GNN-Based Concentration Prediction With Variable Input Flow Rates for Microfluidic Mixers

Recent years have witnessed significant advances brought by microfluidic biochips in automating biochemical protocols. Accurate preparation of fluid samples is an essential component of these protocols, where concentration prediction and generation are critical. Equipped with the advantages of convenient fabrication and control, microfluidic mixers demonstrate huge potential in sample preparation. Although finite element analysis (FEA) is the most commonly used simulation method for accurate concentration prediction of a given microfluidic mixer, it is time-consuming with poor scalability for large biochip sizes. Recently, machine learning models have been adopted in concentration prediction, with great potential in enhancing the efficiency over traditional FEA methods. However, the state-of-the-art machine learning-based method can only predict the concentration of mixers with fixed input flow rates and fixed sizes. In this paper, we propose a new concentration prediction method based on graph neural networks (GNNs), which can predict output concentrations for microfluidic mixters with variable input flow rates. Moreover, a transfer learning method is proposed to transfer the trained model to mixers of different sizes with reduced training data. Experimental results show that, for microfluidic mixers with fixed input flow rates, the proposed method obtains an average reduction of 88% in terms of prediction errors compared with the state-of-the-art method. For microfluidic mixers with variable input flow rates, the proposed method reduces the prediction error by 85% on average. Besides, the proposed transfer learning method reduces the training data by 84% for extending the pre-trained model for microfluidic mixers of different sizes with acceptable prediction error.

Parameter-Efficient Person Re-Identification in the 3D Space

People live in a 3D world. However, existing works on person re-identification (re-id) mostly consider the semantic representation learning in a 2D space, intrinsically limiting the understanding of people. In this work, we address this limitation by exploring the prior knowledge of the 3D body structure. Specifically, we project 2D images to a 3D space and introduce a novel parameter-efficient omni-scale graph network (OG-Net) to learn the pedestrian representation directly from 3D point clouds. OG-Net effectively exploits the local information provided by sparse 3D points and takes advantage of the structure and appearance information in a coherent manner. With the help of 3D geometry information, we can learn a new type of deep re-id feature free from noisy variants, such as scale and viewpoint. To our knowledge, we are among the first attempts to conduct person re-id in the 3D space. We demonstrate through extensive experiments that the proposed method: (1) eases the matching difficulty in the traditional 2D space; 2) exploits the complementary information of 2D appearance and 3D structure; 3) achieves competitive results with limited parameters on four large-scale person re-id datasets; and 4) has good scalability to unseen datasets. Our code, models, and generated 3D human data are publicly available at https://github.com/layumi/person-reid-3d.

Generating High-Precision Force Fields for Molecular Dynamics Simulations to Study Chemical Reaction Mechanisms Using Molecular Configuration Transformer

Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical calculations is the most commonly used method. However, this way is heavily dependent on individual experience and chemical intuition. In our previous study, we proposed a research paradigm that used enhanced sampling in molecular dynamics simulations to study chemical reactions. This approach can directly simulate the entire process of a chemical reaction. However, the computational speed limited the use of high-precision potential energy functions for simulations. To address this issue, we presented a scheme for training high-precision force fields for molecular modeling using a previously developed graph-neural-network-based molecular model, molecular configuration transformer. This potential energy function allowed for highly accurate simulations at a low computational cost, leading to more precise calculations of the mechanism of chemical reactions. We applied this approach to study a Claisen rearrangement reaction and a carbonyl insertion reaction catalyzed by manganese.

Protein-Protein Interfaces: A Graph Neural Network Approach

Protein-protein interactions (PPIs) are fundamental processes governing cellular functions, crucial for understanding biological systems at the molecular level. Compared to experimental methods for PPI prediction and site identification, computational deep learning approaches represent an affordable and efficient solution to tackle these problems. Since protein structure can be summarized as a graph, graph neural networks (GNNs) represent the ideal deep learning architecture for the task. In this work, PPI prediction is modeled as a node-focused binary classification task using a GNN to determine whether a generic residue is part of the interface. Biological data were obtained from the Protein Data Bank in Europe (PDBe), leveraging the Protein Interfaces, Surfaces, and Assemblies (PISA) service. To gain a deeper understanding of how proteins interact, the data obtained from PISA were assembled into three datasets: Whole, Interface, and Chain, consisting of data on the whole protein, couples of interacting chains, and single chains, respectively. These three datasets correspond to three different nuances of the problem: identifying interfaces between protein complexes, between chains of the same protein, and interface regions in general. The results indicate that GNNs are capable of solving each of the three tasks with very good performance levels.

Context-Enhanced Network with Spatial-Aware Graph for Smartphone Screen Defect Detection

Interactive devices such as touch screens have gained widespread usage in daily life; this has directed the attention of researchers to the quality of screen glass. Consequently, defect detection in screen glass is essential for improving the quality of smartphone screens. In recent years, defect detection methods based on deep learning have played a crucial role in improving detection accuracy and robustness. However, challenges have arisen in achieving high-performance detection due to the small size, irregular shapes and low contrast of defects. To address these challenges, this paper proposes CE-SGNet, a Context-Enhanced Network with a Spatial-aware Graph, for smartphone screen defect detection. It consists of two novel components: the Adaptive Receptive Field Attention Module (ARFAM) and the Spatial-aware Graph Reasoning Module (SGRM). The ARFAM enhances defect features by adaptively extracting contextual information to capture the most relevant contextual region of defect features. The SGRM constructs a region-to-region graph and encodes region features with spatial relationships. The connections among defect regions are enhanced during the propagation process through a graph attention network. By enriching the feature representations of defect regions, the CE-SGNet can accurately identify and locate defects of various shapes and scales. Experimental results demonstrate that the CE-SGNet achieves outstanding performance on two public datasets.

Antibody design using deep learning: from sequence and structure design to affinity maturation

Deep learning has achieved impressive results in various fields such as computer vision and natural language processing, making it a powerful tool in biology. Its applications now encompass cellular image classification, genomic studies and drug discovery. While drug development traditionally focused deep learning applications on small molecules, recent innovations have incorporated it in the discovery and development of biological molecules, particularly antibodies. Researchers have devised novel techniques to streamline antibody development, combining in vitro and in silico methods. In particular, computational power expedites lead candidate generation, scaling and potential antibody development against complex antigens. This survey highlights significant advancements in protein design and optimization, specifically focusing on antibodies. This includes various aspects such as design, folding, antibody-antigen interactions docking and affinity maturation.

A comprehensive review and comparison of existing computational methods for protein function prediction

Protein function prediction is critical for understanding the cellular physiological and biochemical processes, and it opens up new possibilities for advancements in fields such as disease research and drug discovery. During the past decades, with the exponential growth of protein sequence data, many computational methods for predicting protein function have been proposed. Therefore, a systematic review and comparison of these methods are necessary. In this study, we divide these methods into four different categories, including sequence-based methods, 3D structure-based methods, PPI network-based methods and hybrid information-based methods. Furthermore, their advantages and disadvantages are discussed, and then their performance is comprehensively evaluated and compared. Finally, we discuss the challenges and opportunities present in this field.

