Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional clustering methods. To address these issues, we propose a deep clustering method, Attention-Enhanced Structural Deep Embedding Graph Clustering (scASDC), which integrates multiple advanced modules to improve clustering accuracy and robustness.Our approach employs a multi-layer graph convolutional network (GCN) to capture high-order structural relationships between cells, termed as the graph autoencoder module. To mitigate the oversmoothing issue in GCNs, we introduce a ZINB-based autoencoder module that extracts content information from the data and learns latent representations of gene expression. These modules are further integrated through an attention fusion mechanism, ensuring effective combination of gene expression and structural information at each layer of the GCN. Additionally, a self-supervised learning module is incorporated to enhance the robustness of the learned embeddings. Extensive experiments demonstrate that scASDC outperforms existing state-of-the-art methods, providing a robust and effective solution for single-cell clustering tasks. Our method paves the way for more accurate and meaningful analysis of single-cell RNA sequencing data, contributing to better understanding of cellular heterogeneity and biological processes. All code and public datasets used in this paper are available at \url{https://github.com/wenwenmin/scASDC} and \url{https://zenodo.org/records/12814320}.

Machine learning in computational pathology (CPath) often aggregates patch-level predictions from multi-gigapixel Whole Slide Images (WSIs) to generate WSI-level prediction scores for crucial tasks such as survival prediction and drug effect prediction. However, current methods do not explicitly characterize distributional differences between patch sets within WSIs. We introduce HistoKernel, a novel Maximum Mean Discrepancy (MMD) kernel that measures distributional similarity between WSIs for enhanced prediction performance on downstream prediction tasks. Our comprehensive analysis demonstrates HistoKernel's effectiveness across various machine learning tasks, including retrieval (n = 9,362), drug sensitivity regression (n = 551), point mutation classification (n = 3,419), and survival analysis (n = 2,291), outperforming existing deep learning methods. Additionally, HistoKernel seamlessly integrates multi-modal data and offers a novel perturbation-based method for patch-level explainability. This work pioneers the use of kernel-based methods for WSI-level predictive modeling, opening new avenues for research. Code is available at https://github.com/pkeller00/HistoKernel.

Various machine learning (ML)-based in-situ monitoring systems have been developed to detect laser additive manufacturing (LAM) process anomalies and defects. Multimodal fusion can improve in-situ monitoring performance by acquiring and integrating data from multiple modalities, including visual and audio data. However, multimodal fusion employs multiple sensors of different types, which leads to higher hardware, computational, and operational costs. This paper proposes a cross-modality knowledge transfer (CMKT) methodology that transfers knowledge from a source to a target modality for LAM in-situ monitoring. CMKT enhances the usefulness of the features extracted from the target modality during the training phase and removes the sensors of the source modality during the prediction phase. This paper proposes three CMKT methods: semantic alignment, fully supervised mapping, and semi-supervised mapping. Semantic alignment establishes a shared encoded space between modalities to facilitate knowledge transfer. It utilizes a semantic alignment loss to align the distributions of the same classes (e.g., visual defective and audio defective classes) and a separation loss to separate the distributions of different classes (e.g., visual defective and audio defect-free classes). The two mapping methods transfer knowledge by deriving the features of one modality from the other modality using fully supervised and semi-supervised learning. The proposed CMKT methods were implemented and compared with multimodal audio-visual fusion in an LAM in-situ anomaly detection case study. The semantic alignment method achieves a 98.4% accuracy while removing the audio modality during the prediction phase, which is comparable to the accuracy of multimodal fusion (98.2%).

Modern machine learning systems have demonstrated substantial abilities with methods that either embrace or ignore human-provided knowledge, but combining benefits of both styles remains a challenge. One particular challenge involves designing learning systems that exhibit built-in responses to specific abstract stimulus patterns, yet are still plastic enough to be agnostic about the modality and exact form of their inputs. In this paper, we investigate what we call The Ungrounded Alignment Problem, which asks How can we build in predefined knowledge in a system where we don't know how a given stimulus will be grounded? This paper examines a simplified version of the general problem, where an unsupervised learner is presented with a sequence of images for the characters in a text corpus, and this learner is later evaluated on its ability to recognize specific (possibly rare) sequential patterns. Importantly, the learner is given no labels during learning or evaluation, but must map images from an unknown font or permutation to its correct class label. That is, at no point is our learner given labeled images, where an image vector is explicitly associated with a class label. Despite ample work in unsupervised and self-supervised loss functions, all current methods require a labeled fine-tuning phase to map the learned representations to correct classes. Finding this mapping in the absence of labels may seem a fool's errand, but our main result resolves this seeming paradox. We show that leveraging only letter bigram frequencies is sufficient for an unsupervised learner both to reliably associate images to class labels and to reliably identify trigger words in the sequence of inputs. More generally, this method suggests an approach for encoding specific desired innate behaviour in modality-agnostic models.

Standardization processes build upon consensus between partners, which depends on their ability to identify points of disagreement and resolving them. Large standardization organizations, like the 3GPP or ISO, rely on leaders of work packages who can correctly, and efficiently, identify disagreements, discuss them and reach a consensus. This task, however, is effort-, labor-intensive and costly. In this paper, we address the problem of identifying similarities, dissimilarities and discussion points using large language models. In a design science research study, we work with one of the organizations which leads several workgroups in the 3GPP standard. Our goal is to understand how well the language models can support the standardization process in becoming more cost-efficient, faster and more reliable. Our results show that generic models for text summarization correlate well with domain expert's and delegate's assessments (Pearson correlation between 0.66 and 0.98), but that there is a need for domain-specific models to provide better discussion materials for the standardization groups.

