Community detection is a fundamental yet important task for characterizing and understanding the structure of attributed graphs. Existing methods mainly focus on the structural tightness and attribute similarity among nodes in a community. However, grouping numerous semantically homogeneous nodes will result in information cocoons and thus reduce the robustness of community structure and the efficiency of node collaboration in real-world applications, such as recommendation systems and collaboration networks. Since nodes with closer connections tend to be more similar, finding communities with dense structures and diverse attributes poses great challenges to mining latent relationships between the graph structure and attribute distribution. To our best knowledge, very little research has been conducted to address this challenge. In this article, we propose a novel three-view graph attention neural networks (TvGANN) model to formally address the attribute diversity aware community detection problem. TvGANN reveals correlations between the graph structure and attributes distribution from the perspective of node organization, attribute co-occurrence, and the node-attribute interaction. It effectively captures structural features and attributes distribution by feeding a structural network and an attribute co-occurrence network into graph attention modules through the encoder–decoder framework. It also learns heterogeneous information by feeding a network into a meta-node attention module. Then, it fuzes the three modules and clusters the embedding representations through a Student's t -distribution approach, which iteratively refines the clustering results. The experiments show that our method not only improves the quality in dense community detection but also performs efficiently for attributed graphs.

Irregularly, asynchronously and sparsely sampled multivariate time series (IASS-MTS) are characterized by sparse and uneven time intervals and nonsynchronous sampling rates, posing significant challenges for machine learning models to learn complex relationships within and beyond IASS-MTS to support various inference tasks. The existing methods typically either focus solely on single-task forecasting or simply concatenate them through a separate preprocessing imputation procedure for the subsequent classification application. However, these methods often ignore valuable annotated labels or fail to discover meaningful patterns from unlabeled data. Moreover, the approach of separate prefilling may introduce errors due to the noise in raw records, and thus degrade the downstream prediction performance. To overcome these challenges, we propose the time-aware dual attention and memory-augmented network (DAMA) with stochastic generative imputation (SGI). Our model constructs a joint task learning architecture that unifies imputation and classification tasks collaboratively. First, we design a new time-aware DAMA that accounts for irregular sampling rates, inherent data nonalignment, and sparse values in IASS-MTS data. The proposed network integrates both attention and memory to effectively analyze complex interactions within and across IASS-MTS for the classification task. Second, we develop the stochastic generative imputation (SGI) network that uses auxiliary information from sequence data for inferring the time series missing observations. By balancing joint tasks, our model facilitates interaction between them, leading to improved performance on both classification and imputation tasks. Third, we evaluate our model on real-world datasets and demonstrate its superior performance in terms of imputation accuracy and classification results, outperforming the baselines.

Labeling sufficient data for supervised learning remains an open challenge in social network analysis. An alternative is to collect self-labeled data, i.e. the data labeled by their owners. Emmery et al show that standard models can be trained and perform well on self-labeled data, suggesting the effectiveness of this approach. In this paper, we argue self-labeled data may not be representative of the population. Taking Twitter demographic prediction as an example, we show the popular FastText model standardly trained on self-labeled data does not generalize well on random testing samples. We then present a new learner DeFastText that aims to correct data bias using the kernel means matching technique. In experiment, we show it achieves lower generalization errors than FastText. This research raises an attention of the data bias problem when learning from self-labeled data in social network analysis.

Data mining in infectious disease pandemic scenarios is a complex giant task involving data from various fields and requirements of real-time and dynamic. In this paper, we propose a graph mining system for the infectious disease pandemic, IDGMS, with one-stop, dynamic, and interactive characteristics. The system has been applied to solve problems from three view scales and performs well. The system is constructed as a loose coupling structure at the front and back ends and can be extended to more graph mining issues. To the best of our knowledge, we are the first graph system especially targeting data mining of infectious diseases.

The advancement of science and technology provides the possibility of personalized intelligent education. Representation learning of students’ behavior data is challenging because whether time sequences and interactive behaviors or the correlation between knowledge points and students carrying important information. Some researchers propose knowledge tracing to provide ideas for solving this dilemma. However, existing knowledge tracing methods are divided into machine learning and deep learning. Machine learning-based methods require manual feature extraction and a large amount of prior knowledge. Although deep learning-based methods can automatically extract features, most methods either only use the time series information of the data, or use the association between knowledge points. All the methods ignore the association between knowledge points and students. To fill this gap, we propose a Gated Heterogeneous Graph Convolutional Network (GHGCN) model. We utilize the encoder-decoder framework to predict student performance using the representations of nodes, which is learned from heterogeneous convolutional networks and gate recurrent unit. To validate the effectiveness of the proposed GHGCN model, we conduct the experiments on three public datasets: Simulated Data, Assistments 2009, and Assistments 2015. The results indicate that our method can achieve better performance compared with state-of-the-art algorithms.