A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation

Artificial intelligence (AI)-driven methods can vastly improve the historically costly drug design process, with various generative models already in widespread use. Generative models for de novo drug design, in particular, focus on the creation of novel biological compounds entirely from scratch, representing a promising future direction. Rapid development in the field, combined with the inherent complexity of the drug design process, creates a difficult landscape for new researchers to enter. In this survey, we organize de novo drug design into two overarching themes: small molecule and protein generation. Within each theme, we identify a variety of subtasks and applications, highlighting important datasets, benchmarks, and model architectures and comparing the performance of top models. We take a broad approach to AI-driven drug design, allowing for both micro-level comparisons of various methods within each subtask and macro-level observations across different fields. We discuss parallel challenges and approaches between the two applications and highlight future directions for AI-driven de novo drug design as a whole. An organized repository of all covered sources is available at https://github.com/gersteinlab/GenAI4Drug.

EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion

Mechanisms of protein-DNA interactions are involved in a wide range of biological activities and processes. Accurately identifying binding sites between proteins and DNA is crucial for analyzing genetic material, exploring protein functions, and designing novel drugs. In recent years, several computational methods have been proposed as alternatives to time-consuming and expensive traditional experiments. However, accurately predicting protein-DNA binding sites still remains a challenge. Existing computational methods often rely on handcrafted features and a single-model architecture, leaving room for improvement. We propose a novel computational method, called EGPDI, based on multi-view graph embedding fusion. This approach involves the integration of Equivariant Graph Neural Networks (EGNN) and Graph Convolutional Networks II (GCNII), independently configured to profoundly mine the global and local node embedding representations. An advanced gated multi-head attention mechanism is subsequently employed to capture the attention weights of the dual embedding representations, thereby facilitating the integration of node features. Besides, extra node features from protein language models are introduced to provide more structural information. To our knowledge, this is the first time that multi-view graph embedding fusion has been applied to the task of protein-DNA binding site prediction. The results of five-fold cross-validation and independent testing demonstrate that EGPDI outperforms state-of-the-art methods. Further comparative experiments and case studies also verify the superiority and generalization ability of EGPDI.

Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks

Spatial transcriptomics data play a crucial role in cancer research, providing a nuanced understanding of the spatial organization of gene expression within tumor tissues. Unraveling the spatial dynamics of gene expression can unveil key insights into tumor heterogeneity and aid in identifying potential therapeutic targets. However, in many large-scale cancer studies, spatial transcriptomics data are limited, with bulk RNA-seq and corresponding Whole Slide Image (WSI) data being more common (e.g. TCGA project). To address this gap, there is a critical need to develop methodologies that can estimate gene expression at near-cell (spot) level resolution from existing WSI and bulk RNA-seq data. This approach is essential for reanalyzing expansive cohort studies and uncovering novel biomarkers that have been overlooked in the initial assessments. In this study, we present STGAT (Spatial Transcriptomics Graph Attention Network), a novel approach leveraging Graph Attention Networks (GAT) to discern spatial dependencies among spots. Trained on spatial transcriptomics data, STGAT is designed to estimate gene expression profiles at spot-level resolution and predict whether each spot represents tumor or non-tumor tissue, especially in patient samples where only WSI and bulk RNA-seq data are available. Comprehensive tests on two breast cancer spatial transcriptomics datasets demonstrated that STGAT outperformed existing methods in accurately predicting gene expression. Further analyses using the TCGA breast cancer dataset revealed that gene expression estimated from tumor-only spots (predicted by STGAT) provides more accurate molecular signatures for breast cancer sub-type and tumor stage prediction, and also leading to improved patient survival and disease-free analysis. Availability: Code is available at https://github.com/compbiolabucf/STGAT.

Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives

Spectrum-structure correlation is playing an increasingly crucial role in spectral analysis and has undergone significant development in recent decades. With the advancement of spectrometers, the high-throughput detection triggers the explosive growth of spectral data, and the research extension from small molecules to biomolecules accompanies massive chemical space. Facing the evolving landscape of spectrum-structure correlation, conventional chemometrics becomes ill-equipped, and deep learning assisted chemometrics rapidly emerges as a flourishing approach with superior ability of extracting latent features and making precise predictions. In this review, the molecular and spectral representations and fundamental knowledge of deep learning are first introduced. We then summarize the development of how deep learning assist to establish the correlation between spectrum and molecular structure in the recent 5 years, by empowering spectral prediction (i.e., forward structure-spectrum correlation) and further enabling library matching and de novo molecular generation (i.e., inverse spectrum-structure correlation). Finally, we highlight the most important open issues persisted with corresponding potential solutions. With the fast development of deep learning, it is expected to see ultimate solution of establishing spectrum-structure correlation soon, which would trigger substantial development of various disciplines.

TSANN-TG: Temporal-Spatial Attention Neural Networks with Task-Specific Graph for EEG Emotion Recognition

Electroencephalography (EEG)-based emotion recognition is increasingly pivotal in the realm of affective brain-computer interfaces. In this paper, we propose TSANN-TG (temporal-spatial attention neural network with a task-specific graph), a novel neural network architecture tailored for enhancing feature extraction and effectively integrating temporal-spatial features. TSANN-TG comprises three primary components: a node-feature-encoding-and-adjacency-matrices-construction block, a graph-aggregation block, and a graph-feature-fusion-and-classification block. Leveraging the distinct temporal scales of features from EEG signals, TSANN-TG incorporates attention mechanisms for efficient feature extraction. By constructing task-specific adjacency matrices, the graph convolutional network with an attention mechanism captures the dynamic changes in dependency information between EEG channels. Additionally, TSANN-TG emphasizes feature integration at multiple levels, leading to improved performance in emotion-recognition tasks. Our proposed TSANN-TG is applied to both our FTEHD dataset and the publicly available DEAP dataset. Comparative experiments and ablation studies highlight the excellent recognition results achieved. Compared to the baseline algorithms, TSANN-TG demonstrates significant enhancements in accuracy and F1 score on the two benchmark datasets for four types of cognitive tasks. These results underscore the significant potential of the TSANN-TG method to advance EEG-based emotion recognition.

Prediction of drug-protein interaction based on dual channel neural networks with attention mechanism

The precise identification of drug-protein inter action (DPI) can significantly speed up the drug discovery process. Bioassay methods are time-consuming and expensive to screen for each pair of drug proteins. Machine-learning-based methods cannot accurately predict a large number of DPIs. Compared with traditional computing methods, deep learning methods need less domain knowledge and have strong data learning ability. In this study, we construct a DPI prediction model based on dual channel neural networks with an efficient path attention mechanism, called DCA-DPI. The drug molecular graph and protein sequence are used as the data input of the model, and the residual graph neural network and the residual convolution network are used to learn the feature representation of the drug and protein, respectively, to obtain the feature vector of the drug and the hidden vector of protein. To get a more accurate protein feature vector, the weighted sum of the hidden vector of protein is applied using the neural attention mechanism. In the end, drug and protein vectors are concatenated and input into the full connection layer for classification. In order to evaluate the performance of DCA-DPI, three widely used public data, Human, C.elegans and DUD-E, are used in the experiment. The evaluation metrics values in the experiment are superior to other relevant methods. Experiments show that our model is efficient for DPI prediction.

