Transcriptome foundation models (TFMs) hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present single cell, Cell-ontology guided TFM (scCello). We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training. The novel loss component guide scCello to learn the cell-type-specific representation and the structural relation between cell types from the cell ontology graph, respectively. We pre-trained scCello on 22 million cells from CellxGene database leveraging their cell-type labels mapped to the cell ontology graph from Open Biological and Biomedical Ontology Foundry. Our TFM demonstrates competitive generalization and transferability performance over the existing TFMs on biologically important tasks including identifying novel cell types of unseen cells, prediction of cell-type-specific marker genes, and cancer drug responses.

This paper studies a factor modeling-based approach for clustering high-dimensional data generated from a mixture of strongly correlated variables. Statistical modeling with correlated structures pervades modern applications in economics, finance, genomics, wireless sensing, etc., with factor modeling being one of the popular techniques for explaining the common dependence. Standard techniques for clustering high-dimensional data, e.g., naive spectral clustering, often fail to yield insightful results as their performances heavily depend on the mixture components having a weakly correlated structure. To address the clustering problem in the presence of a latent factor model, we propose the Factor Adjusted Spectral Clustering (FASC) algorithm, which uses an additional data denoising step via eliminating the factor component to cope with the data dependency. We prove this method achieves an exponentially low mislabeling rate, with respect to the signal to noise ratio under a general set of assumptions. Our assumption bridges many classical factor models in the literature, such as the pervasive factor model, the weak factor model, and the sparse factor model. The FASC algorithm is also computationally efficient, requiring only near-linear sample complexity with respect to the data dimension. We also show the applicability of the FASC algorithm with real data experiments and numerical studies, and establish that FASC provides significant results in many cases where traditional spectral clustering fails.

The analysis and detection of communities in network structures are becoming increasingly relevant for understanding social behavior. One of the principal challenges in this field is the complexity of existing algorithms. The Girvan-Newman algorithm, which uses the betweenness metric as a measure of node similarity, is one of the most representative algorithms in this area. This study employs the same method to evaluate the relevance of using local similarity metrics for community detection. A series of local metrics were tested on a set of networks constructed using the Girvan-Newman basic algorithm. The efficacy of these metrics was evaluated by applying the base algorithm to several real networks with varying community sizes, using modularity and NMI. The results indicate that approaches based on local similarity metrics have significant potential for community detection.

In the downstream information retrieval process of DNA storage technology, specific hybridization techniques, such as Polymerase Chain Reaction (PCR) or magnetic bead separation, are commonly used to access data [1]. However, this technology faces several challenges, including high base error rates (insertions, deletions, substitutions, etc.) and the loss of storage sequences, which pose significant threats to the reliability of stored data [2]. To address these issues, clustering and alignment of sequencing data can be employed. A commonly used feature extraction method is based on k-mer frequency matrices, where the dimensionality of the extracted features increases exponentially with the value of k [3] [4] [5]. Therefore, selecting an appropriate dimensionality reduction technique becomes a critical challenge that needs to be addressed. This study aims to develop an adaptive classification model to identify the optimal dimensionality reduction method, thereby mitigating the curse of dimensionality caused by k-mer feature extraction and enhancing the effectiveness of K-means clustering in restoring the original sequence information. Specifically, among the numerous available algorithms, Principal Component Analysis (PCA) [6], t-distributed Stochastic Neighbor Embedding (t-SNE) [7], and Uniform Manifold Approximation and Projection (UMAP) [8] are particularly prominent in the fields of cell biology, bioinformatics, and data visualization [9]. This study addresses the challenge of selecting the appropriate dimensionality reduction method to mitigate the curse of dimensionality in K-means clustering.

Recent advances in unsupervised deep graph clustering have been significantly promoted by contrastive learning. Despite the strides, most graph contrastive learning models face challenges: 1) graph augmentation is used to improve learning diversity, but commonly used random augmentation methods may destroy inherent semantics and cause noise; 2) the fixed positive and negative sample selection strategy is limited to deal with complex real data, thereby impeding the model's capability to capture fine-grained patterns and relationships. To reduce these problems, we propose the Clustering-guided Curriculum Graph contrastive Learning (CCGL) framework. CCGL uses clustering entropy as the guidance of the following graph augmentation and contrastive learning. Specifically, according to the clustering entropy, the intra-class edges and important features are emphasized in augmentation. Then, a multi-task curriculum learning scheme is proposed, which employs the clustering guidance to shift the focus from the discrimination task to the clustering task. In this way, the sample selection strategy of contrastive learning can be adjusted adaptively from early to late stage, which enhances the model's flexibility for complex data structure. Experimental results demonstrate that CCGL has achieved excellent performance compared to state-of-the-art competitors.

Large vision-language models (VLMs) have shown significant performance boost in various application domains. However, adopting them to deal with several sequentially encountered tasks has been challenging because finetuning a VLM on a task normally leads to reducing its generalization power and the capacity of learning new tasks as well as causing catastrophic forgetting on previously learned tasks. Enabling using VLMs in multimodal continual learning (CL) settings can help to address such scenarios. To improve generalization capacity and prevent catastrophic forgetting, we propose a novel prompt-based CL method for VLMs, namely $\textbf{Clu}$ster-based $\textbf{Mo}$dality Fusion Prompt (\textbf{CluMo}). We design a novel \textbf{Key-Key-Prompt} pair, where each prompt is associated with a visual prompt key and a textual prompt key. We adopt a two-stage training strategy. During the first stage, the single-modal keys are trained via $K$-means clustering algorithm to help select the best semantically matched prompt. During the second stage, the prompt keys are frozen, the selected prompt is attached to the input for training the VLM in the CL scenario. Experiments on two benchmarks demonstrate that our method achieves SOTA performance.

