Drug combination therapy plays a vital role in disease treatment, including cancer, as it contributes to treatment efficacy and can alleviate the effect of drug resistance. Although clinical trials and screening may provide valuable information about synergistic drug combinations, they suffer from challenging combinatorial space. Multiple methods are proposed to address those issues. However, they still fail in making full use of global and local triplet context relationships of known synergistic combinations. To this end, a deep learning model which leverages dual view hypergraph representation fusion for synergistic drug combinations identification is proposed, namely DVHSyn. It first extracts the transcriptome features of cancer cell lines and molecular structures of drugs. Subsequently, by modeling the synergistic effect on a hypergraph, DVHSyn simultaneously learns the local and global context of the sample triplets via a hypergraph view and its expanded heterogeneous graph view. Finally, the learned representations of the above two branches are fused selectively to predict synergistic drug combinations. Experiment results demonstrate that DVHSyn surpasses six other competing methods. One case study also reflects that DVHSyn has the potential to predict novel synergistic drug combinations. Overall, our method is effective in identifying synergistic drug combinations and provides new insights for novel drug development.

With the explosive growth of user-generated content (UGC) in multimedia, multimodal sentiment recognition (MSR) tasks face unprecedented challenges. Specifically, existing MSR models exhibit primary limitations: i) Most approaches rely on predefined cross-modal emotion interaction patterns derived from statistical methods, which may not be applicable to all real-world scenarios; ii) many techniques interpret emotions semantically, hindering the ability to capture the sparsity of emotional transmission; and iii) these techniques overlook discrepancies between emotional expressions in images and text on social media. To address these challenges, we developed a novel cross-modal inconsistency adaptive graph learning network, termed RoseNet.RoseNet employs a token-level image-text mapping relationship (ITTM) to effectively capture cross-modal emotional interaction patterns between images and text. Inspired by the Expectation-Maximization (EM) algorithm, and RoseNet features Graph Learning(GL) and Graph Attention prediction(GAP) modules, which are alternately trained to generate more realistic ITTM. Moreover, a carefully designed loss function ensures the sparsity of emotional transmission. Additionally, RoseNet introduces a semantic-affective contrastive learning strategy that enables more grounded semantic and affective representation learning. Evaluation experiments using two benchmarks derived from real-world social media datasets demonstrate that RoseNet achieves significant and consistent performance in MSR tasks. Furthermore, visualizations confirm the model’s ability to capture ITTM with minimal prior knowledge.

Major depressive disorder (MDD) is a severe psychiatric disorder that currently lacks any objective diagnostic markers. Here, we develop a deep learning approach to discover the mass spectrometric features that can discriminate MDD patients from health controls. Using plasma peptides, the neural network, termed as CMS-Net, can perform diagnosis and prediction with an accuracy of 0.9441. The sensitivity and specificity reached 0.9352 and 0.9517 respectively, and the area under the curve was enhanced to 0.9634. Using the gradient-based feature importance method to interpret crucial features, we identify 28 differential peptide sequences from 14 precursor proteins (e.g. hemoglobin, immunoglobulin, albumin, etc.). This work highlights the possibility of molecular diagnosis of MDD with the aid of chemical and computer science.

Cell type identification plays a vital role in single-cell RNA sequencing (scRNA-seq) data analysis. Although many deep embedded methods to cluster scRNA-seq data have been proposed, they still fail in elucidating the intrinsic properties of cells and genes. Here, we present a novel end-to-end deep graph clustering model for single-cell transcriptomics data based on unsupervised Gene-Cell Collective representation learning and Optimal Transport (scGCOT) which integrates both cell and gene correlations. Specifically, scGCOT learns the latent embedding of cells and genes simultaneously and reconstructs the cell graph, the gene graph, and the gene expression count matrix. A zero-inflated negative binomial (ZINB) model is estimated via the reconstructed count matrix to capture the essential properties of scRNA-seq data. By leveraging the optimal transport-based joint representation alignment, scGCOT learns the clustering process and the latent representations through a mutually supervised self optimization strategy. Extensive experiments with 14 competing methods on 15 real scRNA-seq datasets demonstrate the competitive edges of scGCOT.

