Similar Neighbors Research Articles

Denoised Graph Collaborative Filtering via Neighborhood Similarity and Dynamic Thresholding

Denoised Graph Collaborative Filtering via Neighborhood Similarity and Dynamic Thresholding

Improving airborne laser scanning-based species-specific forest volume estimation using sentinel-2 time series

ABSTRACT Species-specific timber volume estimates are required to support forest planning and conservation. We evaluated whether additional predictors from a Sentinel-2 time series can improve airborne laser scanning (ALS)-based estimation of species-specific timber volumes. Furthermore, we determined the satellite image dates that provided the greatest improvement in accuracy. The Sentinel-2 time series was constructed to cover 1 March–30 November time-period, with a focus on late spring and early summer. The estimation was done using the k Most Similar Neighbor method and predictors extracted from the ALS data and Sentinel-2 images. Our best model included both ALS and Sentinel-2 time-series predictors, and the relative root mean square error (RMSE) values for pine, spruce and deciduous timber volumes were 40.8%, 57.0% and 51.3%, respectively (mean 49.7%). All deciduous trees were treated as one species. When bands from an individual image were used instead of the time series, the best result was obtained with an image from September where the respective relative RMSE values were 42.2% (deciduous), 58.4% (pine) and 60.6% (spruce) with a mean value of 53.7%. A fusion of a Sentinel-2 time-series and ALS data can improve species-specific estimation results compared to the use of individual Sentinel-2 images or ALS only.

Recover then aggregate: unified cross-modal deep clustering with global structural information for single-cell data.

Single-cell cross-modal joint clustering has been extensively utilized to investigate the tumor microenvironment. Although numerous approaches have been suggested, accurate clustering remains the main challenge. First, the gene expression matrix frequently contains numerous missing values due to measurement limitations. The majority of existing clustering methods treat it as a typical multi-modal dataset without further processing. Few methods conduct recovery before clustering and do not sufficiently engage with the underlying research, leading to suboptimal outcomes. Additionally, the existing cross-modal information fusion strategy does not ensure consistency of representations across different modes, potentially leading to the integration of conflicting information, which could degrade performance. To address these challenges, we propose the 'Recover then Aggregate' strategy and introduce the Unified Cross-Modal Deep Clustering model. Specifically, we have developed a data augmentation technique based on neighborhood similarity, iteratively imposing rank constraints on the Laplacian matrix, thus updating the similarity matrix and recovering dropout events. Concurrently, we integrate cross-modal features and employ contrastive learning to align modality-specific representations with consistent ones, enhancing the effective integration of diverse modal information. Comprehensive experiments on five real-world multi-modal datasets have demonstrated this method's superior effectiveness in single-cell clustering tasks.

ANS-SCMC: A matrix completion method based on adaptive neighbourhood similarity and sparse constraints for predicting microbe-disease associations.

The use of matrix completion methods to predict the association between microbes and diseases can effectively improve treatment efficiency. However, the similarity measures used in the existing methods are often influenced by various factors such as neighbourhood size, choice of similarity metric, or multiple parameters for similarity fusion, making it challenging. Additionally, matrix completion is currently limited by the sparsity of the initial association matrix, which restricts its predictive performance. To address these problems, we propose a matrix completion method based on adaptive neighbourhood similarity and sparse constraints (ANS-SCMC) for predict microbe-disease potential associations. Adaptive neighbourhood similarity learning dynamically uses the decomposition results as effective information for the next learning iteration by simultaneously performing local manifold structure learning and decomposition. This approach effectively preserves fine local structure information and avoids the influence of weight parameters directly involved in similarity measurement. Additionally, the sparse constraint-based matrix completion approach can better handle the sparsity challenge in the association matrix. Finally, the algorithm we proposed has achieved significantly higher predictive performance in the validation compared to several commonly used prediction methods proposed to date. Furthermore, in the case study, the prediction algorithm achieved an accuracy of up to 80% for the top 10 microbes associated with type 1 diabetes and 100% for Crohn's disease respectively.

