Matrix Factorization Algorithm Research Articles

Investigating gene signatures associated with immunity in colon adenocarcinoma to predict the immunotherapy effectiveness using NFM and WGCNA algorithms.

Colon adenocarcinoma (COAD), a frequently encountered and highly lethal malignancy of the digestive system, has been the focus of intensive research regarding its prognosis. The intricate immune microenvironment plays a pivotal role in the pathological progression of COAD; nevertheless, the underlying molecular mechanisms remain incompletely understood. This study aims to explore the immune gene expression patterns in COAD, construct a robust prognostic model, and delve into the molecular mechanisms and potential therapeutic targets for COAD liver metastasis, thereby providing critical support for individualized treatment strategies and prognostic evaluation. Initially, we curated a comprehensive dataset by screening 2600 immune-related genes (IRGs) from the ImmPort and InnateDB databases, successfully obtaining a rich data resource. Subsequently, the COAD patient cohort was classified using the non-negative matrix factorization (NMF) algorithm, enabling accurate categorization. Continuing on, utilizing the weighted gene co-expression network analysis (WGCNA) method, we analyzed the top 5000 genes with the smallest p-values among the differentially expressed genes (DEGs) between immune subtypes. Through this rigorous screening process, we identified the gene modules with the strongest correlation to the COAD subpopulation, and the intersection of genes in these modules with DEGs (COAD vs COAD vs Normal colon tissue) is referred to as Differentially Expressed Immune Genes Associated with COAD (DEIGRC). Employing diverse bioinformatics methodologies, we successfully developed a prognostic model (DPM) consisting of six genes derived from the DEIGRC, which was further validated across multiple independent datasets. Not only does this predictive model accurately forecast the prognosis of COAD patients, but it also provides valuable insights for formulating personalized treatment regimens. Within the constructed DPM, we observed a downregulation of CALB2 expression levels in COAD tissues, whereas NOXA1, KDF1, LARS2, GSR, and TIMP1 exhibited upregulated expression levels. These genes likely play indispensable roles in the initiation and progression of COAD and thus represent potential therapeutic targets for patient management. Furthermore, our investigation into the molecular mechanisms and therapeutic targets for COAD liver metastasis revealed associations with relevant processes such as fat digestion and absorption, cancer gene protein polysaccharides, and nitrogen metabolism. Consequently, genes including CAV1, ANXA1, CPS1, EDNRA, and GC emerge as promising candidates as therapeutic targets for COAD liver metastasis, thereby providing crucial insights for future clinical practices and drug development. In summary, this study uncovers the immune gene expression patterns in COAD, establishes a robust prognostic model, and elucidates the molecular mechanisms and potential therapeutic targets for COAD liver metastasis, thereby possessing significant theoretical and clinical implications. These findings are anticipated to offer substantial support for both the treatment and prognosis management of COAD patients.

Abstract PS09-09: Multiomics profiling and molecular classification refine precision treatment strategies for HER2-positive breast cancer