The migration of containerized microservices from virtual machines (VMs) to cloud data centers has become the most advanced deployment technique for large software applications in the cloud. This study investigates the scheduling of instance-intensive workflow (IWF) tasks to be executed in containers on a hybrid cloud when computational resources are limited. The process of scheduling these IWF tasks becomes complicated when considering the deployment time of containers, inter-task communication time, and their dependencies simultaneously, particularly when the task can choose multi-mode executions due to the flexible computational resource allocation of the container. We propose a batch scheduling strategy (BSS) for the IWF task scheduling problem. The BSS prioritizes the execution of IWF tasks with high repetition rates with a certain probability and records the virtual machines and modes selected for task execution, which can reduce the data transfer time and the randomness of computation. Based on this, we use an improved hybrid algorithm combined with BSS to solve the multi-mode IWF task scheduling problem. The experimental results demonstrate that employing the BSS can reduce the scheduling time by 6% when the number of workflows increases to 80. Additionally, we tested the effectiveness of all operators in the algorithm, and the results show that each step of the algorithm yields good performance. Compared to similar algorithms in related studies, the overall algorithm can achieve a maximum reduction of approximately 18% in the target value.

Providing potential next point-of-interest (POI) suggestions for users has become a prominent task in location-based social networks, which receives more and more attention from the industry and academia and it remains challenging due to highly dynamic and personalized interactions in user movements. Currently, state-of-the-art works develop various graph- and sequential-based learning methods to model user-POI interactions and transition regularities. However, there are still two significant shortcomings in these works: (1) ignoring personalized spatial and temporal-aspect interactive characteristics capable of exhibiting periodic interests of users and (2) insufficiently leveraging the sequential patterns of interactions for beyond-pairwise high-order collaborative signals among users’ sequences. To jointly address these challenges, we propose a novel multi-view hypergraph learning with spatial-temporal periodic interests for next POI recommendation (MvStHgL). In the local view, we attempt to learn the POI representation of each interaction via jointing periodic characteristics of spatial and temporal aspects. In the global view, we design a hypergraph by regarding interactive sequences as hyperedges to capture high-order collaborative signals across users, for further POI representations. More specifically, the output of POI representations in the local view is used for the initialized embedding, and the aggregation and propagation in the hypergraph are performed by a novel Node-to-Hypergraph-to-Node scheme. Furthermore, the captured POI embeddings are applied to achieve sequential dependency modeling for next POI prediction. Extensive experiments on three real-world datasets demonstrate that our proposed model outperforms the state-of-the-art models.

MOTIVATION: Chromothripsis, associated with poor clinical outcomes, is prognostically vital in multiple myeloma. The catastrophic event is reported to be detectable prior to the progression of multiple myeloma. As a result, chromothripsis detection can contribute to risk estimation and early treatment guidelines for multiple myeloma patients. However, manual diagnosis remains the gold standard approach to detect chromothripsis events with the whole-genome sequencing technology to retrieve both copy number variation (CNV) and structural variation data. Meanwhile, CNV data are much easier to obtain than structural variation data. Hence, in order to reduce the reliance on human experts' efforts and structural variation data extraction, it is necessary to establish a reliable and accurate chromothripsis detection method based on CNV data. RESULTS: To address those issues, we propose a method to detect chromothripsis solely based on CNV data. With the help of structure learning, the intrinsic relationship-directed acyclic graph of CNV features is inferred to derive a CNV embedding graph (i.e. CNV-DAG). Subsequently, a neural network based on Graph Transformer, local feature extraction, and non-linear feature interaction, is proposed with the embedding graph as the input to distinguish whether the chromothripsis event occurs. Ablation experiments, clustering, and feature importance analysis are also conducted to enable the proposed model to be explained by capturing mechanistic insights. AVAILABILITY AND IMPLEMENTATION: The source code and data are freely available at https://github.com/luvyfdawnYu/CNV_chromothripsis.

Abstract Bullet screen comments (BSCs) are user‐generated short comments that appear as real‐time overlays on many video platforms, expressing the audience opinions and emotions about different aspects of the ongoing video. Unlike traditional long comments after a show, BSCs are often incomplete, ambiguous in context, and correlated over time. Current studies in sentiment analysis of BSCs rarely address these challenges, motivating us to develop an aspect‐level sentiment analysis framework. Our framework, BSCNET, is a pre‐trained language encoder‐based deep neural classifier designed to enhance semantic understanding. A novel neighbor context construction method is proposed to uncover latent contextual correlation among BSCs over time, and we also incorporate semi‐supervised learning to reduce labeling costs. The framework increases F1 (Macro) and accuracy by up to 10% and 10.2%, respectively. Additionally, we have developed two novel downstream tasks. The first is noisy BSCs identification, which reached F1 (Macro) and accuracy of 90.1% and 98.3%, respectively, through fine‐tuning the BSCNET. The second is the prediction of future episode popularity, where the MAPE is reduced by 11%–19.0% when incorporating sentiment features. Overall, this study provides a methodology reference for aspect‐level sentiment analysis of BSCs and highlights its potential for viewing experience or forthcoming content optimization.