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1.
J Comput Chem ; 2024 Sep 02.
Article in English | MEDLINE | ID: mdl-39223071

ABSTRACT

Predicting protein-ligand binding affinity is a crucial and challenging task in structure-based drug discovery. With the accumulation of complex structures and binding affinity data, various machine-learning scoring functions, particularly those based on deep learning, have been developed for this task, exhibiting superiority over their traditional counterparts. A fusion model sequentially connecting a graph neural network (GNN) and a convolutional neural network (CNN) to predict protein-ligand binding affinity is proposed in this work. In this model, the intermediate outputs of the GNN layers, as supplementary descriptors of atomic chemical environments at different levels, are concatenated with the input features of CNN. The model demonstrates a noticeable improvement in performance on CASF-2016 benchmark compared to its constituent CNN models. The generalization ability of the model is evaluated by setting a series of thresholds for ligand extended-connectivity fingerprint similarity or protein sequence similarity between the training and test sets. Masking experiment reveals that model can capture key interaction regions. Furthermore, the fusion model is applied to a virtual screening task for a novel target, PI5P4Kα. The fusion strategy significantly improves the ability of the constituent CNN model to identify active compounds. This work offers a novel approach to enhancing the accuracy of deep learning models in predicting binding affinity through fusion strategies.

2.
Neural Netw ; 180: 106651, 2024 Aug 23.
Article in English | MEDLINE | ID: mdl-39217862

ABSTRACT

Graph neural networks (GNNs) have achieved state-of-the-art performance in graph representation learning. Message passing neural networks, which learn representations through recursively aggregating information from each node and its neighbors, are among the most commonly-used GNNs. However, a wealth of structural information of individual nodes and full graphs is often ignored in such process, which restricts the expressive power of GNNs. Various graph data augmentation methods that enable the message passing with richer structure knowledge have been introduced as one main way to tackle this issue, but they are often focused on individual structure features and difficult to scale up with more structure features. In this work we propose a novel approach, namely collective structure knowledge-augmented graph neural network (CoS-GNN), in which a new message passing method is introduced to allow GNNs to harness a diverse set of node- and graph-level structure features, together with original node features/attributes, in augmented graphs. In doing so, our approach largely improves the structural knowledge modeling of GNNs in both node and graph levels, resulting in substantially improved graph representations. This is justified by extensive empirical results where CoS-GNN outperforms state-of-the-art models in various graph-level learning tasks, including graph classification, anomaly detection, and out-of-distribution generalization.

3.
Molecules ; 29(15)2024 Jul 31.
Article in English | MEDLINE | ID: mdl-39125019

ABSTRACT

Identifying the catalytic regioselectivity of enzymes remains a challenge. Compared to experimental trial-and-error approaches, computational methods like molecular dynamics simulations provide valuable insights into enzyme characteristics. However, the massive data generated by these simulations hinder the extraction of knowledge about enzyme catalytic mechanisms without adequate modeling techniques. Here, we propose a computational framework utilizing graph-based active learning from molecular dynamics to identify the regioselectivity of ginsenoside hydrolases (GHs), which selectively catalyze C6 or C20 positions to obtain rare deglycosylated bioactive compounds from Panax plants. Experimental results reveal that the dynamic-aware graph model can excellently distinguish GH regioselectivity with accuracy as high as 96-98% even when different enzyme-substrate systems exhibit similar dynamic behaviors. The active learning strategy equips our model to work robustly while reducing the reliance on dynamic data, indicating its capacity to mine sufficient knowledge from short multi-replica simulations. Moreover, the model's interpretability identified crucial residues and features associated with regioselectivity. Our findings contribute to the understanding of GH catalytic mechanisms and provide direct assistance for rational design to improve regioselectivity. We presented a general computational framework for modeling enzyme catalytic specificity from simulation data, paving the way for further integration of experimental and computational approaches in enzyme optimization and design.


Subject(s)
Ginsenosides , Molecular Dynamics Simulation , Ginsenosides/chemistry , Ginsenosides/metabolism , Substrate Specificity , Hydrolases/chemistry , Hydrolases/metabolism , Panax/chemistry , Panax/enzymology
4.
Stud Health Technol Inform ; 316: 575-579, 2024 Aug 22.
Article in English | MEDLINE | ID: mdl-39176807

ABSTRACT

Developing novel predictive models with complex biomedical information is challenging due to various idiosyncrasies related to heterogeneity, standardization or sparseness of the data. We previously introduced a person-centric ontology to organize information about individual patients, and a representation learning framework to extract person-centric knowledge graphs (PKGs) and to train Graph Neural Networks (GNNs). In this paper, we propose a systematic approach to examine the results of GNN models trained with both structured and unstructured information from the MIMIC-III dataset. Through ablation studies on different clinical, demographic, and social data, we show the robustness of this approach in identifying predictive features in PKGs for the task of readmission prediction.