Abstract Background: Anti-HER2 targeted therapy has achieved a series of breakthroughs. However, the current treatment strategy regarding HER2-positive breast cancer remains indiscriminate and lacks specificity, which limits the further improvement of overall treatment response and may lead to overtreatment and extra cost for some patients. Our study aims to reveal the molecular heterogeneity of HER2-positive breast cancer to guide a more precise treatment. Patients and methods: We selected HER2-positive breast cancer patients treated at Fudan University Shanghai Cancer Center between 2013 and 2014 and conducted genomic, transcriptomic, proteomic and metabolomic profiling. We then applied a non-negative matrix factorization algorithm on transcriptomic data to obtain an unsupervised classification. And we further studied the correlation between subtypes and corresponding treatment strategies in multiple cohorts of adjuvant and neoadjuvant therapy. For clinical accessibility, we developed convolutional neural network models through deep learning algorithm based on digital pathology to identify different subtypes. Additionally, we explored novel treatment strategies using the patient-derived organoids (PDOs) models. Results: We established a novel multiomics cohort of 180 HER2- breast cancer patients and classified them into four clinically significant molecular subtypes: (1) A classical HER2-enriched (HER2-CLA, N=51) subtype characterized by strong ERBB2 signaling and remarkable sensitivity to anti-HER2-targeted therapy (pathologic complete response with dual-targeted therapy: 93%). (2) an immunomodulatory (HER2-IM, N=36) subtype characterized by an immune-activated microenvironment and excellent prognosis with current treatment (no relapse in 97% of patients with a median follow-up of 86 months). Tumors of this subtype were therefore candidates for de-escalatory treatment. (3) A luminal-like (HER2-LUM, N=55) subtype distinguished by activated estrogen receptor signaling and (4) a basal/mesenchymal-like (HER2-BM, N=38) subtype enriched in activated receptor tyrosine kinase pathways. HER2-LUM and HER2- BM showed limited benefit from anti-HER2 therapy, and thus, add-on therapies might be needed. The overall area under the curve (AUC) of the convolutional neural network model based on digital pathology for identifying different subtypes is 0.77. In the exploration of novel treatment strategies, we found in the PDO model that the HER2-LUM subtype is more sensitive to a treatment regimen combining standard (chemotherapy and targeted therapy) with subsequent endocrine therapy and CDK4/6 inhibitors compared to other subtypes. Additionally, the HER2-BM subtype demonstrated greater sensitivity to treatment with a combination of EGFR inhibitors, PDGFR inhibitors or VEGFR inhibitors. Conclusion: We uncovered a high degree of molecular heterogeneity in HER2-positive breast cancer and illustrated its impact on treatment response. More precise treatment can be given according to the characteristics of different subtypes, which may achieve good efficacy and simultaneously reduce overtreatment and extra cost. The comprehensive profiling of HER2-positive breast cancers could also serve as an important resource for further exploration. Key Words: HER2-positive breast cancer cohort; molecular classification; targeted therapy; precision treatment; de-escalatory treatment. Citation Format: Yu-Wei Li, Ding Ma, Xiang-Rong Wu, Lei-Jie Dai, Shen Zhao, Yu-Zheng Xu, Xi Jin, Xiao Yi, Ying Wang, Cai-Jin Lin, Yi-Fan Zhou, Tong Fu, Wen-Tao Yang, Ming Li, Hong Lv, Yi-Zhou Jiang, Zhi-Ming Shao. Multiomics profiling and molecular classification refine precision treatment strategies for HER2-positive breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS09-09.

Personalised Outfit Recommendation System Using Deep Learning

Abstract: Fashion engineering presents a significant challenge in efficiently coordinating outfits to suit personal preferences. In this study, we introduce a Fashion Coordination Assistant featuring a hybrid recommendation system. Our approach combines content-based and collaborative filtering techniques, utilizing Singular Value Decomposition (SVD) and Non-negative Matrix Factorization (NMF) algorithms. By thoroughly analyzing clothing characteristics and user behavior, we address the technical complexities of fashion coordination. Leveraging the latent features identified by SVD and the non-linear relationships captured by NMF, our system generates tailored outfit suggestions based on individual preferences and style profiles. Extensive testing validates the system's ability to provide diverse and efficient recommendations. By integrating innovative recommendation methods, the Fashion Coordination Assistant adapts to evolving fashion trends and user preferences, enhancing its practical utility in real-world scenarios

Semi-supervised Multi-view Clustering based on NMF with Fusion Regularization

Multi-view clustering has attracted significant attention and application. Nonnegative matrix factorization is one popular feature of learning technology in pattern recognition. In recent years, many semi-supervised nonnegative matrix factorization algorithms were proposed by considering label information, which has achieved outstanding performance for multi-view clustering. However, most of these existing methods have either failed to consider discriminative information effectively or included too much hyper-parameters. Addressing these issues, a semi-supervised multi-view nonnegative matrix factorization with a novel fusion regularization (FRSMNMF) is developed in this article. In this work, we uniformly constrain alignment of multiple views and discriminative information among clusters with designed fusion regularization. Meanwhile, to align the multiple views effectively, two kinds of compensating matrices are used to normalize the feature scales of different views. Additionally, we preserve the geometry structure information of labeled and unlabeled samples by introducing the graph regularization simultaneously. Due to the proposed methods, two effective optimization strategies based on multiplicative update rules are designed. Experiments implemented on six real-world datasets have demonstrated the effectiveness of our FRSMNMF comparing with several state-of-the-art unsupervised and semi-supervised approaches.

Integrating machine learning algorithms and single-cell analysis to identify gut microbiota-related macrophage biomarkers in atherosclerotic plaques.