BTR: a bioinformatics tool recommendation system

MOTIVATION

The rapid expansion of Bioinformatics research has led to a proliferation of computational tools for scientific analysis pipelines. However, constructing these pipelines is a demanding task, requiring extensive domain knowledge and careful consideration. As the Bioinformatics landscape evolves, researchers, both novice and expert, may feel overwhelmed in unfamiliar fields, potentially leading to the selection of unsuitable tools during workflow development.

RESULTS

In this article, we introduce the Bioinformatics Tool Recommendation system (BTR), a deep learning model designed to recommend suitable tools for a given workflow-in-progress. BTR leverages recent advances in graph neural network technology, representing the workflow as a graph to capture essential context. Natural language processing techniques enhance tool recommendations by analyzing associated tool descriptions. Experiments demonstrate that BTR outperforms the existing Galaxy tool recommendation system, showcasing its potential to streamline scientific workflow construction.

AVAILABILITY AND IMPLEMENTATION

The Python source code is available at https://github.com/ryangreenj/bioinformatics_tool_recommendation.

Computational drug repositioning with attention walking

Drug repositioning aims to identify new therapeutic indications for approved medications. Recently, the importance of computational drug repositioning has been highlighted because it can reduce the costs, development time, and risks compared to traditional drug discovery. Most approaches in this area use networks for systematic analysis. Inferring drug-disease associations is then defined as a link prediction problem in a heterogeneous network composed of drugs and diseases. In this article, we present a novel method of computational drug repositioning, named drug repositioning with attention walking (DRAW). DRAW proceeds as follows: first, a subgraph enclosing the target link for prediction is extracted. Second, a graph convolutional network captures the structural features of the labeled nodes in the subgraph. Third, the transition probabilities are computed using attention mechanisms and converted into random walk profiles. Finally, a multi-layer perceptron takes random walk profiles and predicts whether a target link exists. As an experiment, we constructed two heterogeneous networks with drug-drug similarities based on chemical structures and anatomical therapeutic chemical classification (ATC) codes. Using 10-fold cross-validation, DRAW achieved an area under the receiver operating characteristic (ROC) curve of 0.903 and outperformed state-of-the-art methods. Moreover, we demonstrated the results of case studies for selected drugs and diseases to further confirm the capability of DRAW to predict drug-disease associations.

Multiview hyperedge-aware hypergraph embedding learning for multisite, multiatlas fMRI based functional connectivity network analysis

Recently, functional magnetic resonance imaging (fMRI) based functional connectivity network (FCN) analysis via graph convolutional networks (GCNs) has shown promise for automated diagnosis of brain diseases by regarding the FCNs as irregular graph-structured data. However, multiview information and site influences of the FCNs in a multisite, multiatlas fMRI scenario have been understudied. In this paper, we propose a Class-consistency and Site-independence Multiview Hyperedge-Aware HyperGraph Embedding Learning (CcSi-MHAHGEL) framework to integrate FCNs constructed on multiple brain atlases in a multisite fMRI study. Specifically, for each subject, we first model brain network as a hypergraph for every brain atlas to characterize high-order relations among multiple vertexes, and then introduce a multiview hyperedge-aware hypergraph convolutional network (HGCN) to extract a multiatlas-based FCN embedding where hyperedge weights are adaptively learned rather than employing the fixed weights precalculated in traditional HGCNs. In addition, we formulate two modules to jointly learn the multiatlas-based FCN embeddings by considering the between-subject associations across classes and sites, respectively, i.e., a class-consistency module to encourage both compactness within every class and separation between classes for promoting discrimination in the embedding space, and a site-independence module to minimize the site dependence of the embeddings for mitigating undesired site influences due to differences in scanning platforms and/or protocols at multiple sites. Finally, the multiatlas-based FCN embeddings are fed into a few fully connected layers followed by the soft-max classifier for diagnosis decision. Extensive experiments on the ABIDE demonstrate the effectiveness of our method for autism spectrum disorder (ASD) identification. Furthermore, our method is interpretable by revealing ASD-relevant brain regions that are biologically significant.

Brave the Wind and the Waves: Discovering Robust and Generalizable Graph Lottery Tickets

The training and inference of Graph Neural Networks (GNNs) are costly when scaling up to large-scale graphs. Graph Lottery Ticket (GLT) has presented the first attempt to accelerate GNN inference on large-scale graphs by jointly pruning the graph structure and the model weights. Though promising, GLT encounters robustness and generalization issues when deployed in real-world scenarios, which are also long-standing and critical problems in deep learning ideology. In real-world scenarios, the distribution of unseen test data is typically diverse. We attribute the failures on out-of-distribution (OOD) data to the incapability of discerning causal patterns, which remain stable amidst distribution shifts. In traditional spase graph learning, the model performance deteriorates dramatically as the graph/network sparsity exceeds a certain high level. Worse still, the pruned GNNs are hard to generalize to unseen graph data due to limited training set at hand. To tackle these issues, we propose the Resilient Graph Lottery Ticket (RGLT) to find more robust and generalizable GLT in GNNs. Concretely, we reactivate a fraction of weights/edges by instantaneous gradient information at each pruning point. After sufficient pruning, we conduct environmental interventions to extrapolate potential test distribution. Finally, we perform last several rounds of model averages to further improve generalization. We provide multiple examples and theoretical analyses that underpin the universality and reliability of our proposal. Further, RGLT has been experimentally verified across various independent identically distributed (IID) and out-of-distribution (OOD) graph benchmarks.

Edge-relational window-attentional graph neural network for gene expression prediction in spatial transcriptomics analysis

Spatial transcriptomics (ST), containing gene expression with fine-grained (i.e., different windows) spatial location within tissue samples, has become vital in developing innovative treatments. Traditional ST technology, however, rely on costly specialized commercial equipment. Addressing this, our article aims to creates a cost-effective, virtual ST approach using standard tissue images for gene expression prediction, eliminating the need for expensive equipment. Conventional approaches in this field often overlook the long-distance spatial dependencies between different sample windows or need prior gene expression data. To overcome these limitations, we propose the Edge-Relational Window-Attentional Network (ErwaNet), enhancing gene prediction by capturing both local interactions and global structural information from tissue images, without prior gene expression data. ErwaNet innovatively constructs heterogeneous graphs to model local window interactions and incorporates an attention mechanism for global information analysis. This dual framework not only provides a cost-effective solution for gene expression predictions but also obviates the necessity of prior knowledge gene expression information, a significant advantage in the field of cancer research where it enables a more efficient and accessible analytical paradigm. ErwaNet stands out as a prior-free and easy-to-implement Graph Convolution Network (GCN) method for predicting gene expression from tissue images. Evaluation of the two public breast cancer datasets shows that ErwaNet, without additional information, outperforms the state-of-the-art (SOTA) methods. Code is available at https://github.com/biyecc/ErwaNet.