A unified framework of semi-supervised community detection integrating network topology and node content

Detecting the community structure within networks is important because it aids in the analysis of complex networks. However, the existence of diverse complex structures in the network topology can limit the topological information’s ability to represent communities. For instance, the accuracy of many traditional methods based on topology alone decreases sharply when a link is missing or noisy. To solve the above-mentioned issues simultaneously, we propose a unified framework of semi-supervised community detection integrating content information. Three models are proposed, instead of a special model-handling problem. The framework used performs the same interpretation for a target problem. The inputs contain the adjacent and node content matrix. The proposed models describe the network topology using a non-negative matrix factorization (NMF) algorithm–based generative model or modularity maximization algorithm. Additionally, we use the equivalence theory of the pLSI, and NMF models the content information based on NMF. Community membership is also used as the relationship between communities and node contents. The models uniformly integrate content information and network topology. Further, a constraint matrix that depicts must-links is built by calculating the similarity of neighbors between any two nodes. Must-link pairs can represent the network topology’s prior information. The models’ community memberships are adjusted by using a strong constraint based on the connected component of this matrix. The models also introduce prior information into the topological and content information in the mentioned models. We compared the proposed models with the state-of-the-art community detection models on artificial networks and five real networks. The experimental results show that the proposed models outperformed the models combining topology and content and semi-supervised models. Fusing the topology with the content and the prior information in the models was also effective for community detection. Thus, the models under the framework are more advantageous than other semi-supervised models when incorporating the same amount of prior information into the models. The semi-supervised framework used also has a certain level of competitiveness in detecting communities.

DECNet: Dense embedding contrast for unsupervised semantic segmentation

Unsupervised semantic segmentation is important for understanding that each pixel belongs to known categories without annotation. Recent studies have demonstrated promising outcomes by employing a vision transformer backbone pre-trained on an image-level dataset in a self-supervised manner. However, those methods always depend on complex architectures or meticulously designed inputs. Naturally, we are attempting to explore the investment with a straightforward approach. To prevent over-complication, we introduce a simple Dense Embedding Contrast network (DECNet) for unsupervised semantic segmentation in this paper. Specifically, we propose a Nearest Neighbor Similarity strategy (NNS) to establish well-defined positive and negative pairs for dense contrastive learning. Meanwhile, we optimize a contrastive objective named Ortho-InfoNCE to alleviate the false negative problem inherent in contrastive learning for further enhancing dense representations. Finally, extensive experiments conducted on COCO-Stuff and Cityscapes datasets demonstrate that our approach outperforms state-of-the-art methods.

Taxonomic study of wasp species in the Polybia (Myrapetra) occidentalis group morphologically related to P. scrobalis and P. flavifrons, with description of a new species (Hymenoptera, Vespidae, Polistinae)

Polybia is a genus of neotropical swarming wasps, and the largest within the Epiponini (Vespidae). The genus is dominant in the Neotropics, with more than 59 described species and eleven recognized subgenera. Myrapetra is the largest subgenus, currently with twenty-four valid species and fourteen subspecies, most of them allocated in the “P. occidentalis species-group”. Several species within Myrapetra are poorly characterized, with imprecise limits, and subspecies are largely based on color, that is highly variable feature, even among nest mates. This study is about those species of the P. occidentalis species-group which are morphologically more distinct from P. occidentalis (and its more similar neighbors), which we refer to as the species related to P. scrobalis and P. flavifrons. We describe a new species (P. rosalinae Amorim & Santos, sp. nov.) and for three subspecies we recognize the need to treat as distinct species (P. brevitarsus Richards, stat. nov.; P. hecuba Richards, stat. nov.; and P. surinama Richards, stat. nov.). In addition, we describe the males of two species and provide the first data (description and photos) on male genitalia of four taxa. P. dimorpha Richards, previously an isolated species within Myrapetra is treated as a member of the P. occidentalis species-group. Additionally, we provide a new identification key for the studied species.