The relationship between macrophages and the gut microbiota in patients with atherosclerosis remains poorly defined, and effective biological markers are lacking. This study aims to elucidate the interplay between gut microbial communities and macrophages, and to identify biomarkers associated with the destabilization of atherosclerotic plaques. The goal is to enhance our understanding of the underlying molecular pathways and to pave new avenues for diagnostic approaches and therapeutic strategies in the disease. This study employed Weighted Gene Co-expression Network Analysis (WGCNA) and differential expression analysis on atherosclerosis datasets to identify macrophage-associated genes and quantify the correlation between these genes and gut microbiota gene sets. The Random Forest algorithm was utilized to pinpoint PLEK, IRF8, BTK, CCR1, and CD68 as gut microbiota-related macrophage genes, and a nomogram was constructed. Based on the top five genes, a Non-negative Matrix Factorization (NMF) algorithm was applied to construct gut microbiota-related macrophage clusters and analyze their potential biological alterations. Subsequent single-cell analyses were conducted to observe the expression patterns of the top five genes and the interactions between immune cells. Finally, the expression profiles of key molecules were validated using clinical samples from atherosclerosis patients. Utilizing the Random Forest algorithm, we ultimately identified PLEK, IRF8, CD68, CCR1, and BTK as gut microbiota-associated macrophage genes that are upregulated in atherosclerotic plaques. A nomogram based on the expression of these five genes was constructed for use as an auxiliary tool in clinical diagnosis. Single-cell analysis confirmed the specific expression of gut microbiota-associated macrophage genes in macrophages. Clinical samples substantiated the high expression of PLEK in unstable atherosclerotic plaques. Gut microbiota-associated macrophage genes (PLEK, IRF8, CD68, CCR1, and BTK) may be implicated in the pathogenesis of atherosclerotic plaques and could serve as diagnostic markers to aid patients with atherosclerosis.

Identification of two distinct head and neck squamous cell carcinoma subtypes based on fatty acid metabolism-related signatures: Implications for immunotherapy and chemotherapy.

The dysregulation of lipid metabolism is a critical factor in the initiation and progression of tumors. In this investigation, we aim to characterize the molecular subtypes of head and neck squamous cell carcinoma (HNSCC) based on their association with fatty acid metabolism and develop a prognostic risk model. The transcriptomic and clinical data about HNSCC were obtained from public databases. Clustering analysis was conducted on fatty acid metabolism genes (FAMG) associated with prognosis, utilizing the non-negative matrix factorization algorithm. The immune infiltration, response to immune therapy, and drug sensitivity between molecular subtypes were evaluated. Differential expression genes were identified between subtypes, and a prognostic model was constructed using Cox regression analyses. A nomogram for HNSCC was constructed and evaluated. Thirty FAMGs have been found to exhibit differential expression in HNSCC, out of which three are associated with HNSCC prognosis. By performing clustering analysis on these 3 genes, 2 distinct molecular subtypes of HNSCC were identified that exhibit significant heterogeneity in prognosis, immune landscape, and treatment response. Using a set of 7778 genes that displayed differential expression between the 2 molecular subtypes, a prognostic risk model for HNSCC was constructed comprising 11 genes. This model has the ability to stratify HNSCC patients into high-risk and low-risk groups, which exhibit significant differences in prognosis, immune infiltration, and immune therapy response. Moreover, our data suggest that this risk model is negatively correlated with B cells and most T cells, but positively correlated with macrophages, mast cells, and dendritic cells. Ultimately, we constructed a nomogram incorporating both the risk signature and radiotherapy, which has demonstrated exceptional performance in predicting prognosis for HNSCC patients. A molecular classification system and prognostic risk models were developed for HNSCC based on FAMGs. This study revealed the potential involvement of FAMGs in modulating tumor immune microenvironment and response to treatment.

Integrating Multi-omics Data for Alzheimer's Disease to Explore Its Biomarkers Via the Hypergraph-Regularized Joint Deep Semi-Non-Negative Matrix Factorization Algorithm.