Weisfeiler-Lehman goes dynamic: An analysis of the expressive power of Graph Neural Networks for attributed and dynamic graphs

Graph Neural Networks (GNNs) are a large class of relational models for graph processing. Recent theoretical studies on the expressive power of GNNs have focused on two issues. On the one hand, it has been proven that GNNs are as powerful as the Weisfeiler-Lehman test (1-WL) in their ability to distinguish graphs. Moreover, it has been shown that the equivalence enforced by 1-WL equals unfolding equivalence. On the other hand, GNNs turned out to be universal approximators on graphs modulo the constraints enforced by 1-WL/unfolding equivalence. However, these results only apply to Static Attributed Undirected Homogeneous Graphs (SAUHG) with node attributes. In contrast, real-life applications often involve a much larger variety of graph types. In this paper, we conduct a theoretical analysis of the expressive power of GNNs for two other graph domains that are particularly interesting in practical applications, namely dynamic graphs and SAUGHs with edge attributes. Dynamic graphs are widely used in modern applications; hence, the study of the expressive capability of GNNs in this domain is essential for practical reasons and, in addition, it requires a new analyzing approach due to the difference in the architecture of dynamic GNNs compared to static ones. On the other hand, the examination of SAUHGs is of particular relevance since they act as a standard form for all graph types: it has been shown that all graph types can be transformed without loss of information to SAUHGs with both attributes on nodes and edges. This paper considers generic GNN models and appropriate 1-WL tests for those domains. Then, the known results on the expressive power of GNNs are extended to the mentioned domains: it is proven that GNNs have the same capability as the 1-WL test, the 1-WL equivalence equals unfolding equivalence and that GNNs are universal approximators modulo 1-WL/unfolding equivalence. Moreover, the proof of the approximation capability is mostly constructive and allows us to deduce hints on the architecture of GNNs that can achieve the desired approximation.

A Comprehensive Survey on Deep Graph Representation Learning

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future.

Geometric Multimodal Deep Learning With Multiscaled Graph Wavelet Convolutional Network

Multimodal data provide complementary information of a natural phenomenon by integrating data from various domains with very different statistical properties. Capturing the intramodality and cross-modality information of multimodal data is the essential capability of multimodal learning methods. The geometry-aware data analysis approaches provide these capabilities by implicitly representing data in various modalities based on their geometric underlying structures. Also, in many applications, data are explicitly defined on an intrinsic geometric structure. Generalizing deep learning methods to the non-Euclidean domains is an emerging research field, which has recently been investigated in many studies. Most of those popular methods are developed for unimodal data. In this article, a multimodal graph wavelet convolutional network (M-GWCN) is proposed as an end-to-end network. M-GWCN simultaneously finds intramodality representation by applying the multiscale graph wavelet transform to provide helpful localization properties in the graph domain of each modality and cross-modality representation by learning permutations that encode correlations among various modalities. M-GWCN is not limited to either the homogeneous modalities with the same number of data or any prior knowledge indicating correspondences between modalities. Several semisupervised node classification experiments have been conducted on three popular unimodal explicit graph-based datasets and five multimodal implicit ones. The experimental results indicate the superiority and effectiveness of the proposed methods compared with both spectral graph domain convolutional neural networks and state-of-the-art multimodal methods.

TinyNS: Platform-Aware Neurosymbolic Auto Tiny Machine Learning

Machine learning at the extreme edge has enabled a plethora of intelligent, time-critical, and remote applications. However, deploying interpretable artificial intelligence systems that can perform high-level symbolic reasoning and satisfy the underlying system rules and physics within the tight platform resource constraints is challenging. In this paper, we introduce TinyNS, the first platform-aware neurosymbolic architecture search framework for joint optimization of symbolic and neural operators. TinyNS provides recipes and parsers to automatically write microcontroller code for five types of neurosymbolic models, combining the context awareness and integrity of symbolic techniques with the robustness and performance of machine learning models. TinyNS uses a fast, gradient-free, black-box Bayesian optimizer over discontinuous, conditional, numeric, and categorical search spaces to find the best synergy of symbolic code and neural networks within the hardware resource budget. To guarantee deployability, TinyNS talks to the target hardware during the optimization process. We showcase the utility of TinyNS by deploying microcontroller-class neurosymbolic models through several case studies. In all use cases, TinyNS outperforms purely neural or purely symbolic approaches while guaranteeing execution on real hardware.

Graph-based social relation inference with multi-level conditional attention

Social relation inference intrinsically requires high-level semantic understanding. In order to accurately infer relations of persons in images, one needs not only to understand scenes and objects in images, but also to adaptively attend to important clues. Unlike prior works of classifying social relations using attention on detected objects, we propose a MUlti-level Conditional Attention (MUCA) mechanism for social relation inference, which attends to scenes, objects and human interactions based on each person pair. Then, we develop a transformer-style network to achieve the MUCA mechanism. The novel network named as Graph-based Relation Inference Transformer (i.e., GRIT) consists of two modules, i.e., a Conditional Query Module (CQM) and a Relation Attention Module (RAM). Specifically, we design a graph-based CQM to generate informative relation queries for all person pairs, which fuses local features and global context for each person pair. Moreover, we fully take advantage of transformer-style networks in RAM for multi-level attentions in classifying social relations. To our best knowledge, GRIT is the first for inferring social relations with multi-level conditional attention. GRIT is end-to-end trainable and significantly outperforms existing methods on two benchmark datasets, e.g., with performance improvement of 7.8% on PIPA and 9.6% on PISC.

Modification and completion of geological structure knowledge graph based on pattern matching

As a knowledge representation method, knowledge graph is widely used in intelligent question answering systems and recommendation systems. At present, the research on knowledge graph mainly focuses on information query and retrieval based on knowledge graph. In some domain knowledge graphs, specific subgraph structures (patterns) have specific physical meanings. Aiming at this problem, this paper proposes a method and framework of knowledge graph pattern mining based on gat. Firstly, the patterns with specific physical meaning were transformed into subgraph structures containing topological structures and entity attributes. Secondly, the subgraph structure of the pattern is regarded as the query graph, and the knowledge graph is regarded as the data graph, so that the problem is transformed into an approximate subgraph matching problem. Then, the improved relational graph attention network is used to fuse the adaptive edge deletion mechanism to realize the approximate subgraph matching of subgraph structure and attribute, so as to obtain the best matching subgraph. The proposed method is trained in an end-to-end manner. The approximate subgraph matching is realized on the existing data set, and the research work of key pattern mining of complex geological structure knowledge graph is carried out.

TITAN: Combining a bidirectional forwarding graph and GCN to detect saturation attack targeted at SDN

The decoupling of control and forwarding layers brings Software-Defined Networking (SDN) the network programmability and global control capability, but it also poses SDN security risks. The adversaries can use the forwarding and control decoupling character of SDN to forge legitimate traffic, launching saturation attacks targeted at SDN switches. These attacks can cause the overflow of switch flow tables, thus making the switch cannot forward benign network traffic. How to effectively detect saturation attack is a research hotspot. There are only a few graph-based saturation attack detection methods. Meanwhile, the current graph generation methods may take useless or misleading information to the attack detection, thus decreasing the attack detection accuracy. To solve the above problems, this paper proposes TITAN, a bidirecTional forwardIng graph-based saturaTion Attack detectioN method. TITAN defines flow forwarding rules and topology information, and designs flow statistical features. Based on these definitions, TITAN generates nodes of the bi-forwarding graph based on the flow statistics features and edges of the bi-forwarding graph based on the network traffic routing paths. In this way, each traffic flow in the network is transformed into a bi-directional forwarding graph. Then TITAN feeds the above bidirectional forwarding graph into a Graph Convolutional Network (GCN) to detect whether the flow is a saturation attack flow. The experimental results show that TITAN can effectively detect saturation attacks in SDNs with a detection accuracy of more than 97%.

