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Statistical-Neural Interaction Networks for Interpretable Mixed-Type Data Imputation
Deng, Ou, Nishimura, Shoji, Ogihara, Atsushi, Jin, Qun
Real-world tabular databases routinely combine continuous measurements and categorical records, yet missing entries are pervasive and can distort downstream analysis. We propose Statistical-Neural Interaction (SNI), an interpretable mixed-type imputation framework that couples correlation-derived statistical priors with neural feature attention through a Controllable-Prior Feature Attention (CPFA) module. CPFA learns head-wise prior-strength coefficients $\{λ_h\}$ that softly regularize attention toward the prior while allowing data-driven deviations when nonlinear patterns appear to be present in the data. Beyond imputation, SNI aggregates attention maps into a directed feature-dependency matrix that summarizes which variables the imputer relied on, without requiring post-hoc explainers. We evaluate SNI against six baselines (Mean/Mode, MICE, KNN, MissForest, GAIN, MIWAE) on six datasets spanning ICU monitoring, population surveys, socio-economic statistics, and engineering applications. Under MCAR/strict-MAR at 30\% missingness, SNI is generally competitive on continuous metrics but is often outperformed by accuracy-first baselines (MissForest, MIWAE) on categorical variables; in return, it provides intrinsic dependency diagnostics and explicit statistical-neural trade-off parameters. We additionally report MNAR stress tests (with a mask-aware variant) and discuss computational cost, limitations -- particularly for severely imbalanced categorical targets -- and deployment scenarios where interpretability may justify the trade-off.
Murmur2Vec: A Hashing Based Solution For Embedding Generation Of COVID-19 Spike Sequences
Early detection and characterization of coronavirus disease (COVID-19), caused by SARS-CoV-2, remain critical for effective clinical response and public-health planning. The global availability of large-scale viral sequence data presents significant opportunities for computational analysis; however, existing approaches face notable limitations. Phylogenetic tree-based methods are computationally intensive and do not scale efficiently to today's multi-million-sequence datasets. Similarly, current embedding-based techniques often rely on aligned sequences or exhibit suboptimal predictive performance and high runtime costs, creating barriers to practical large-scale analysis. In this study, we focus on the most prevalent SARS-CoV-2 lineages associated with the spike protein region and introduce a scalable embedding method that leverages hashing to generate compact, low-dimensional representations of spike sequences. These embeddings are subsequently used to train a variety of machine learning models for supervised lineage classification. We conduct an extensive evaluation comparing our approach with multiple baseline and state-of-the-art biological sequence embedding methods across diverse metrics. Our results demonstrate that the proposed embeddings offer substantial improvements in efficiency, achieving up to 86.4\% classification accuracy while reducing embedding generation time by as much as 99.81\%. This highlights the method's potential as a fast, effective, and scalable solution for large-scale viral sequence analysis.
Fuzzy Label: From Concept to Its Application in Label Learning
Luoa, Chenxi, Zhaoa, Zhuangzhuang, Denga, Zhaohong, Zhangb, Te
Label learning is a fundamental task in machine learning that aims to construct intelligent models using labeled data, encompassing traditional single-label and multi-label classification models. Traditional methods typically rely on logical labels, such as binary indicators (e.g., "yes/no") that specify whether an instance belongs to a given category. However, in practical applications, label annotations often involve significant uncertainty due to factors such as data noise, inherent ambiguity in the observed entities, and the subjectivity of human annotators. Therefore, representing labels using simplistic binary logic can obscure valuable information and limit the expressiveness of label learning models. To overcome this limitation, this paper introduces the concept of fuzzy labels, grounded in fuzzy set theory, to better capture and represent label uncertainty. We further propose an efficient fuzzy labeling method that mines and generates fuzzy labels from the original data, thereby enriching the label space with more informative and nuanced representations. Based on this foundation, we present fuzzy-label-enhanced algorithms for both single-label and multi-label learning, using the classical K-Nearest Neighbors (KNN) and multi-label KNN algorithms as illustrative examples. Experimental results indicate that fuzzy labels can more effectively characterize the real-world labeling information and significantly enhance the performance of label learning models.