Alzheimer's disease (AD) is a progressive and irreversible neurodegenerative disorder. Its etiology may be associated with genetic, environmental, and lifestyle factors. With the advancement of technology, the integration of genomics, transcriptomics, and imaging data related to AD allows simultaneous exploration of molecular information at different levels and their interaction within the organism. This paper proposes a hypergraph-regularized joint deep semi-non-negative matrix factorization (HR-JDSNMF) algorithm to integrate positron emission tomography (PET), single-nucleotide polymorphism (SNP), and gene expression data for AD. The method employs matrix factorization techniques to nonlinearly decompose the original data at multiple layers, extracting deep features from different omics data, and utilizes hypergraph mining to uncover high-order correlations among the three types of data. Experimental results demonstrate that this approach outperforms several matrix factorization-based algorithms and effectively identifies multi-omics biomarkers for AD. Additionally, single-cell RNA sequencing (scRNA-seq) data for AD were collected, and genes within significant modules were used to categorize different types of cell clusters into high and low-risk cell groups. Finally, the study extensively explores the differences in differentiation and communication between these two cell types. The multi-omics biomarkers unearthed in this study can serve as valuable references for the clinical diagnosis and drug target discovery for AD. The realization of the algorithm in this paper code is available at https://github.com/ShubingKong/HR-JDSNMF .

A prognostic signature established based on genes related to tumor microenvironment for patients with hepatocellular carcinoma.

Complex cellular signaling network in the tumor microenvironment (TME) could serve as an indicator for the prognostic classification of hepatocellular carcinoma (HCC) patients. Univariate Cox regression analysis was performed to screen prognosis-related TME-related genes (TRGs), based on which HCC samples were clustered by running non-negative matrix factorization (NMF) algorithm. Furthermore, the correlation between different molecular HCC subtypes and immune cell infiltration level was analyzed. Finally, a risk score (RS) model was established by LASSO and Cox regression analyses (CRA) using these TRGs. Functional enrichment analysis was performed using gene set enrichment analysis (GSEA). HCC patients were divided into three molecular subtypes (C1, C2, and C3) based on 704 prognosis-related TRGs. HCC subtype C1 had significantly better OS than C2 and C3. We selected 13 TRGs to construct the RS model. Univariate and multivariate CRA showed that the RS could independently predict patients' prognosis. A nomogram integrating the RS and clinicopathologic features of the patients was further created. We also validated the reliability of the model according to the area under the receiver operating characteristic (ROC) curve value, concordance index (C-index), and decision curve analysis. The current findings demonstrated that the RS was significantly correlated with CD8+ T cells, monocytic lineage, and myeloid dendritic cells. This study provided TRGs to help classify patients with HCC and predict their prognoses, contributing to personalized treatments for patients with HCC.

Electronic Information System Signal Noise for Noise Reduction using Variational Bayesian based Robust Adaptive Filter

The most significant issues for a thousand users is the unwanted or loud signals in sound files, it is impossible to eliminate or minimize these noise signals without knowledge their types and ranges. To overcome this issue, present an Electronic Information System Signal Noise for Noise Reduction using Variational Bayesian based Robust Adaptive Filter (EIS-SNR-VBRAF) is proposed. Initially, the data is collected from Adaptive Myriad Filter using Time-Varying Noise and Signal-Dependent Parameters dataset. Then, the data is given for Pre-processing section, Variational Bayesian based Robust Adaptive Filter (VBRAF) is used to reduce the signal noise from Gaussian Noise, Traffic noise and Audio signal back ground noise. The proposed technique is implemented and efficacy of EIS-SNR-VBRAF technique is assessed by support of numerous performances such as BER, Signal-to-Noise-Ratio (SNR), Mean Squared Error, Peak Signal-to-Noise Ratio (PSNR), Root Mean Square Error, Structural Similarity Index, Cross-Correlation and Computational Complexity is analyzed. The proposed EIS-SNR-VBRAF method attains 21.18%, 23.52% and 23.65% lower RMSE, 21.52%, 21.76% and 23.24% higher PSNR, 21.19%, 21.73% and 20.48% higher Structural Similarity Index are compared with existing methods like early detection of mechanical malfunctions in vehicles utilizing sound signal processing (ED-MMV-SSP),noise reduction in infrasound signals based on mask coefficient binary weighting generalized cross correlation non-negative matrix factorization algorithm (NRID-MCWG-NMFA) and Click-event sound detection in automotive industry using machine/deep learning (CE-SDSI-DL) respectively.