Exploring Chemical Reaction Space with Machine Learning Models: Representation and Feature Perspective

Chemical reactions serve as foundational building blocks for organic chemistry and drug design. In the era of large AI models, data-driven approaches have emerged to innovate the design of novel reactions, optimize existing ones for higher yields, and discover new pathways for synthesizing chemical structures comprehensively. To effectively address these challenges with machine learning models, it is imperative to derive robust and informative representations or engage in feature engineering using extensive data sets of reactions. This work aims to provide a comprehensive review of established reaction featurization approaches, offering insights into the selection of representations and the design of features for a wide array of tasks. The advantages and limitations of employing SMILES, molecular fingerprints, molecular graphs, and physics-based properties are meticulously elaborated. Solutions to bridge the gap between different representations will also be critically evaluated. Additionally, we introduce a new frontier in chemical reaction pretraining, holding promise as an innovative yet unexplored avenue.

Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer

Colorectal cancer (CRC) is the third most diagnosed cancer and the second deadliest cancer worldwide representing a major public health problem. In recent years, increasing evidence has shown that microRNA (miRNA) can control the expression of targeted human messenger RNA (mRNA) by reducing their abundance or translation, acting as oncogenes or tumor suppressors in various cancers, including CRC. Due to the significant up-regulation of oncogenic miRNAs in CRC, elucidating the underlying mechanism and identifying dysregulated miRNA targets may provide a basis for improving current therapeutic interventions. In this paper, we proposed Gra-CRC-miRTar, a pre-trained nucleotide-to-graph neural network framework, for identifying potential miRNA targets in CRC. Different from previous studies, we constructed two pre-trained models to encode RNA sequences and transformed them into de Bruijn graphs. We employed different graph neural networks to learn the latent representations. The embeddings generated from de Bruijn graphs were then fed into a Multilayer Perceptron (MLP) to perform the prediction tasks. Our extensive experiments show that Gra-CRC-miRTar achieves better performance than other deep learning algorithms and existing predictors. In addition, our analyses also successfully revealed 172 out of 201 functional interactions through experimentally validated miRNA-mRNA pairs in CRC. Collectively, our effort provides an accurate and efficient framework to identify potential miRNA targets in CRC, which can also be used to reveal miRNA target interactions in other malignancies, facilitating the development of novel therapeutics.

GCMSFormer: A Fully Automatic Method for the Resolution of Overlapping Peaks in Gas Chromatography-Mass Spectrometry

Gas chromatography-mass spectrometry (GC-MS) is one of the most important instruments for analyzing volatile organic compounds. However, the complexity of real samples and the limitations of chromatographic separation capabilities lead to coeluting compounds without ideal separation. In this study, a Transformer-based automatic resolution method (GCMSFormer) is proposed to resolve mass spectra from GC-MS peaks in an end-to-end manner, predicting the mass spectra of components directly from the raw overlapping peaks data. Furthermore, orthogonal projection resolution (OPR) was integrated into GCMSFormer to resolve minor components. The GCMSFormer model was trained, validated, and tested using 100,000 augmented data. It achieves 99.88% of the bilingual evaluation understudy (BLEU) value on the test set, significantly higher than the 97.68% BLEU value of the baseline sequence-to-sequence model long short-term memory (LSTM). GCMSFormer was also compared with two nondeep learning resolution tools (MZmine and AMDIS) and two deep learning resolution tools (PARAFAC2 with DL and MSHub/GNPS) on a real plant essential oil GC-MS data set. Their resolution results were compared on evaluation metrics, including the number of compounds resolved, mass spectral match score, correlation coefficient, explained variance, and resolution speed. The results demonstrate that GCMSFormer has better resolution performance, higher automation, and faster resolution speed. In summary, GCMSFormer is an end-to-end, fast, fully automatic, and accurate method for analyzing GC-MS data of complex samples.

Unbiasing Enhanced Sampling on a High-Dimensional Free Energy Surface with a Deep Generative Model

Biased enhanced sampling methods that utilize collective variables (CVs) are powerful tools for sampling conformational ensembles. Due to their large intrinsic dimensions, efficiently generating conformational ensembles for complex systems requires enhanced sampling on high-dimensional free energy surfaces. While temperature-accelerated molecular dynamics (TAMD) can trivially adopt many CVs in a simulation, unbiasing the simulation to generate unbiased conformational ensembles requires accurate modeling of a high-dimensional CV probability distribution, which is challenging for traditional density estimation techniques. Here we propose an unbiasing method based on the score-based diffusion model, a deep generative learning method that excels in density estimation across complex data landscapes. We demonstrate that this unbiasing approach, tested on multiple TAMD simulations, significantly outperforms traditional unbiasing methods and can generate accurate unbiased conformational ensembles. With the proposed approach, TAMD can adopt CVs that focus on improving sampling efficiency and the proposed unbiasing method enables accurate evaluation of ensemble averages of important chemical features.

Dual-channel deep graph convolutional neural networks

The dual-channel graph convolutional neural networks based on hybrid features jointly model the different features of networks, so that the features can learn each other and improve the performance of various subsequent machine learning tasks. However, current dual-channel graph convolutional neural networks are limited by the number of convolution layers, which hinders the performance improvement of the models. Graph convolutional neural networks superimpose multi-layer graph convolution operations, which would occur in smoothing phenomena, resulting in performance decreasing as the increasing number of graph convolutional layers. Inspired by the success of residual connections on convolutional neural networks, this paper applies residual connections to dual-channel graph convolutional neural networks, and increases the depth of dual-channel graph convolutional neural networks. Thus, a dual-channel deep graph convolutional neural network (D2GCN) is proposed, which can effectively avoid over-smoothing and improve model performance. D2GCN is verified on CiteSeer, DBLP, and SDBLP datasets, the results show that D2GCN performs better than the comparison algorithms used in node classification tasks.

Multimodal Transformer for Property Prediction in Polymers

In this work, we designed a multimodal transformer that combines both the Simplified Molecular Input Line Entry System (SMILES) and molecular graph representations to enhance the prediction of polymer properties. Three models with different embeddings (SMILES, SMILES + monomer, and SMILES + dimer) were employed to assess the performance of incorporating multimodal features into transformer architectures. Fine-tuning results across five properties (i.e., density, glass-transition temperature (Tg), melting temperature (Tm), volume resistivity, and conductivity) demonstrated that the multimodal transformer with both the SMILES and the dimer configuration as inputs outperformed the transformer using only SMILES across all five properties. Furthermore, our model facilitates in-depth analysis by examining attention scores, providing deeper insights into the relationship between the deep learning model and the polymer attributes. We believe that our work, shedding light on the potential of multimodal transformers in predicting polymer properties, paves a new direction for understanding and refining polymer properties.