Attributed graph subspace clustering with residual compensation guided by adaptive dual manifold regularization

As an important technology for recommendation system, attributed graph clustering has received extensive attention recently. Attributed graph clustering methods based on graph neural networks are the mainstream methods . However, their assumption that the attributes of adjacent nodes are similar is often not satisfied in the real world, which influences the clustering performance. To this end, this paper proposes an attributed graph subspace clustering algorithm with residual compensation guided by adaptive dual manifold regularization (ADMRGC). On the basis of the low rank representation subspace clustering (LRR) model, ADMRGC introduces attributed manifold regularization, topological manifold regularization and residual compensation, which make ADMRGC possible to utilize attributed similarity and topological similarity at the same time, thus solving the problem that traditional subspace clustering only considers attributed information. In addition, ADMRGC balances the contribution of node attributes and topology by adaptively weighting the dual manifold regularization, and uses the residual representation matrix to describe the difference between node attributed similarity and topological neighbor relationship. Therefore, ADMRGC can avoid the limitation of graph neural network models assuming that the attributes of adjacent nodes are similar. Experimental results on 7 public graph datasets show that ADMRGC can achieve the best clustering performance on both high-homophily and low-homophily datasets. Especially, for datasets with low homophily, ADMRGC as a shallow model can also achieve better clustering performance than state-of-the-art deep neural network models.

‘If I tell them that I live near the neighborhood, they’re like, oh are you poor?’ Differences in young people’s reactions to territorial stigma in the Helsinki metropolitan area, Finland

ABSTRACT Geographers have long been interested in how place is a crucial element of exclusion in society. In this study, we examine the reactions to neighborhood stigma of two groups of young people whose lives are intertwined with a stigmatized neighborhood at different levels. The first group lives, goes to school and spends leisure time in the neighborhoods and the second group goes to school there. Theoretically, we draw on Wacquant's concept of territorial stigmatization and Pryor and Reeder's taxonomy of different types of stigma: public stigma, self-stigma, and stigma by association. Our ethnographic data comprise interviews with young people (aged 13–15) and daily observations from two schools located in disadvantaged neighborhoods in the Helsinki metropolitan area in Finland. We found three differences in stigma reactions between the two groups of young people, which were intertwined with spatial and social inequalities. The first difference arose from the uneven ways in which they struggled with neighborhood stigma. The second difference related to disengagement from the source of stigma, by detachment either from certain places or from the entire neighborhood. The third difference emerged in the different ways in which they used the neighborhood normalization strategy, to indicate neighborhood similarities or differences.

Fuzzy Neighborhood-Based Manifold Learning and Feature Weight Matrix for Multilabel Feature Selection

In recent years, it has been difficult to determine neighborhood radii with almost all feature selection methodologies, and the existing multilabel feature selection approaches neglect these correlations among labels, which results in poor classification efficiency. To address these flaws, a fuzzy neighborhood-based manifold learning model and a feature weight matrix are developed to study multilabel feature selection in this article. First, the difference coefficient of the given samples and the new classification margin of each sample are defined to construct an adaptive fuzzy neighborhood radius. While considering the influences of features and labels on the similarity relationships of samples, a novel fuzzy neighborhood similarity relationship is developed by combining it with the label similarity approach that uses the Jaccard similarity coefficient. Second, the least-squares regression model is introduced to design a loss function for learning the mapping relationship between the feature and label spaces. To constrain the objective function, a regularization term based on the fuzzy neighborhood similarity relationship matrix is developed to establish a manifold learning model. To reduce the complexity of the loss function and to reduce the induced structural risk, the final objective function is constructed by incorporating two graph Laplacian matrices. Third, positive and negative confidence values are presented to incorporate the frequency parameter and to form the dependencies between labels into a new label correlation matrix. A new feature weight matrix integrated with the dependencies between labels is defined to learn the correlations between features and labels. Finally, an embedded feature selection method with an objective function is designed, where the objective function is optimized by the gradient descent scheme. Experiments conducted on 12 multilabel datasets reveal that the proposed approach yields better classification results than do other algorithms.