In this paper the accuracy and robustness of quality measures for the assessment of machine learning models are investigated. The prediction quality of a machine learning model is evaluated model-independent based on a cross-validation approach, where the approximation error is estimated for unknown data. The presented measures quantify the amount of explained variation in the model prediction. The reliability of these measures is assessed by means of several numerical examples, where an additional data set for the verification of the estimated prediction error is available. Furthermore, the confidence bounds of the presented quality measures are estimated and local quality measures are derived from the prediction residuals obtained by the cross-validation approach.

This paper addresses the challenge of out-of-distribution (OOD) generalization in graph machine learning, a field rapidly advancing yet grappling with the discrepancy between source and target data distributions. Traditional graph learning algorithms, based on the assumption of uniform distribution between training and test data, falter in real-world scenarios where this assumption fails, resulting in suboptimal performance. A principal factor contributing to this suboptimal performance is the inherent simplicity bias of neural networks trained through Stochastic Gradient Descent (SGD), which prefer simpler features over more complex yet equally or more predictive ones. This bias leads to a reliance on spurious correlations, adversely affecting OOD performance in various tasks such as image recognition, natural language understanding, and graph classification. Current methodologies, including subgraph-mixup and information bottleneck approaches, have achieved partial success but struggle to overcome simplicity bias, often reinforcing spurious correlations. To tackle this, we propose DIVE, training a collection of models to focus on all label-predictive subgraphs by encouraging the models to foster divergence on the subgraph mask, which circumvents the limitation of a model solely focusing on the subgraph corresponding to simple structural patterns. Specifically, we employs a regularizer to punish overlap in extracted subgraphs across models, thereby encouraging different models to concentrate on distinct structural patterns. Model selection for robust OOD performance is achieved through validation accuracy. Tested across four datasets from GOOD benchmark and one dataset from DrugOOD benchmark, our approach demonstrates significant improvement over existing methods, effectively addressing the simplicity bias and enhancing generalization in graph machine learning.

Previous studies yielded discouraging results for item-level locally differentially private linear regression with $s^*$-sparsity assumption, where the minimax rate for $nm$ samples is $\mathcal{O}(s^{*}d / nm\varepsilon^2)$. This can be challenging for high-dimensional data, where the dimension $d$ is extremely large. In this work, we investigate user-level locally differentially private sparse linear regression. We show that with $n$ users each contributing $m$ samples, the linear dependency of dimension $d$ can be eliminated, yielding an error upper bound of $\mathcal{O}(s^{*2} / nm\varepsilon^2)$. We propose a framework that first selects candidate variables and then conducts estimation in the narrowed low-dimensional space, which is extendable to general sparse estimation problems with tight error bounds. Experiments on both synthetic and real datasets demonstrate the superiority of the proposed methods. Both the theoretical and empirical results suggest that, with the same number of samples, locally private sparse estimation is better conducted when multiple samples per user are available.

Pneumonia, a severe respiratory disease, poses significant diagnostic challenges, especially in underdeveloped regions. Traditional diagnostic methods, such as chest X-rays, suffer from variability in interpretation among radiologists, necessitating reliable automated tools. In this study, we propose a novel approach combining deep learning and transformer-based attention mechanisms to enhance pneumonia detection from chest X-rays. Our method begins with lung segmentation using a TransUNet model that integrates our specialized transformer module, which has fewer parameters compared to common transformers while maintaining performance. This model is trained on the "Chest Xray Masks and Labels" dataset and then applied to the Kermany and Cohen datasets to isolate lung regions, enhancing subsequent classification tasks. For classification, we employ pre-trained ResNet models (ResNet-50 and ResNet-101) to extract multi-scale feature maps, processed through our modified transformer module. By employing our specialized transformer, we attain superior results with significantly fewer parameters compared to common transformer models. Our approach achieves high accuracy rates of 92.79% on the Kermany dataset and 95.11% on the Cohen dataset, ensuring robust and efficient performance suitable for resource-constrained environments. "https://github.com/amirrezafateh/Multi-Scale-Transformer-Pneumonia"

Sparse estimation for Gaussian graphical models is a crucial technique for making the relationships among numerous observed variables more interpretable and quantifiable. Various methods have been proposed, including graphical lasso, which utilizes the $\ell_1$ norm as a regularization term, as well as methods employing non-convex regularization terms. However, most of these methods approximate the $\ell_0$ norm with convex functions. To estimate more accurate solutions, it is desirable to treat the $\ell_0$ norm directly as a regularization term. In this study, we formulate the sparse estimation problem for Gaussian graphical models using the $\ell_0$ norm and propose a method to solve this problem using the Difference of Convex functions Algorithm (DCA). Specifically, we convert the $\ell_0$ norm constraint into an equivalent largest-$K$ norm constraint, reformulate the constrained problem into a penalized form, and solve it using the DC algorithm (DCA). Furthermore, we designed an algorithm that efficiently computes using graphical lasso. Experimental results with synthetic data show that our method yields results that are equivalent to or better than existing methods. Comparisons of model learning through cross-validation confirm that our method is particularly advantageous in selecting true edges.