Online Multi-Agent Forecasting With Interpretable Collaborative Graph Neural Networks

This article considers predicting future statuses of multiple agents in an online fashion by exploiting dynamic interactions in the system. We propose a novel collaborative prediction unit (CoPU), which aggregates the predictions from multiple collaborative predictors according to a collaborative graph. Each collaborative predictor is trained to predict the agent status by integrating the impact of another agent. The edge weights of the collaborative graph reflect the importance of each predictor. The collaborative graph is adjusted online by multiplicative update, which can be motivated by minimizing an explicit objective. With this objective, we also conduct regret analysis to indicate that, along with training, our CoPU achieves similar performance with the best individual collaborative predictor in hindsight. This theoretical interpretability distinguishes our method from many other graph networks. To progressively refine predictions, multiple CoPUs are stacked to form a collaborative graph neural network. Extensive experiments are conducted on three tasks: online simulated trajectory prediction, online human motion prediction, and online traffic speed prediction, and our methods outperform state-of-the-art works on the three tasks by 28.6%, 17.4%, and 21.0% on average, respectively; in addition, the proposed CoGNNs have lower average time costs in one online training/testing iteration than most previous methods.

A Meta-Learning Approach for Training Explainable Graph Neural Networks

In this article, we investigate the degree of explainability of graph neural networks (GNNs). The existing explainers work by finding global/local subgraphs to explain a prediction, but they are applied after a GNN has already been trained. Here, we propose a meta-explainer for improving the level of explainability of a GNN directly at training time, by steering the optimization procedure toward minima that allow post hoc explainers to achieve better results, without sacrificing the overall accuracy of GNN. Our framework (called MATE, MetA-Train to Explain) jointly trains a model to solve the original task, e.g., node classification, and to provide easily processable outputs for downstream algorithms that explain the model's decisions in a human-friendly way. In particular, we meta-train the model's parameters to quickly minimize the error of an instance-level GNNExplainer trained on-the-fly on randomly sampled nodes. The final internal representation relies on a set of features that can be "better" understood by an explanation algorithm, e.g., another instance of GNNExplainer. Our model-agnostic approach can improve the explanations produced for different GNN architectures and use any instance-based explainer to drive this process. Experiments on synthetic and real-world datasets for node and graph classification show that we can produce models that are consistently easier to explain by different algorithms. Furthermore, this increase in explainability comes at no cost to the accuracy of the model.

A Laplacian regularized graph neural network for predictive modeling of multiple chronic conditions

BACKGROUND AND GOALS

One of the biggest difficulties facing healthcare systems today is the prevalence of multiple chronic diseases (MCC). Mortality and the development of new chronic illnesses are more likely in those with MCC. Pre-existing diseases and risk factors specific to the patient have an impact on the complex stochastic process that guides the evolution of MCC. This study's goal is to use a brand-new Graph Neural Network (GNN) model to examine the connections between specific chronic illnesses, patient-level risk factors, and pre-existing conditions.

METHODS

We propose a graph neural network model to analyze the relationship between five chronic conditions (diabetes, obesity, cognitive impairment, hyperlipidemia, and hypertension). The proposed model adds a graph Laplacian regularization term to the loss function, which aims to improve the parameter learning process and accuracy of the GNN based on the graph structure. For validation, we used historical data from the Cameron County Hispanic Cohort (CCHC).

RESULTS

Evaluating the Laplacian regularized GNN on data from 600 patients, we expanded our analysis from two chronic conditions to five chronic conditions. The proposed model consistently surpassed a baseline GNN model, achieving an average accuracy of ≥89% across all combinations. In contrast, the performance of the standard model declined more markedly with the addition of more chronic conditions. The Laplacian regularization provided consistent predictions for adjacent nodes, beneficial in cases with shared attributes among nodes.

CONCLUSIONS

The incorporation of Laplacian regularization in our GNN model is essential, resulting in enhanced node categorization and better predictive performance by harnessing the graph structure. This study underscores the significance of considering graph structure when designing neural networks for graph data. Future research might further explore and refine this regularization method for various tasks using graph-structured data.

Graph Neural Networks for Graph Drawing

Graph drawing techniques have been developed in the last few years with the purpose of producing esthetically pleasing node-link layouts. Recently, the employment of differentiable loss functions has paved the road to the massive usage of gradient descent and related optimization algorithms. In this article, we propose a novel framework for the development of Graph Neural Drawers (GNDs), machines that rely on neural computation for constructing efficient and complex maps. GND is Graph Neural Networks (GNNs) whose learning process can be driven by any provided loss function, such as the ones commonly employed in Graph Drawing. Moreover, we prove that this mechanism can be guided by loss functions computed by means of feedforward neural networks, on the basis of supervision hints that express beauty properties, like the minimization of crossing edges. In this context, we show that GNNs can nicely be enriched by positional features to deal also with unlabeled vertexes. We provide a proof-of-concept by constructing a loss function for the edge crossing and provide quantitative and qualitative comparisons among different GNN models working under the proposed framework.

Two-Level Graph Neural Network

Graph neural networks (GNNs) are recently proposed neural network structures for the processing of graph-structured data. Due to their employed neighbor aggregation strategy, existing GNNs focus on capturing node-level information and neglect high-level information. Existing GNNs, therefore, suffer from representational limitations caused by the local permutation invariance (LPI) problem. To overcome these limitations and enrich the features captured by GNNs, we propose a novel GNN framework, referred to as the two-level GNN (TL-GNN). This merges subgraph-level information with node-level information. Moreover, we provide a mathematical analysis of the LPI problem, which demonstrates that subgraph-level information is beneficial to overcoming the problems associated with LPI. A subgraph counting method based on the dynamic programming algorithm is also proposed, and this has the time complexity of O(n3) , where n is the number of nodes of a graph. Experiments show that TL-GNN outperforms existing GNNs and achieves state-of-the-art performance.

GNDAN: Graph Navigated Dual Attention Network for Zero-Shot Learning

Zero-shot learning (ZSL) tackles the unseen class recognition problem by transferring semantic knowledge from seen classes to unseen ones. Typically, to guarantee desirable knowledge transfer, a direct embedding is adopted for associating the visual and semantic domains in ZSL. However, most existing ZSL methods focus on learning the embedding from implicit global features or image regions to the semantic space. Thus, they fail to: 1) exploit the appearance relationship priors between various local regions in a single image, which corresponds to the semantic information and 2) learn cooperative global and local features jointly for discriminative feature representations. In this article, we propose the novel graph navigated dual attention network (GNDAN) for ZSL to address these drawbacks. GNDAN employs a region-guided attention network (RAN) and a region-guided graph attention network (RGAT) to jointly learn a discriminative local embedding and incorporate global context for exploiting explicit global embeddings under the guidance of a graph. Specifically, RAN uses soft spatial attention to discover discriminative regions for generating local embeddings. Meanwhile, RGAT employs an attribute-based attention to obtain attribute-based region features, where each attribute focuses on the most relevant image regions. Motivated by the graph neural network (GNN), which is beneficial for structural relationship representations, RGAT further leverages a graph attention network to exploit the relationships between the attribute-based region features for explicit global embedding representations. Based on the self-calibration mechanism, the joint visual embedding learned is matched with the semantic embedding to form the final prediction. Extensive experiments on three benchmark datasets demonstrate that the proposed GNDAN achieves superior performances to the state-of-the-art methods. Our code and trained models are available at https://github.com/shiming-chen/GNDAN.