Integrating transcriptomics and machine learning for immunotherapy assessment in colorectal cancer

Colorectal cancer (CRC) is a highly prevalent and lethal malignancy worldwide. Although immunotherapy has substantially improved CRC outcomes, intolerance remains a major concern among most patients. Considering the pivotal role of the tumor microenvironment (TME) in tumor progression and treatment outcomes, profiling the TME at the transcriptomic level can provide novel insights for developing CRC treatment strategies. Seventy-seven TME-associated signatures were acquired from previous studies. To elucidate variations in prognosis, clinical features, genomic alterations, and responses to immunotherapy in CRC, we employed a non-negative matrix factorization algorithm to categorize 2595 CRC samples of 27 microarrays from the Gene Expression Omnibus database. Three machine learning techniques were employed to identify a signature specific to immunotherapy. Subsequently, the mechanisms by which this signature interacts with TME subtypes and immunotherapy were investigated. Our findings revealed five distinct TME subtypes (TMESs; TMES1–TMES5) in CRC, each exhibiting a unique pattern of immunotherapy response. TMES1, TMES4, and TMES5 had relatively inferior outcomes, TMES2 was associated with the poorest prognosis, and TMES3 had a superior outcome. Subsequent investigations revealed that activated dendritic cells could enhance the immunotherapy response rate, with their augmentation effect closely associated with the activation of CD8+T cells. We successfully classified CRC into five TMESs, each demonstrating varying response rates to immunotherapy. Notably, the application of machine learning to identify activated dendritic cells helped elucidate the underlying mechanisms contributing to these differences. We posit that these TMESs hold promising clinical implications for prognostic evaluation and guidance of immunotherapy strategies, thereby providing valuable insights to inform clinical decision-making.

Abstract 3494: KINOMO: A non-negative matrix factorization framework for recovering intra- and inter-tumoral heterogeneity from single-cell RNA-seq data

Abstract Single-cell RNA-sequencing (scRNA-seq) is a powerful technology to uncover cellular heterogeneity in tumor ecosystems. Due to differences in underlying gene load, direct comparison between patient samples is challenging, and this is further complicated by the sparsity of data matrices in scRNA-seq. Here, we present a factorization method called KINOMO (Kernel dIfferentiability correlation-based NOn- negative Matrix factorization algorithm using Kullback-Leibler divergence loss Optimization). This tool uses quadratic approximation approach for error correction and an iterative multiplicative approach, which improves the quality assessment of NMF-identified factorization, while mitigating biases introduced by inter-patient genomic variability. We benchmarked this new approach against nine different methods across 150 scRNA-seq experiments and find that KINOMO outperforms prior methods when evaluated with an adjusted Rand index (ARI), ranging 0.82-0.91 compared to 0.68-0.77. Thus, KINOMO provides an improved approach for determining coherent transcriptional programs (and meta-programs) from scRNA- seq data of cancer tissues, enabling comparison of patients with variable genomic backgrounds. Citation Format: Somnath Tagore, Yiping Wang, Jana Biermann, Edridge K. D'Souza, Karan D. Luthria, Raul Rabadan, Elham Azizi, Benjamin Izar. KINOMO: A non-negative matrix factorization framework for recovering intra- and inter-tumoral heterogeneity from single-cell RNA-seq data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3494.

Optimizing Matrix Factorization for Personalized Recommendations Using Ridge Regularization

Personalized recommendation systems have become indispensable tools for enhancing user engagement and satisfaction in various online platforms. Matrix Factorization (MF) algorithms serve as fundamental techniques in these systems, allowing for the efficient modeling of user-item interactions and the generation of tailored recommendations. However, ensuring the robustness and generalization capability of MF models remains a challenge, particularly in the presence of sparse and noisy datasets. In this study, we focus on optimizing MF for personalized recommendations through the incorporation of L2 regularization techniques. By introducing a penalty term based on the squared Frobenius norm of the user and item matrices, L2 regularization promotes the learning of more stable and generalized latent representations, thereby mitigating overfitting. We aim to investigate the impact of L2 regularization on recommendation performance and to demonstrate its effectiveness in improving the accuracy and robustness of MF-based recommendation systems. We conduct comprehensive experiments on real-world datasets, evaluating the performance of L2-regularized MF models against baseline approaches. Our results indicate that L2 regularization significantly enhances recommendation accuracy and generalization performance, highlighting its potential to optimize MF for personalized recommendations in diverse application domains

Bulk and single-cell RNA sequencing analysis with 101 machine learning combinations reveal neutrophil extracellular trap involvement in hepatic ischemia-reperfusion injury and early allograft dysfunction