LMFLS: A new fast local multi-factor node scoring and label selection-based algorithm for community detection

Community detection is still regarded as one of the most applicable approaches for discovering latent information in complex networks. To meet the needs of processing large networks in today's world, it is important to propose fast methods that have low execution time and fast convergence speed, while maintaining algorithmic accuracy. To overcome these issues, a fast local multi-factor node scoring and label selection-based (LMFLS) method with low time complexity and fast convergence is proposed. Node scoring step incorporates diverse metrics to better assess impact of nodes from different aspects and obtain more meaningful order of nodes. In second step, to construct and stabilize initial structure of communities, an efficient label assignment technique based on the selection of the most similar neighbor is suggested. Moreover, two label selection strategies are proposed to significantly enhance the accuracy and improve convergence of the algorithm. During the label selection step, each node in graph tends to choose the most appropriate label based on a multi-criteria label influence from its surrounding nodes. Finally, by utilizing a novel merge method, small group of nodes are merged to form the final communities. Meanwhile, since drug repositioning is one of the popular research fields in therapeutics, to extend the application of the proposed algorithm in practical context, the LMFLS algorithm is applied on Drug-Drug network to find potential repositioning for drugs. Thorough experiments are conducted on both actual real-world networks and synthetic networks to assess the algorithm's performance and accuracy. The findings demonstrate that the proposed method outperforms state-of-the-art algorithms in terms of both accuracy and execution time.

Neighbors selective Graph Convolutional Network for homophily and heterophily

Graph Convolutional Networks (GCNs) gain remarkable success in graph-related tasks under homophily graph assumption—most connected nodes have the same label. However, this assumption is fragile since heterophily is common in real-world networks, where most linked nodes have different labels. Some methods address heterophily using graph-level weighted combinations of multi-hop neighbor representations. However, they introduce noise and irrelevant information from two aspects: (1) higher-order neighborhoods may include more neighbors with different labels than those with the same label; (2) graph-level weighted combination fails to capture distinct node properties. To address these issues, firstly, a Neighborhood Distribution-induced Similarity (NDS) measure is developed to identify potential similar neighbors for nodes. Secondly, a node-level fusion mechanism Selective-Neighbors Gated Unit (SNGU) is designed to adaptively aggregate potential neighbors, first-hop neighbors, and the node itself by learning distinct weights for nodes. By combining the above two designs, this work proposes a novel Neighbors Selective Graph Convolutional Network (NSGCN), which allows nodes to selectively receive relevant neighbor information for better node representations, effectively modeling homophily and heterophily. Experiments on 10 widely used real-world datasets with varying properties demonstrate the superiority of the NSGCN, surpassing a strong baseline with an absolute increase of 9.83% in classification accuracy. The code is available at https://github.com/GGA23/NSGCN.

A novel similarity measure SF-IPF for CBKNN with implicit feedback data

PurposeThe increasing popularity of music streaming services also increases the need to customize the services for each user to attract and retain customers. Most of the music streaming services will not have explicit ratings for songs; they will have only implicit feedback data, i.e user listening history. For efficient music recommendation, the preferences of the users have to be infered, which is a challenging task.Design/methodology/approachPreferences of the users can be identified from the users' listening history. In this paper, a hybrid music recommendation system is proposed that infers features from user's implicit feedback and uses the hybrid of content-based and collaborative filtering method to recommend songs. A Content Boosted K-Nearest Neighbours (CBKNN) filtering technique was proposed, which used the users' listening history, popularity of songs, song features, and songs of similar interested users for recommending songs. The song features are taken as content features. Song Frequency–Inverse Popularity Frequency (SF-IPF) metric is proposed to find the similarity among the neighbours in collaborative filtering. Million Song Dataset and Echo Nest Taste Profile Subset are used as data sets.FindingsThe proposed CBKNN technique with SF-IPF similarity measure to identify similar interest neighbours performs better than other machine learning techniques like linear regression, decision trees, random forest, support vector machines, XGboost and Adaboost. The performance of proposed SF-IPF was tested with other similarity metrics like Pearson and Cosine similarity measures, in which SF-IPF results in better performance.Originality/valueThis method was devised to infer the user preferences from the implicit feedback data and it is converted as rating preferences. The importance of adding content features with collaborative information is analysed in hybrid filtering. A new similarity metric SF-IPF is formulated to identify the similarity between the users in collaborative filtering.