Empowering Simple Graph Convolutional Networks

Many neural networks for graphs are based on the graph convolution (GC) operator, proposed more than a decade ago. Since then, many alternative definitions have been proposed, which tend to add complexity (and nonlinearity) to the model. Recently, however, a simplified GC operator, dubbed simple graph convolution (SGC), which aims to remove nonlinearities was proposed. Motivated by the good results reached by this simpler model, in this article we propose, analyze, and compare simple graph convolution operators of increasing complexity that rely on linear transformations or controlled nonlinearities, and that can be implemented in single-layer graph convolutional networks (GCNs). Their computational expressiveness is characterized as well. We show that the predictive performance of the proposed GC operators is competitive with the ones of other widely adopted models on the considered node classification benchmark datasets.

Graph-Based Contrastive Learning for Description and Detection of Local Features

Confronted with the task environment full of repetitive textures, the state-of-art description and detection methods for local features greatly suffer from the "pseudo-negatives," bringing inconsistent optimization objectives during training. To address this problem, this article develops a self-supervised graph-based contrastive learning framework to train the model for local features, GCLFeat. The proposed approach learns to alleviate the pseudo-negatives specifically from three aspects: 1) designing a graph neural network (GNN), which focuses on mining the local transformational invariance across different views and global textual knowledge within individual images; 2) generating the dense correspondence annotations from a diverse natural dataset with a self-supervised paradigm; and 3) adopting a keypoints-aware sampling strategy to compute the loss across the whole dataset. The experimental results show that the unsupervised framework outperforms the state-of-the-art supervised baselines on diverse downstream benchmarks including image matching, 3-D reconstruction and visual localization. The code will be made public and available at https://github.com/RealZihaoWang/GCLFeat.

Debiased Graph Neural Networks With Agnostic Label Selection Bias

Most existing graph neural networks (GNNs) are proposed without considering the selection bias in data, i.e., the inconsistent distribution between the training set with the test set. In reality, the test data are not even available during the training process, making selection bias agnostic. Training GNNs with biased selected nodes leads to significant parameter estimation bias and greatly impacts the generalization ability on test nodes. In this article, we first present an experimental investigation, which clearly shows that the selection bias drastically hinders the generalization ability of GNNs, and theoretically proves that the selection bias will cause the biased estimation on GNN parameters. Then to remove the bias in GNN estimation, we propose a novel debiased GNNs (DGNN) with a differentiated decorrelation regularizer. The differentiated decorrelation regularizer estimates a sample weight for each labeled node such that the spurious correlation of learned embeddings could be eliminated. We analyze the regularizer in causal view and it motivates us to differentiate the weights of the variables based on their contribution to the confounding bias. Then, these sample weights are used for reweighting GNNs to eliminate the estimation bias, and thus, help to improve the stability of prediction on unknown test nodes. Comprehensive experiments are conducted on several challenging graph datasets with two kinds of label selection biases. The results well verify that our proposed model outperforms the state-of-the-art methods and DGNN is a flexible framework to enhance existing GNNs.

DyGCN: Efficient Dynamic Graph Embedding With Graph Convolutional Network

Graph embedding, aiming to learn low-dimensional representations (aka. embeddings) of nodes in graphs, has received significant attention. In recent years, there has been a surge of efforts, among which graph convolutional networks (GCNs) have emerged as an effective class of models. However, these methods mainly focus on the static graph embedding. In the present work, an efficient dynamic graph embedding approach is proposed, called dynamic GCN (DyGCN), which is an extension of the GCN-based methods. The embedding propagation scheme of GCN is naturally generalized to a dynamic setting in an efficient manner, which propagates the change in topological structure and neighborhood embeddings along the graph to update the node embeddings. The most affected nodes are updated first, and then their changes are propagated to further nodes, which in turn are updated. Extensive experiments on various dynamic graphs showed that the proposed model can update the node embeddings in a time-saving and performance-preserving way.

Flexible Bayesian inference on partially observed epidemics

Individual-based models of contagious processes are useful for predicting epidemic trajectories and informing intervention strategies. In such models, the incorporation of contact network information can capture the non-randomness and heterogeneity of realistic contact dynamics. In this article, we consider Bayesian inference on the spreading parameters of an SIR contagion on a known, static network, where information regarding individual disease status is known only from a series of tests (positive or negative disease status). When the contagion model is complex or information such as infection and removal times is missing, the posterior distribution can be difficult to sample from. Previous work has considered the use of Approximate Bayesian Computation (ABC), which allows for simulation-based Bayesian inference on complex models. However, ABC methods usually require the user to select reasonable summary statistics. Here, we consider an inference scheme based on the Mixture Density Network compressed ABC, which minimizes the expected posterior entropy in order to learn informative summary statistics. This allows us to conduct Bayesian inference on the parameters of a partially observed contagious process while also circumventing the need for manual summary statistic selection. This methodology can be extended to incorporate additional simulation complexities, including behavioural change after positive tests or false test results.

Structure-Aware Prototypical Neural Process for Few-Shot Graph Classification

Graph classification plays an important role in a wide range of applications from biological prediction to social analysis. Traditional graph classification models built on graph kernels are hampered by the challenge of poor generalization as they are heavily dependent on the dedicated design of handcrafted features. Recently, graph neural networks (GNNs) become a new class of tools for analyzing graph data and have achieved promising performance. However, it is necessary to collect a large number of labeled graph data for training an accurate GNN, which is often unaffordable in real-world applications. Therefore, it is an open question to build GNNs under the condition of few-shot learning where only a few labeled graphs are available. In this article, we introduce a new Structure-aware Prototypical Neural Process (SPNP for short) for a few-shot graph classification. Specifically, at the encoding stage, SPNP first employs GNNs to capture graph structure information. Then, SPNP incorporates such structural priors into the latent path and the deterministic path for representing stochastic processes. At the decoding stage, SPNP uses a new prototypical decoder to define a metric space where unseen graphs can be predicted effectively. The proposed decoder, which contains a self-attention mechanism to learn the intraclass dependence between graphs, can enhance the class-level representations, especially for new classes. Furthermore, benefited from such a flexible encoding-decoding architecture, SPNP can directly map the context samples to a predictive distribution without any complicated operations used in previous methods. Extensive experiments demonstrate that SPNP achieves consistent and significant improvements over state-of-the-art methods. Further discussions are provided toward model efficiency and more detailed analysis.