BackgroundHepatic ischaemia–reperfusion injury (HIRI) is a major clinical concern during the perioperative period and is closely associated with early allograft dysfunction (EAD), acute rejection (AR) and long-term graft survival. Neutrophil extracellular traps (NETs) are extracellular structures formed by the release of decondensed chromatin and granular proteins following neutrophil stimulation. There is growing evidence that NETs are involved in the progression of various liver transplantation complications, including ischaemia–reperfusion injury (IRI). This study aimed to comprehensively analyse the expression patterns of NET-related genes (NRGs) in HIRI, identify HIRI subtypes with distinct characteristics, and develop a reliable EAD prediction model. MethodsMicroarray, bulk RNA-seq, and single-cell sequencing datasets were obtained from the GEO database. Initially, differentially expressed NRGs (DE-NRGs) were identified using differential gene expression analyses. We then utilised a non-negative matrix factorisation (NMF) algorithm to classify HIRI samples. Subsequently, we employed machine learning algorithms to screen the hub NRGs related to EAD and developed an EAD prediction model based on these hub NRGs. Concurrently, we assessed the expression patterns of hub NRGs at the single-cell level using the HIRI. Additionally, we validated C5AR1 expression and its effect on HIRI and NETs formation in a rat orthotopic liver transplantation (OLT) model. ResultsIn this study, we identified 11 DE-NRGs in the HIRI context. Based on these 11 DE-NRGs, HIRI samples were classified into two distinct clusters. Cluster1 exhibited a low expression of DE-NRGs, minimal neutrophil infiltration, mild inflammation, and a low incidence of EAD. Conversely, Cluster2 displayed the opposite phenotype, with an activated inflammatory subtype and a higher incidence of EAD. Furthermore, an EAD prediction model was developed using the four hub NRGs associated with EAD. Based on risk scores, HIRI samples were classified into high- and low-risk groups. The OLT model confirmed substantial upregulation of C5AR1 expression in the liver tissue, accompanied by increased formation of NETs. Treatment with a C5AR1 antagonist improved liver function, reduced tissue inflammation, and decreased NETs formation. ConclusionsThis study distinguished two apparent HIRI subtypes, established a predictive model for EAD, and validated the effect of C5AR1 on HIRI. These findings provide novel perspectives for the development of advanced clinical strategies to enhance the outcomes of liver transplant recipients.

Edge-cloud computing oriented large-scale online music education mechanism driven by neural networks

With the advent of the big data era, edge cloud computing has developed rapidly. In this era of popular digital music, various technologies have brought great convenience to online music education. But vast databases of digital music prevent educators from making specific-purpose choices. Music recommendation will be a potential development direction for online music education. In this paper, we propose a deep learning model based on multi-source information fusion for music recommendation under the scenario of edge-cloud computing. First, we use the music latent factor vector obtained by the Weighted Matrix Factorization (WMF) algorithm as the ground truth. Second, we build a neural network model to fuse multiple sources of music information, including music spectrum extracted from extra music information to predict the latent spatial features of music. Finally, we predict the user’s preference for music through the inner product of the user vector and the music vector for recommendation. Experimental results on public datasets and real music data collected by edge devices demonstrate the effectiveness of the proposed method in music recommendation.

Identification and validation of a novel nine-gene prognostic signature of stem cell characteristic in hepatocellular carcinoma.

Currently, cancer stem cells (CSCs) are regarded as the most promising target for cancer therapy due to their close association with tumor resistance, invasion, and recurrence. Thus, identifying CSCs-related genes and constructing a prognostic risk model associated with CSCs may be crucial for hepatocellular carcinoma (HCC) therapy. Xena Browser was used to download gene expression profiles and clinical data, while MSigDB was used to obtain genes associated with CSCs. Firstly, the non-negative matrix factorization (NMF) algorithm was used to cluster the HCC samples based on CSCs-related genes. To evaluate the predictive performance of the risk model, the receiver operating characteristic curves (ROC) and Kaplan-Meier analysis were used. The R package "rms" was used to construct the final nomogram based on risk scores and clinical characteristics. Based on 449 CSCs-related genes, a total of 588 HCC samples from TCGA-LIHC and ICGC-LIRI_JP were classified into four molecular subtypes with marked differences in survival and mRNA stemness index (mRNAsi) between subtypes. Univariate Cox regression, multivariate Cox regression, and LASSO regression analyses were performed on a total of 1417 differentially expressed genes (DEGs) between subtypes, and a nine-gene prognostic model was constructed with TTK, ST6GALNAC4, SPP1, SGCB, MEP1A, HTRA1, CD79A, C6, and ATP2A3. In both the training and testing sets and the external validation cohort, the risk model performed well in predicting HCC patients' survival. A nomogram was constructed and had high predictive efficacy in short-term survival. In comparison with the other two prognostic models, our nine-gene signature model performed best. We constructed a nine-gene signature model to predict the survival of HCC patients, which has good predictive efficacy and stability. The model may contribute to guiding the prognostic assessment of HCC patients in clinical practice.