Subject(s)
Neural Networks, Computer , Humans , Patient Readmission
5.
Neural Netw ; 179: 106567, 2024 Jul 23.
Article in English | MEDLINE | ID: mdl-39089155

ABSTRACT

While Graph Neural Networks (GNNs) have demonstrated their effectiveness in processing non-Euclidean structured data, the neighborhood fetching of GNNs is time-consuming and computationally intensive, making them difficult to deploy in low-latency industrial applications. To address the issue, a feasible solution is graph knowledge distillation (KD), which can learn high-performance student Multi-layer Perceptrons (MLPs) to replace GNNs by mimicking the superior output of teacher GNNs. However, state-of-the-art graph knowledge distillation methods are mainly based on distilling deep features from intermediate hidden layers, this leads to the significance of logit layer distillation being greatly overlooked. To provide a novel viewpoint for studying logits-based KD methods, we introduce the idea of decoupling into graph knowledge distillation. Specifically, we first reformulate the classical graph knowledge distillation loss into two parts, i.e., the target class graph distillation (TCGD) loss and the non-target class graph distillation (NCGD) loss. Next, we decouple the negative correlation between GNN's prediction confidence and NCGD loss, as well as eliminate the fixed weight between TCGD and NCGD. We named this logits-based method Decoupled Graph Knowledge Distillation (DGKD). It can flexibly adjust the weights of TCGD and NCGD for different data samples, thereby improving the prediction accuracy of the student MLP. Extensive experiments conducted on public benchmark datasets show the effectiveness of our method. Additionally, DGKD can be incorporated into any existing graph knowledge distillation framework as a plug-and-play loss function, further improving distillation performance. The code is available at https://github.com/xsk160/DGKD.

6.
Brief Bioinform ; 25(5)2024 Jul 25.
Article in English | MEDLINE | ID: mdl-39175132

ABSTRACT

Numerous studies have demonstrated that microRNAs (miRNAs) are critically important for the prediction, diagnosis, and characterization of diseases. However, identifying miRNA-disease associations through traditional biological experiments is both costly and time-consuming. To further explore these associations, we proposed a model based on hybrid high-order moments combined with element-level attention mechanisms (HHOMR). This model innovatively fused hybrid higher-order statistical information along with structural and community information. Specifically, we first constructed a heterogeneous graph based on existing associations between miRNAs and diseases. HHOMR employs a structural fusion layer to capture structure-level embeddings and leverages a hybrid high-order moments encoder layer to enhance features. Element-level attention mechanisms are then used to adaptively integrate the features of these hybrid moments. Finally, a multi-layer perceptron is utilized to calculate the association scores between miRNAs and diseases. Through five-fold cross-validation on HMDD v2.0, we achieved a mean AUC of 93.28%. Compared with four state-of-the-art models, HHOMR exhibited superior performance. Additionally, case studies on three diseases-esophageal neoplasms, lymphoma, and prostate neoplasms-were conducted. Among the top 50 miRNAs with high disease association scores, 46, 47, and 45 associated with these diseases were confirmed by the dbDEMC and miR2Disease databases, respectively. Our results demonstrate that HHOMR not only outperforms existing models but also shows significant potential in predicting miRNA-disease associations.


Subject(s)
MicroRNAs , MicroRNAs/genetics , Humans , Computational Biology/methods , Genetic Predisposition to Disease , Algorithms , Prostatic Neoplasms/genetics , Models, Genetic
7.
Neural Netw ; 180: 106635, 2024 Aug 14.
Article in English | MEDLINE | ID: mdl-39173205

ABSTRACT

Graph neural networks (GNNs) have become a popular approach for semi-supervised graph representation learning. GNNs research has generally focused on improving methodological details, whereas less attention has been paid to exploring the importance of labeling the data. However, for semi-supervised learning, the quality of training data is vital. In this paper, we first introduce and elaborate on the problem of training data selection for GNNs. More specifically, focusing on node classification, we aim to select representative nodes from a graph used to train GNNs to achieve the best performance. To solve this problem, we are inspired by the popular lottery ticket hypothesis, typically used for sparse architectures, and we propose the following subset hypothesis for graph data: "There exists a core subset when selecting a fixed-size dataset from the dense training dataset, that can represent the properties of the dataset, and GNNs trained on this core subset can achieve a better graph representation". Equipped with this subset hypothesis, we present an efficient algorithm to identify the core data in the graph for GNNs. Extensive experiments demonstrate that the selected data (as a training set) can obtain performance improvements across various datasets and GNNs architectures.