Irregularly, asynchronously and sparsely sampled multivariate time series (IASS-MTS) are characterized by sparse non-uniform time intervals between successive observations and different sampling rates amongst series. Those properties pose substantial challenges to mainstream machine learning models for learning complicated relations within and across IASS-MTS. This is because that most of the models assume that the time series in question are even, complete (fixed-dimensional features) and synchronous. To address these challenges, we present a novel time-aware Dual-Attention and Memory-Augmented Network (DAMA-Net). The proposed model can leverage both time irregularity, multi-sampling rates and global temporal patterns information inherent in IASS-MTS so as to learn more effective representations for improving prediction performance. Comprehensive experiments on real datasets show that the DAMA-Net outperforms the state-of-the-art methods in multivariate time series classification task.

MOTIVATION: The accumulation of somatic mutations plays critical roles in cancer development and progression. However, the global patterns of somatic mutations, especially non-coding mutations, and their roles in defining molecular subtypes of cancer have not been well characterized due to the computational challenges in analysing the complex mutational patterns. RESULTS: Here, we develop a new algorithm, called MutSpace, to effectively extract patient-specific mutational features using an embedding framework for larger sequence context. Our method is motivated by the observation that the mutation rate at megabase scale and the local mutational patterns jointly contribute to distinguishing cancer subtypes, both of which can be simultaneously captured by MutSpace. Simulation evaluations show that MutSpace can effectively characterize mutational features from known patient subgroups and achieve superior performance compared with previous methods. As a proof-of-principle, we apply MutSpace to 560 breast cancer patient samples and demonstrate that our method achieves high accuracy in subtype identification. In addition, the learned embeddings from MutSpace reflect intrinsic patterns of breast cancer subtypes and other features of genome structure and function. MutSpace is a promising new framework to better understand cancer heterogeneity based on somatic mutations. AVAILABILITY AND IMPLEMENTATION: Source code of MutSpace can be accessed at: https://github.com/ma-compbio/MutSpace. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

In eukaryotes, polyadenylation (poly(A)) is an essential process during mRNA maturation. Identifying the cis-determinants of poly(A) signal (PAS) on the DNA sequence is the key to understand the mechanism of translation regulation and mRNA metabolism. Although machine learning methods were widely used in computationally identifying PAS, the need for tremendous amounts of annotation data hinder applications of existing methods in species without experimental data on PAS. Therefore, cross-species PAS identification, which enables the possibility to predict PAS from untrained species, naturally becomes a promising direction. In our works, we propose a novel deep learning method named Poly(A)-DG for cross-species PAS identification. Poly(A)-DG consists of a Convolution Neural Network-Multilayer Perceptron (CNN-MLP) network and a domain generalization technique. It learns PAS patterns from the training species and identifies PAS in target species without re-training. To test our method, we use four species and build cross-species training sets with two of them and evaluate the performance of the remaining ones. Moreover, we test our method against insufficient data and imbalanced data issues and demonstrate that Poly(A)-DG not only outperforms state-of-the-art methods but also maintains relatively high accuracy when it comes to a smaller or imbalanced training set.

Motivation: The three dimensional organization of chromosomes within the cell nucleus is highly regulated. It is known that CCCTC-binding factor (CTCF) is an important architectural protein to mediate long-range chromatin loops. Recent studies have shown that the majority of CTCF binding motif pairs at chromatin loop anchor regions are in convergent orientation. However, it remains unknown whether the genomic context at the sequence level can determine if a convergent CTCF motif pair is able to form a chromatin loop. Results: In this article, we directly ask whether and what sequence-based features (other than the motif itself) may be important to establish CTCF-mediated chromatin loops. We found that motif conservation measured by 'branch-of-origin' that accounts for motif turn-over in evolution is an important feature. We developed a new machine learning algorithm called CTCF-MP based on word2vec to demonstrate that sequence-based features alone have the capability to predict if a pair of convergent CTCF motifs would form a loop. Together with functional genomic signals from CTCF ChIP-seq and DNase-seq, CTCF-MP is able to make highly accurate predictions on whether a convergent CTCF motif pair would form a loop in a single cell type and also across different cell types. Our work represents an important step further to understand the sequence determinants that may guide the formation of complex chromatin architectures. Availability and implementation: The source code of CTCF-MP can be accessed at: https://github.com/ma-compbio/CTCF-MP. Supplementary information: Supplementary data are available at Bioinformatics online.

Changes in cis-regulatory element composition that result in novel patterns of gene expression are thought to be a major contributor to the evolution of lineage-specific traits. Although transcription factor binding events show substantial variation across species, most computational approaches to study regulatory elements focus primarily upon highly conserved sites, and rely heavily upon multiple sequence alignments. However, sequence conservation based approaches have limited ability to detect lineage-specific elements that could contribute to species-specific traits. In this paper, we describe a novel framework that utilizes a birth-death model to trace the evolution of lineage-specific binding sites without relying on detailed base-by-base cross-species alignments. Our model was applied to analyze the evolution of binding sites based on the ChIP-seq data for six transcription factors (GATA1, SOX2, CTCF, MYC, MAX, ETS1) along the lineage toward human after human-mouse common ancestor. We estimate that a substantial fraction of binding sites (∼58-79% for each factor) in humans have origins since the divergence with mouse. Over 15% of all binding sites are unique to hominids. Such elements are often enriched near genes associated with specific pathways, and harbor more common SNPs than older binding sites in the human genome. These results support the ability of our method to identify lineage-specific regulatory elements and help understand their roles in shaping variation in gene regulation across species.