On incomplete matrix information completion methods and opinion evolution: Matrix factorization towards adjacency preferences

Completeness and consistency are widely acknowledged as indispensable prerequisites for applying fuzzy preference relations in resolving real-world problems. Interactions between decision-makers in the field of group decision-making can have a profound effect on preference changes, especially in situations of incomplete information. However, preference matrices generated using existing models often suffer from low consistency during opinion evolution, which further increases the risk of wrong decisions. To cope with these problems, this paper proposes an opinion evolution method under incomplete information. The method consists of two main components: (1) A preference prediction model based on matrix factorization algorithm and social trust networks under incomplete information, and (2) A model for decision-makers’ preference evolution under dynamic trust scenarios. In Part (1), to simplify the preference collection method and reduce the occurrence of inconsistent information, this paper presents the concept of a consistent adjacency fuzzy preference matrix. To advance the utilization of machine learning algorithms for consistent preference relations, this paper employs the matrix factorization method with stochastic gradient descent to predict missing preferences in adjacency fuzzy preference matrix. In Part (2), to address the shortcomings in past opinion evolution models, this paper simulates the change of decision-makers’ opinions in different stages of interactions under variable trust weights by using alternative ranking similarity and trust thresholds. To illustrate the practical application of the proposed model, this article uses the enterprise supplier selection problem as a case study. The model’s effectiveness and feasibility are then validated through a comparative analysis with existing methods.

Identification of circadian rhythm-related gene classification patterns and immune infiltration analysis in heart failure based on machine learning

BackgroundCircadian rhythms play a key role in the failing heart, but the exact molecular mechanisms linking changes in the expression of circadian rhythm-related genes to heart failure (HF) remain unclear. MethodsBy intersecting differentially expressed genes (DEGs) between normal and HF samples in the Gene Expression Omnibus (GEO) database with circadian rhythm-related genes (CRGs), differentially expressed circadian rhythm-related genes (DE-CRGs) were obtained. Machine learning algorithms were used to screen for feature genes, and diagnostic models were constructed based on these feature genes. Subsequently, consensus clustering algorithms and non-negative matrix factorization (NMF) algorithms were used for clustering analysis of HF samples. On this basis, immune infiltration analysis was used to score the immune infiltration status between HF and normal samples as well as among different subclusters. Gene Set Variation Analysis (GSVA) evaluated the biological functional differences among subclusters. Results13 CRGs showed differential expression between HF patients and normal samples. Nine feature genes were obtained through cross-referencing results from four distinct machine learning algorithms. Multivariate LASSO regression and external dataset validation were performed to select five key genes with diagnostic value, including NAMPT, SERPINA3, MAPK10, NPPA, and SLC2A1. Moreover, consensus clustering analysis could divide HF patients into two distinct clusters, which exhibited different biological functions and immune characteristics. Additionally, two subgroups were distinguished using the NMF algorithm based on circadian rhythm associated differentially expressed genes. Studies on immune infiltration showed marked variances in levels of immune infiltration between these subgroups. Subgroup A had higher immune scores and more widespread immune infiltration. Finally, the Weighted Gene Co-expression Network Analysis (WGCNA) method was utilized to discern the modules that had the closest association with the two observed subgroups, and hub genes were pinpointed via protein-protein interaction (PPI) networks. GRIN2A, DLG1, ERBB4, LRRC7, and NRG1 were circadian rhythm-related hub genes closely associated with HF. ConclusionThis study provides valuable references for further elucidating the pathogenesis of HF and offers beneficial insights for targeting circadian rhythm mechanisms to regulate immune responses and energy metabolism in HF treatment. Five genes identified by us as diagnostic features could be potential targets for therapy for HF.

