model employs multi-task learning to concurrently segment regions in images that correspond to tumors. Thirdly, the proposed approach outputs quantified contributions of each BI-RADS descriptor toward predicting the benign or malignant class using post-hoc explanations with Shapley Values.

eess.IV↗

arXiv2023

Breast Ultrasound Tumor Classification Using a Hybrid Multitask CNN-Transformer Network

Capturing global contextual information plays a critical role in breast ultrasound (BUS) image classification. Although convolutional neural networks (CNNs) have demonstrated reliable performance in tumor classification, they have inherent limitations for modeling global and long-range dependencies due to the localized nature of convolution operations. Vision Transformers have an improved capability of capturing global contextual information but may distort the local image patterns due to the tokenization operations. In this study, we proposed a hybrid multitask deep neural network called Hybrid-MT-ESTAN, designed to perform BUS tumor classification and segmentation using a hybrid architecture composed of CNNs and Swin Transformer components. The proposed approach was compared to nine BUS classification methods and evaluated using seven quantitative metrics on a dataset of 3,320 BUS images. The results indicate that Hybrid-MT-ESTAN achieved the highest accuracy, sensitivity, and F1 score of 82.7%, 86.4%, and 86.0%, respectively.

eess.IV↗

arXiv2023

Evaluation of Complexity Measures for Deep Learning Generalization in Medical Image Analysis

The generalization performance of deep learning models for medical image analysis often decreases on images collected with different devices for data acquisition, device settings, or patient population. A better understanding of the generalization capacity on new images is crucial for clinicians' trustworthiness in deep learning. Although significant research efforts have been recently directed toward establishing generalization bounds and complexity measures, still, there is often a significant discrepancy between the predicted and actual generalization performance. As well, related large empirical studies have been primarily based on validation with general-purpose image datasets. This paper presents an empirical study that investigates the correlation between 25 complexity measures and the generalization abilities of supervised deep learning classifiers for breast ultrasound images. The results indicate that PAC-Bayes flatness-based and path norm-based measures produce the most consistent explanation for the combination of models and data. We also investigate the use of multi-task classification and segmentation approach for breast images, and report that such learning approach acts as an implicit regularizer and is conducive toward improved generalization.

cs.CV↗

arXiv2023

Machine Learning Methods for Cancer Classification Using Gene Expression Data: A Review

Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after cardiovascular diseases. Gene expression can play a fundamental role in the early detection of cancer, as it is indicative of the biochemical processes in tissue and cells, as well as the genetic characteristics of an organism. Deoxyribonucleic Acid (DNA) microarrays and Ribonucleic Acid (RNA)- sequencing methods for gene expression data allow quantifying the expression levels of genes and produce valuable data for computational analysis. This study reviews recent progress in gene expression analysis for cancer classification using machine learning methods. Both conventional and deep learning-based approaches are reviewed, with an emphasis on the ap-plication of deep learning models due to their comparative advantages for identifying gene patterns that are distinctive for various types of cancers. Relevant works that employ the most commonly used deep neural network architectures are covered, including multi-layer perceptrons, convolutional, recurrent, graph, and transformer networks. This survey also presents an overview of the data collection methods for gene expression analysis and lists important datasets that are commonly used for supervised machine learning for this task. Furthermore, reviewed are pertinent techniques for feature engineering and data preprocessing that are typically used to handle the high dimensionality of gene expression data, caused by a large number of genes present in data samples. The paper concludes with a discussion of future research directions for machine learning-based gene expression analysis for cancer classification.

cs.LG↗

arXiv2023

SIAN: Style-Guided Instance-Adaptive Normalization for Multi-Organ Histopathology Image Synthesis

Existing deep neural networks for histopathology image synthesis cannot generate image styles that align with different organs, and cannot produce accurate boundaries of clustered nuclei. To address these issues, we propose a style-guided instance-adaptive normalization (SIAN) approach to synthesize realistic color distributions and textures for histopathology images from different organs. SIAN contains four phases, semantization, stylization, instantiation, and modulation. The first two phases synthesize image semantics and styles by using semantic maps and learned image style vectors. The instantiation module integrates geometrical and topological information and generates accurate nuclei boundaries. We validate the proposed approach on a multiple-organ dataset, Extensive experimental results demonstrate that the proposed method generates more realistic histopathology images than four state-of-the-art approaches for five organs. By incorporating synthetic images from the proposed approach to model training, an instance segmentation network can achieve state-of-the-art performance.

eess.IV↗