8.
Mol Pharm ; 21(9): 4356-4371, 2024 Sep 02.
Article in English | MEDLINE | ID: mdl-39132855

ABSTRACT

We present a novel computational approach for predicting human pharmacokinetics (PK) that addresses the challenges of early stage drug design. Our study introduces and describes a large-scale data set of 11 clinical PK end points, encompassing over 2700 unique chemical structures to train machine learning models. To that end multiple advanced training strategies are compared, including the integration of in vitro data and a novel self-supervised pretraining task. In addition to the predictions, our final model provides meaningful epistemic uncertainties for every data point. This allows us to successfully identify regions of exceptional predictive performance, with an absolute average fold error (AAFE/geometric mean fold error) of less than 2.5 across multiple end points. Together, these advancements represent a significant leap toward actionable PK predictions, which can be utilized early on in the drug design process to expedite development and reduce reliance on nonclinical studies.


Subject(s)
Drug Design , Machine Learning , Humans , Pharmacokinetics , Pharmaceutical Preparations/chemistry
9.
Protein Sci ; 33(7): e5076, 2024 Jul.
Article in English | MEDLINE | ID: mdl-39196703

ABSTRACT

Antimicrobial resistance is a critical public health concern, necessitating the exploration of alternative treatments. While antimicrobial peptides (AMPs) show promise, assessing their toxicity using traditional wet lab methods is both time-consuming and costly. We introduce tAMPer, a novel multi-modal deep learning model designed to predict peptide toxicity by integrating the underlying amino acid sequence composition and the three-dimensional structure of peptides. tAMPer adopts a graph-based representation for peptides, encoding ColabFold-predicted structures, where nodes represent amino acids and edges represent spatial interactions. Structural features are extracted using graph neural networks, and recurrent neural networks capture sequential dependencies. tAMPer's performance was assessed on a publicly available protein toxicity benchmark and an AMP hemolysis data we generated. On the latter, tAMPer achieves an F1-score of 68.7%, outperforming the second-best method by 23.4%. On the protein benchmark, tAMPer exhibited an improvement of over 3.0% in the F1-score compared to current state-of-the-art methods. We anticipate tAMPer to accelerate AMP discovery and development by reducing the reliance on laborious toxicity screening experiments.


Subject(s)
Deep Learning , Antimicrobial Peptides/chemistry , Antimicrobial Peptides/pharmacology , Antimicrobial Peptides/toxicity , Neural Networks, Computer , Hemolysis/drug effects
10.
Front Artif Intell ; 7: 1408843, 2024.
Article in English | MEDLINE | ID: mdl-39118787

ABSTRACT

Cancer research encompasses data across various scales, modalities, and resolutions, from screening and diagnostic imaging to digitized histopathology slides to various types of molecular data and clinical records. The integration of these diverse data types for personalized cancer care and predictive modeling holds the promise of enhancing the accuracy and reliability of cancer screening, diagnosis, and treatment. Traditional analytical methods, which often focus on isolated or unimodal information, fall short of capturing the complex and heterogeneous nature of cancer data. The advent of deep neural networks has spurred the development of sophisticated multimodal data fusion techniques capable of extracting and synthesizing information from disparate sources. Among these, Graph Neural Networks (GNNs) and Transformers have emerged as powerful tools for multimodal learning, demonstrating significant success. This review presents the foundational principles of multimodal learning including oncology data modalities, taxonomy of multimodal learning, and fusion strategies. We delve into the recent advancements in GNNs and Transformers for the fusion of multimodal data in oncology, spotlighting key studies and their pivotal findings. We discuss the unique challenges of multimodal learning, such as data heterogeneity and integration complexities, alongside the opportunities it presents for a more nuanced and comprehensive understanding of cancer. Finally, we present some of the latest comprehensive multimodal pan-cancer data sources. By surveying the landscape of multimodal data integration in oncology, our goal is to underline the transformative potential of multimodal GNNs and Transformers. Through technological advancements and the methodological innovations presented in this review, we aim to chart a course for future research in this promising field. This review may be the first that highlights the current state of multimodal modeling applications in cancer using GNNs and transformers, presents comprehensive multimodal oncology data sources, and sets the stage for multimodal evolution, encouraging further exploration and development in personalized cancer care.