Clustering algorithm based on DINNSM and its application in gene expression data analysis.

Selecting an appropriate similarity measurement method is crucial for obtaining biologically meaningful clustering modules. Commonly used measurement methods are insufficient in capturing the complexity of biological systems and fail to accurately represent their intricate interactions. This study aimed to obtain biologically meaningful gene modules by using the clustering algorithm based on a similarity measurement method. A new algorithm called the Dual-Index Nearest Neighbor Similarity Measure (DINNSM) was proposed. This algorithm calculated the similarity matrix between genes using Pearson's or Spearman's correlation. It was then used to construct a nearest-neighbor table based on the similarity matrix. The final similarity matrix was reconstructed using the positions of shared genes in the nearest neighbor table and the number of shared genes. Experiments were conducted on five different gene expression datasets and compared with five widely used similarity measurement techniques for gene expression data. The findings demonstrate that when utilizing DINNSM as the similarity measure, the clustering results performed better than using alternative measurement techniques. DINNSM provided more accurate insights into the intricate biological connections among genes, facilitating the identification of more accurate and biological gene co-expression modules.

DMS: Low-overlap Registration of 3D Point Clouds with Double-layer Multi-scale Star-graph.

Registering 3D point clouds with low overlap is challenging in 3D computer vision, primarily due to difficulties in identifying small overlap regions and removing correspondence outliers. We observe that the neighborhood similarity can be utilized to detect point correspondence, and the consistent neighborhood correspondence can be used as a criterion to detect robust overlapping regions. So that a Double-layer Multi-scale Star-graph (DMS) structure is proposed to detect robust correspondences using two different types of multi-scale star-graphs. The first-layer Multi-scale Neighbor Feature Star-graphs (MNFS) takes each point as the center and its multi-scale nearest neighbors as the leaves. The MNFS enables to establish the initial correspondence candidate set between the two point clouds based on multi-scale neighborhood topology and feature similarity. Subsequently, each pair of corresponding points find their nearest neighbors within the correspondence sets to construct a Multi-scale Matching Star-graphs (MMS) on each side, so the mutual correspondence relationships between the MMS vertices are identified. These identified mutual correspondences are treated as vertices to construct the Multi-scale Correspondence Star-graphs (MCS), that indicate the relationships among the correspondences. We design edge weight and vertex weight criterion in MCS to detect only the robust correspondence set that has strong neighborhood consistency, so as to reject the outliers. Finally, the point cloud registration is conducted based on the detected robust correspondence. The experimental results demonstrate clearly that the proposed DMS method exhibits superior robustness when compared to existing state-of-the-art registration algorithms. The code of this study will be available at https://github.com/HualongCao/DMS.

Improved GMMKNN Hybrid Recommendation Algorithm

This paper proposes a hybrid recommendation algorithm that combines the advantages of Gaussian Mixture Model (GMM) and K-Nearest Neighbors (KNN) algorithms. The algorithm first applies GMM to cluster the training data, grouping users with similar interests using clustering techniques. It then utilizes the KNN algorithm for prediction. During the KNN recommendation process for a target user, the algorithm searches for neighboring users with similar interests and features within the same cluster. This significantly reduces the search scope of the nearest neighbors, thanks to the assistance of the GMM algorithm. The algorithm then selects the K most similar neighbors from the target user’s cluster as the candidate pool for personalized recommendations. Additionally, the algorithm improves the weight calculation method by incorporating a Gaussian kernel function for weight estimation. Experimental results on the dataset demonstrate that the proposed improved algorithm effectively enhances the accuracy of prediction results.

Maximum open-set entropy optimization via uncertainty measure for universal domain adaptation

Universal Domain Adaptation (UniDA) is a technology that enables the intelligent model to transfer knowledge learned from labeled source domains to related but unlabeled target domains without any prior label set relationship. The key to UniDA lies in rejecting target domain-specific “unknown” samples to achieve domain alignment on shared classes. In this paper, we propose the Maximum Open-set Entropy Optimization via uncertainty measure to adaptively reject “unknown” samples. Specifically, MOEO sets a transition region within the most easily confused class in the open-set space. We optimize the maximum open-set entropy of simple samples outside the transition region to further improve their confidence and separate difficult samples within the transition region by aggregating similar neighbors. Accordingly, a secure boundary is formed between shared samples and “unknown” samples, promoting domain alignment within shared classes. Experiments on four benchmarks show that MOEO outperforms the previous state-of-the-art significantly.