Fusing modalities by multiplexed graph neural networks for outcome prediction from medical data and beyond

With the emergence of multimodal electronic health records, the evidence for diseases, events, or findings may be present across multiple modalities ranging from clinical to imaging and genomic data. Developing effective patient-tailored therapeutic guidance and outcome prediction will require fusing evidence across these modalities. Developing general-purpose frameworks capable of modeling fine-grained and multi-faceted complex interactions, both within and across modalities is an important open problem in multimodal fusion. Generalized multimodal fusion is extremely challenging as evidence for outcomes may not be uniform across all modalities, not all modality features may be relevant, or not all modalities may be present for all patients, due to which simple methods of early, late, or intermediate fusion may be inadequate. In this paper, we present a novel approach that uses the machinery of multiplexed graphs for fusion. This allows for modalities to be represented through their targeted encodings. We model their relationship between explicitly via multiplexed graphs derived from salient features in a combined latent space. We then derive a new graph neural network for multiplex graphs for task-informed reasoning. We compare our framework against several state-of-the-art approaches for multi-graph reasoning and multimodal fusion. As a sanity check on the neural network design, we evaluate the multiplexed GNN on two popular benchmark datasets, namely the AIFB and the MUTAG dataset against several state-of-the-art multi-relational GNNs for reasoning. Second, we evaluate our multiplexed framework against several state-of-the-art multimodal fusion frameworks on two large clinical datasets for two separate applications. The first is the NIH-TB portals dataset for treatment outcome prediction in Tuberculosis, and the second is the ABIDE dataset for Autism Spectrum Disorder classification. Through rigorous experimental evaluation, we demonstrate that the multiplexed GNN provides robust performance improvements in all of these diverse applications.

A Novel Local-Global Graph Convolutional Method for Point Cloud Semantic Segmentation

Although convolutional neural networks (CNNs) have shown good performance on grid data, they are limited in the semantic segmentation of irregular point clouds. This article proposes a novel and effective graph CNN framework, referred to as the local-global graph convolutional method (LGGCM), which can achieve short- and long-range dependencies on point clouds. The key to this framework is the design of local spatial attention convolution (LSA-Conv). The design includes two parts: generating a weighted adjacency matrix of the local graph composed of neighborhood points, and updating and aggregating the features of nodes to obtain the spatial geometric features of the local point cloud. In addition, a smooth module for central points is incorporated into the process of LSA-Conv to enhance the robustness of the convolution against noise interference by adjusting the position coordinates of the points adaptively. The learned robust LSA-Conv features are then fed into a global spatial attention module with the gated unit to extract long-range contextual information and dynamically adjust the weights of features from different stages. The proposed framework, consisting of both encoding and decoding branches, is an end-to-end trainable network for semantic segmentation of 3-D point clouds. The theoretical analysis of the approximation capabilities of LSA-Conv is discussed to determine whether the features of the point cloud can be accurately represented. Experimental results on challenging benchmarks of the 3-D point cloud demonstrate that the proposed framework achieves excellent performance.

Unsupervised graph anomaly detection with discriminative embedding similarity for viscoelastic sandwich cylindrical structures

In the detection of slipping anomalies in viscoelastic sandwich cylindrical structures (VSCS), conventional methods may encounter challenges due to the extremely rare and weak nature of slipping signals. This study focuses on normal signals and introduces unsupervised graph representation learning (UGRL) with discriminative embedding similarity for VSCS's detection. UGRL involves data preprocessing, model embedding, and matrix reconstructing. Association graphs are constructed based on sample similarities for yielding adjacency and attribute matrices. Subsequently, the matrices undergo embedding and reconstruction via various network modules to enhance graph data characterization. Detection indicators are derived by calculating embedding similarities and reconstruction errors, and thresholds are constructed using these indicators to enable efficient anomaly detection. The experiments in VSCS slipping dataset effectively indicate the superiority of the proposed method.

Application of artificial intelligence and machine learning in drug repurposing

The purpose of drug repurposing is to leverage previously approved drugs for a particular disease indication and apply them to another disease. It can be seen as a faster and more cost-effective approach to drug discovery and a powerful tool for achieving precision medicine. In addition, drug repurposing can be used to identify therapeutic candidates for rare diseases and phenotypic conditions with limited information on disease biology. Machine learning and artificial intelligence (AI) methodologies have enabled the construction of effective, data-driven repurposing pipelines by integrating and analyzing large-scale biomedical data. Recent technological advances, especially in heterogeneous network mining and natural language processing, have opened up exciting new opportunities and analytical strategies for drug repurposing. In this review, we first introduce the challenges in repurposing approaches and highlight some success stories, including those during the COVID-19 pandemic. Next, we review some existing computational frameworks in the literature, organized on the basis of the type of biomedical input data analyzed and the computational algorithms involved. In conclusion, we outline some exciting new directions that drug repurposing research may take, as pioneered by the generative AI revolution.

GraphKM: machine and deep learning for KM prediction of wildtype and mutant enzymes

Michaelis constant (KM) is one of essential parameters for enzymes kinetics in the fields of protein engineering, enzyme engineering, and synthetic biology. As overwhelming experimental measurements of KM are difficult and time-consuming, prediction of the KM values from machine and deep learning models would increase the pace of the enzymes kinetics studies. Existing machine and deep learning models are limited to the specific enzymes, i.e., a minority of enzymes or wildtype enzymes. Here, we used a deep learning framework PaddlePaddle to implement a machine and deep learning approach (GraphKM) for KM prediction of wildtype and mutant enzymes. GraphKM is composed by graph neural networks (GNN), fully connected layers and gradient boosting framework. We represented the substrates through molecular graph and the enzymes through a pretrained transformer-based language model to construct the model inputs. We compared the difference of the model results made by the different GNN (GIN, GAT, GCN, and GAT-GCN). The GAT-GCN-based model generally outperformed. To evaluate the prediction performance of the GraphKM and other reported KM prediction models, we collected an independent KM dataset (HXKm) from literatures.

Vulnerability detection in Java source code using a quantum convolutional neural network with self-attentive pooling, deep sequence, and graph-based hybrid feature extraction

Software vulnerabilities pose a significant threat to system security, necessitating effective automatic detection methods. Current techniques face challenges such as dependency issues, language bias, and coarse detection granularity. This study presents a novel deep learning-based vulnerability detection system for Java code. Leveraging hybrid feature extraction through graph and sequence-based techniques enhances semantic and syntactic understanding. The system utilizes control flow graphs (CFG), abstract syntax trees (AST), program dependencies (PD), and greedy longest-match first vectorization for graph representation. A hybrid neural network (GCN-RFEMLP) and the pre-trained CodeBERT model extract features, feeding them into a quantum convolutional neural network with self-attentive pooling. The system addresses issues like long-term information dependency and coarse detection granularity, employing intermediate code representation and inter-procedural slice code. To mitigate language bias, a benchmark software assurance reference dataset is employed. Evaluations demonstrate the system's superiority, achieving 99.2% accuracy in detecting vulnerabilities, outperforming benchmark methods. The proposed approach comprehensively addresses vulnerabilities, including improper input validation, missing authorizations, buffer overflow, cross-site scripting, and SQL injection attacks listed by common weakness enumeration (CWE).