Breaking the Euclidean Barrier: Hyperboloid-Based Biological Sequence Analysis
Ali, Sarwan, Mansoor, Haris, Patterson, Murray
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working in high-dimensional Euclidean spaces. This limitation hinders accurate sequence classification and similarity measurement. To address these challenges, this research proposes a method to transform the feature representation of biological sequences into the hyperboloid space. By applying a transformation, the sequences are mapped onto the hyperboloid, preserving their inherent structural information. Once the sequences are represented in the hyperboloid space, a kernel matrix is computed based on the hyperboloid features. The kernel matrix captures the pairwise similarities between sequences, enabling more effective analysis of biological sequence relationships. This approach leverages the inner product of the hyperboloid feature vectors to measure the similarity between pairs of sequences. The experimental evaluation of the proposed approach demonstrates its efficacy in capturing important sequence correlations and improving classification accuracy.
The Impact of Feature Scaling In Machine Learning: Effects on Regression and Classification Tasks
Pinheiro, João Manoel Herrera, de Oliveira, Suzana Vilas Boas, Silva, Thiago Henrique Segreto, Saraiva, Pedro Antonio Rabelo, de Souza, Enzo Ferreira, Godoy, Ricardo V., Ambrosio, Leonardo André, Becker, Marcelo
This research addresses the critical lack of comprehensive studies on feature scaling by systematically evaluating 12 scaling techniques - including several less common transformations - across 14 different Machine Learning algorithms and 16 datasets for classification and regression tasks. We meticulously analyzed impacts on predictive performance (using metrics such as accuracy, MAE, MSE, and $R^2$) and computational costs (training time, inference time, and memory usage). Key findings reveal that while ensemble methods (such as Random Forest and gradient boosting models like XGBoost, CatBoost and LightGBM) demonstrate robust performance largely independent of scaling, other widely used models such as Logistic Regression, SVMs, TabNet, and MLPs show significant performance variations highly dependent on the chosen scaler. This extensive empirical analysis, with all source code, experimental results, and model parameters made publicly available to ensure complete transparency and reproducibility, offers model-specific crucial guidance to practitioners on the need for an optimal selection of feature scaling techniques.
Data Augmentation via Diffusion Model to Enhance AI Fairness
Blow, Christina Hastings, Qian, Lijun, Gibson, Camille, Obiomon, Pamela, Dong, Xishuang
AI fairness seeks to improve the transparency and explainability of AI systems by ensuring that their outcomes genuinely reflect the best interests of users. Data augmentation, which involves generating synthetic data from existing datasets, has gained significant attention as a solution to data scarcity. In particular, diffusion models have become a powerful technique for generating synthetic data, especially in fields like computer vision. This paper explores the potential of diffusion models to generate synthetic tabular data to improve AI fairness. The Tabular Denoising Diffusion Probabilistic Model (Tab-DDPM), a diffusion model adaptable to any tabular dataset and capable of handling various feature types, was utilized with different amounts of generated data for data augmentation. Additionally, reweighting samples from AIF360 was employed to further enhance AI fairness. Five traditional machine learning models-Decision Tree (DT), Gaussian Naive Bayes (GNB), K-Nearest Neighbors (KNN), Logistic Regression (LR), and Random Forest (RF)-were used to validate the proposed approach. Experimental results demonstrate that the synthetic data generated by Tab-DDPM improves fairness in binary classification.
Position Specific Scoring Is All You Need? Revisiting Protein Sequence Classification Tasks
Ali, Sarwan, Murad, Taslim, Chourasia, Prakash, Mansoor, Haris, Khan, Imdad Ullah, Chen, Pin-Yu, Patterson, Murray
Understanding the structural and functional characteristics of proteins are crucial for developing preventative and curative strategies that impact fields from drug discovery to policy development. An important and popular technique for examining how amino acids make up these characteristics of the protein sequences with position-specific scoring (PSS). While the string kernel is crucial in natural language processing (NLP), it is unclear if string kernels can extract biologically meaningful information from protein sequences, despite the fact that they have been shown to be effective in the general sequence analysis tasks. In this work, we propose a weighted PSS kernel matrix (or W-PSSKM), that combines a PSS representation of protein sequences, which encodes the frequency information of each amino acid in a sequence, with the notion of the string kernel. This results in a novel kernel function that outperforms many other approaches for protein sequence classification. We perform extensive experimentation to evaluate the proposed method. Our findings demonstrate that the W-PSSKM significantly outperforms existing baselines and state-of-the-art methods and achieves up to 45.1\% improvement in classification accuracy.