Federated Learning (FL) represents a paradigm shift in the field of machine learning, offering an approach for a decentralized training of models across a multitude of devices while maintaining the privacy of local data. However, the dynamic nature of FL systems, characterized by the ongoing incorporation of new clients with potentially diverse data distributions and computational capabilities, poses a significant challenge to the stability and efficiency of these distributed learning networks. The seamless integration of new clients is imperative to sustain and enhance the performance and robustness of FL systems. This paper looks into the complexities of integrating new clients into existing FL systems and explores how data heterogeneity and varying data distribution (not independent and identically distributed) among them can affect model training, system efficiency, scalability and stability. Despite these challenges, the integration of new clients into FL systems presents opportunities to enhance data diversity, improve learning performance, and leverage distributed computational power. In contrast to other fields of application such as the distributed optimization of word predictions on Gboard (where federated learning once originated), there are usually only a few clients in the production environment, which is why information from each new client becomes all the more valuable. This paper outlines strategies for effective client selection strategies and solutions for ensuring system scalability and stability. Using the example of images from optical quality inspection, it offers insights into practical approaches. In conclusion, this paper proposes that addressing the challenges presented by new client integration is crucial to the advancement and efficiency of distributed learning networks, thus paving the way for the adoption of Federated Learning in production environments.

Federated Learning (FL) is a pivotal approach in decentralized machine learning, especially when data privacy is crucial and direct data sharing is impractical. While FL is typically associated with supervised learning, its potential in unsupervised scenarios is underexplored. This paper introduces a novel unsupervised federated learning methodology designed to identify the complete set of categories (global K) across multiple clients within label-free, non-uniform data distributions, a process known as Federated Clustering. Our approach, Federated Cluster-Wise Refinement (FedCRef), involves clients that collaboratively train models on clusters with similar data distributions. Initially, clients with diverse local data distributions (local K) train models on their clusters to generate compressed data representations. These local models are then shared across the network, enabling clients to compare them through reconstruction error analysis, leading to the formation of federated groups.In these groups, clients collaboratively train a shared model representing each data distribution, while continuously refining their local clusters to enhance data association accuracy. This iterative process allows our system to identify all potential data distributions across the network and develop robust representation models for each. To validate our approach, we compare it with traditional centralized methods, establishing a performance baseline and showcasing the advantages of our distributed solution. We also conduct experiments on the EMNIST and KMNIST datasets, demonstrating FedCRef's ability to refine and align cluster models with actual data distributions, significantly improving data representation precision in unsupervised federated settings.

Fairness in clustering has been considered extensively in the past; however, the trade-off between the two objectives -- e.g., can we sacrifice just a little in the quality of the clustering to significantly increase fairness, or vice-versa? -- has rarely been addressed. We introduce novel algorithms for tracing the complete trade-off curve, or Pareto front, between quality and fairness in clustering problems; that is, computing all clusterings that are not dominated in both objectives by other clusterings. Unlike previous work that deals with specific objectives for quality and fairness, we deal with all objectives for fairness and quality in two general classes encompassing most of the special cases addressed in previous work. Our algorithm must take exponential time in the worst case as the Pareto front itself can be exponential. Even when the Pareto front is polynomial, our algorithm may take exponential time, and we prove that this is inevitable unless P = NP. However, we also present a new polynomial-time algorithm for computing the entire Pareto front when the cluster centers are fixed, and for perhaps the most natural fairness objective: minimizing the sum, over all clusters, of the imbalance between the two groups in each cluster.

The swift advancement of single-cell RNA sequencing (scRNA-seq) technologies enables the investigation of cellular-level tissue heterogeneity. Cell annotation significantly contributes to the extensive downstream analysis of scRNA-seq data. However, The analysis of scRNA-seq for biological inference presents challenges owing to its intricate and indeterminate data distribution, characterized by a substantial volume and a high frequency of dropout events. Furthermore, the quality of training samples varies greatly, and the performance of the popular scRNA-seq data clustering solution GNN could be harmed by two types of low-quality training nodes: 1) nodes on the boundary; 2) nodes that contribute little additional information to the graph. To address these problems, we propose a single-cell curriculum learning-based deep graph embedding clustering (scCLG). We first propose a Chebyshev graph convolutional autoencoder with multi-decoder (ChebAE) that combines three optimization objectives corresponding to three decoders, including topology reconstruction loss of cell graphs, zero-inflated negative binomial (ZINB) loss, and clustering loss, to learn cell-cell topology representation. Meanwhile, we employ a selective training strategy to train GNN based on the features and entropy of nodes and prune the difficult nodes based on the difficulty scores to keep the high-quality graph. Empirical results on a variety of gene expression datasets show that our model outperforms state-of-the-art methods.