Molecular subtype identification and prognosis stratification by a immunogenic cell death-related gene expression signature in colorectal cancer

ABSTRACT Objectives This study intended to develop a new immunogenic cell death (ICD)-related prognostic signature for colorectal cancer (CRC) patients. Research design and methods The Non-Negative Matrix Factorization (NMF) algorithm was adopted to cluster tumor samples based on ICD gene expression to obtain ICD-related subtypes. Survival analysis and immune microenvironment analysis were conducted among different subtypes. Regression analysis was used to construct the model. Based on riskscore median, cancer patients were classified into high and low risk groups, and independent prognostic ability of the model was analyzed. The CIBERSORT algorithm was adopted to determine the immune infiltration level of both groups. Results We analyzed the differential genes between cluster 4 and cluster 1–3 and obtained 12 genes with the best prognostic features finally (NLGN1, SLC30A3, C3orf20, ADAD2, ATOH1, ATP6V1B1, KCNQ2, MUCL3, RGCC, CLEC17A, COL6A5, and INSL4). In addition, patients with lower risk had higher levels of infiltration of most immune cells, lower Tumor Immune Dysfunction and Exclusion (TIDE) level and higher immunophenscore (IPS) level than those with higher risk. Conclusions This study constructed and validated the ICD feature signature predicting CRC prognosis and provide a reference criteria for guiding the prognosis and immunotherapy of CRC cancer patients.

Efficient Blind Hyperspectral Unmixing Framework Based on CUR Decomposition (CUR-HU)

Hyperspectral imaging captures detailed spectral data for remote sensing. However, due to the limited spatial resolution of hyperspectral sensors, each pixel of a hyperspectral image (HSI) may contain information from multiple materials. Although the hyperspectral unmixing (HU) process involves estimating endmembers, identifying pure spectral components, and estimating pixel abundances, existing algorithms mostly focus on just one or two tasks. Blind source separation (BSS) based on nonnegative matrix factorization (NMF) algorithms identify endmembers and their abundances at each pixel of HSI simultaneously. Although they perform well, the factorization results are unstable, require high computational costs, and are difficult to interpret from the original HSI. CUR matrix decomposition selects specific columns and rows from a dataset to represent it as a product of three small submatrices, resulting in interpretable low-rank factorization. In this paper, we propose a new blind HU framework based on CUR factorization called CUR-HU that performs the entire HU process by exploiting the low-rank structure of given HSIs. CUR-HU incorporates several techniques to perform the HU process with a performance comparable to state-of-the-art methods but with higher computational efficiency. We adopt a deterministic sampling method to select the most informative pixels and spectrum components in HSIs. We use an incremental QR decomposition method to reduce computation complexity and estimate the number of endmembers. Various experiments on synthetic and real HSIs are conducted to evaluate the performance of CUR-HU. CUR-HU performs comparably to state-of-the-art methods for estimating the number of endmembers and abundance maps, but it outperforms other methods for estimating the endmembers and the computational efficiency. It has a 9.4 to 249.5 times speedup over different methods for different real HSIs.

Whole leg compression garments influence lower limb kinematics and associated muscle synergies during running.

The utilization of compression garments (CGs) has demonstrated the potential to improve athletic performance; however, the specific mechanisms underlying this enhancement remain a subject of further investigation. This study aimed to examine the impact of CGs on running mechanics and muscle synergies from a neuromuscular control perspective. Twelve adult males ran on a treadmill at 12km/h, while data pertaining to lower limb kinematics, kinetics, and electromyography were collected under two clothing conditions: whole leg compression garments and control. The Non-negative matrix factorization algorithm was employed to extract muscle synergy during running, subsequently followed by cluster analysis and correlation analysis. The findings revealed that the CGs increased knee extension and reduced hip flexion at foot strike compared with the control condition. Moreover, CGs were found to enhance stance-phase peak knee extension, while diminishing hip flexion and maximal hip extension during the stance-phase, and the ankle kinematics remained unaltered. We extracted and classified six synergies (SYN1-6) during running and found that only five SYNs were observed after wearing CGs. CGs altered the structure of the synergies and changed muscle activation weights and durations. The current study is the first to apply muscle synergy to discuss the effect of CGs on running biomechanics. Our findings provide neuromuscular evidence for the idea of previous studies that CGs alter the coordination of muscle groups, thereby affecting kinematic characteristics during running.