Nearest Neighbor CCP-Based Molecular Sequence Analysis
Ali, Sarwan, Chourasia, Prakash, Koirala, Bipin, Patterson, Murray
Molecular sequence analysis is crucial for comprehending several biological processes, including protein-protein interactions, functional annotation, and disease classification. The large number of sequences and the inherently complicated nature of protein structures make it challenging to analyze such data. Finding patterns and enhancing subsequent research requires the use of dimensionality reduction and feature selection approaches. Recently, a method called Correlated Clustering and Projection (CCP) has been proposed as an effective method for biological sequencing data. The CCP technique is still costly to compute even though it is effective for sequence visualization. Furthermore, its utility for classifying molecular sequences is still uncertain. To solve these two problems, we present a Nearest Neighbor Correlated Clustering and Projection (CCP-NN)-based technique for efficiently preprocessing molecular sequence data. To group related molecular sequences and produce representative supersequences, CCP makes use of sequence-to-sequence correlations. As opposed to conventional methods, CCP doesn't rely on matrix diagonalization, therefore it can be applied to a range of machine-learning problems. We estimate the density map and compute the correlation using a nearest-neighbor search technique. We performed molecular sequence classification using CCP and CCP-NN representations to assess the efficacy of our proposed approach. Our findings show that CCP-NN considerably improves classification task accuracy as well as significantly outperforms CCP in terms of computational runtime.
Unifying and extending Precision Recall metrics for assessing generative models
Sykes, Benjamin, Simon, Loic, Rabin, Julien
With the recent success of generative models in image and text, the evaluation of generative models has gained a lot of attention. Whereas most generative models are compared in terms of scalar values such as Frechet Inception Distance (FID) or Inception Score (IS), in the last years (Sajjadi et al., 2018) proposed a definition of precision-recall curve to characterize the closeness of two distributions. Since then, various approaches to precision and recall have seen the light (Kynkaanniemi et al., 2019; Naeem et al., 2020; Park & Kim, 2023). They center their attention on the extreme values of precision and recall, but apart from this fact, their ties are elusive. In this paper, we unify most of these approaches under the same umbrella, relying on the work of (Simon et al., 2019). Doing so, we were able not only to recover entire curves, but also to expose the sources of the accounted pitfalls of the concerned metrics. We also provide consistency results that go well beyond the ones presented in the corresponding literature. Last, we study the different behaviors of the curves obtained experimentally.
Medical Image Classification Using Transfer Learning and Chaos Game Optimization on the Internet of Medical Things
Mabrouk, Alhassan, Dahou, Abdelghani, Elaziz, Mohamed Abd, Redondo, Rebeca P. Díaz, Kayed, Mohammed
The Internet of Medical Things (IoMT) has dramatically benefited medical professionals that patients and physicians can access from all regions. Although the automatic detection and prediction of diseases such as melanoma and leukemia is still being researched and studied in IoMT, existing approaches are not able to achieve a high degree of efficiency. Thus, with a new approach that provides better results, patients would access the adequate treatments earlier and the death rate would be reduced. Therefore, this paper introduces an IoMT proposal for medical images classification that may be used anywhere, i.e. it is an ubiquitous approach. It was design in two stages: first, we employ a Transfer Learning (TL)-based method for feature extraction, which is carried out using MobileNetV3; second, we use the Chaos Game Optimization (CGO) for feature selection, with the aim of excluding unnecessary features and improving the performance, which is key in IoMT. Our methodology was evaluated using ISIC-2016, PH2, and Blood-Cell datasets. The experimental results indicated that the proposed approach obtained an accuracy of 88.39% on ISIC-2016, 97.52% on PH2, and 88.79% on Blood-cell. Moreover, our approach had successful performances for the metrics employed compared to other existing methods.