Adaptive knowledge transfer-based particle swarm optimization for constrained multitask optimization

Constrained multitask optimization (CMTO) problems are frequently encountered in practical applications. However, since the feasible regions of different tasks are difficult to match under constraints, it is hard to obtain and transfer effective knowledge among different tasks, resulting in poor convergence performance. To address this issue, a constrained multitask particle swarm optimization algorithm with knowledge transfer-based adaptive penalty function (CMTPSO-APF) is proposed to improve the convergence performance. The main contributions of CMTPSO-APF are three-fold. First, a dynamic particle topology is designed to improve the neighborhood similarity for different tasks with constrained conditions. Then, the particles with similar spatial structures can facilitate the knowledge transfer between different tasks. Second, a covariance matrix learning mechanism is proposed to obtain valid knowledge with constrained conditions. Then, the proposed method can promote the population to move in the direction of the optimal solution. Third, a knowledge transfer-based adaptive penalty function for constrained multitask optimization is designed to achieve the dynamical change of penalty factor according to the evolution state. Then, the adaptive penalty function can promote the transfer of effective knowledge and improve the convergence. Finally, some simulation experiments are carried out on the CMTO benchmark test suites and the practical application of the wastewater treatment process. The results indicate that CMTPSO-APF can improve the convergence performance.

Time-Aware Similarity Integration for User-Based Collaborative Filtering

A time-aware collaborative filtering-based recommender system provides item recommendations for the current user by prioritizing recent items preferred by similar neighbors over past preferred items. The similarity measure critically affects the performance of the system, and this study focuses on measuring the similarity between users that changes over time. After dividing the users’ rating time into intervals and computing similarity for each time interval, the final similarity is generated as a weighted sum by assigning lower weights to past similarity values and higher weights to more recent similarity values. Additionally, to ensure continuity of similarity measurement, consecutive time intervals are set to overlap. As a result of experiments applying the proposed method to the existing similarity measures, significant performance improvement was achieved in terms of some of the major performance metrics. In particular, the degree of coverage improvement was the highest, and the performance improvement effect was higher when the overlap size between time intervals was large rather than when it was small.

K1K2NN: A novel multi-label classification approach based on neighbors for predicting COVID-19 drug side effects

COVID-19, a novel ailment, has received comparatively fewer drugs for its treatment. Side Effects (SE) of a COVID-19 drug could cause long-term health issues. Hence, SE prediction is essential in COVID-19 drug development. Efficient models are also needed to predict COVID-19 drug SE since most existing research has proposed many classifiers to predict SE for diseases other than COVID-19. This work proposes a novel classifier based on neighbors named K1 K2 Nearest Neighbors (K1K2NN) to predict the SE of the COVID-19 drug from 17 molecules' descriptors and the chemical 1D structure of the drugs. The model is implemented based on the proposition that chemically similar drugs may be assigned similar drug SE, and co-occurring SE may be assigned to chemically similar drugs. The K1K2NN model chooses the first K1 neighbors to the test drug sample by calculating its similarity with the train drug samples. It then assigns the test sample with the SE label having the majority count on the SE labels of these K1 neighbor drugs obtained through a voting mechanism. The model then calculates the SE-SE similarity using the Jaccard similarity measure from the SE co-occurrence values. Finally, the model chooses the most similar K2 SE neighbors for those SE determined by the K1 neighbor drugs and assigns these SE to that test drug sample. The proposed K1K2NN model has showcased promising performance with the highest accuracy of 97.53% on chemical 1D drug structure and outperforms the state-of-the-art multi-label classifiers. In addition, we demonstrate the successful application of the proposed model on gene expression signature datasets, which aided in evaluating its performance and confirming its accuracy and robustness.