11.
Med Image Anal ; 97: 103286, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39111266

ABSTRACT

We present a novel graph-based approach for labeling the anatomical branches of a given airway tree segmentation. The proposed method formulates airway labeling as a branch classification problem in the airway tree graph, where branch features are extracted using convolutional neural networks and enriched using graph neural networks. Our graph neural network is structure-aware by having each node aggregate information from its local neighbors and position-aware by encoding node positions in the graph. We evaluated the proposed method on 220 airway trees from subjects with various severity stages of Chronic Obstructive Pulmonary Disease (COPD). The results demonstrate that our approach is computationally efficient and significantly improves branch classification performance than the baseline method. The overall average accuracy of our method reaches 91.18% for labeling 18 segmental airway branches, compared to 83.83% obtained by the standard CNN method and 87.37% obtained by the existing method. Furthermore, the reader study done on an additional set of 40 subjects shows that our algorithm performs comparably to human experts in labeling segmental-airways. We published our source code at https://github.com/DIAGNijmegen/spgnn. The proposed algorithm is also publicly available at https://grand-challenge.org/algorithms/airway-anatomical-labeling/.


Subject(s)
Algorithms , Neural Networks, Computer , Pulmonary Disease, Chronic Obstructive , Humans , Pulmonary Disease, Chronic Obstructive/diagnostic imaging , Tomography, X-Ray Computed/methods
12.
Sensors (Basel) ; 24(16)2024 Aug 08.
Article in English | MEDLINE | ID: mdl-39204839

ABSTRACT

Federated learning (FL) has emerged as a pivotal paradigm for training machine learning models across decentralized devices while maintaining data privacy. In the healthcare domain, FL enables collaborative training among diverse medical devices and institutions, enhancing model robustness and generalizability without compromising patient privacy. In this paper, we propose DPS-GAT, a novel approach integrating graph attention networks (GATs) with differentially private client selection and resource allocation strategies in FL. Our methodology addresses the challenges of data heterogeneity and limited communication resources inherent in medical applications. By employing graph neural networks (GNNs), we effectively capture the relational structures among clients, optimizing the selection process and ensuring efficient resource distribution. Differential privacy mechanisms are incorporated, to safeguard sensitive information throughout the training process. Our extensive experiments, based on the Regensburg pediatric appendicitis open dataset, demonstrated the superiority of our approach, in terms of model accuracy, privacy preservation, and resource efficiency, compared to traditional FL methods. The ability of DPS-GAT to maintain a high and stable number of client selections across various rounds and differential privacy budgets has significant practical implications, indicating that FL systems can achieve strong privacy guarantees without compromising client engagement and model performance. This balance is essential for real-world applications where both privacy and performance are paramount. This study suggests a promising direction for more secure and efficient FL medical applications, which could improve patient care through enhanced predictive models and collaborative data utilization.


Subject(s)
Machine Learning , Neural Networks, Computer , Humans , Resource Allocation , Privacy , Algorithms
13.
Sensors (Basel) ; 24(16)2024 Aug 22.
Article in English | MEDLINE | ID: mdl-39205126

ABSTRACT

Accurate recognition of tool state is important for maximizing tool life. However, the tool sensor data collected in real-life scenarios has unbalanced characteristics. Additionally, although graph neural networks (GNNs) show excellent performance in feature extraction in the spatial dimension of data, it is difficult to extract features in the temporal dimension efficiently. Therefore, we propose a tool state recognition method based on the Pruned Optimized Graph Neural Network-Gated Recurrent Unit (POGNN-GRU) under unbalanced data. Firstly, design the Improved-Majority Weighted Minority Oversampling Technique (IMWMOTE) by introducing an adaptive noise removal strategy and improving the MWMOTE to alleviate the unbalanced problem of data. Subsequently, propose a POG graph data construction method based on a multi-scale multi-metric basis and a Gaussian kernel weight function to solve the problem of one-sided description of graph data under a single metric basis. Then, construct the POGNN-GRU model to deeply mine the spatial and temporal features of the data to better identify the state of the tool. Finally, validation and ablation experiments on the PHM 2010 and HMoTP datasets show that the proposed method outperforms the other models in terms of identification, and the highest accuracy improves by 1.62% and 1.86% compared with the corresponding optimal baseline model.

14.
J Comput Biol ; 31(9): 871-885, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39117342

ABSTRACT

Recent technological advancements have enabled spatially resolved transcriptomic profiling but at a multicellular resolution that is more cost-effective. The task of cell type deconvolution has been introduced to disentangle discrete cell types from such multicellular spots. However, existing benchmark datasets for cell type deconvolution are either generated from simulation or limited in scale, predominantly encompassing data on mice and are not designed for human immuno-oncology. To overcome these limitations and promote comprehensive investigation of cell type deconvolution for human immuno-oncology, we introduce a large-scale spatial transcriptomic deconvolution benchmark dataset named SpatialCTD, encompassing 1.8 million cells and 12,900 pseudo spots from the human tumor microenvironment across the lung, kidney, and liver. In addition, SpatialCTD provides more realistic reference than those generated from single-cell RNA sequencing (scRNA-seq) data for most reference-based deconvolution methods. To utilize the location-aware SpatialCTD reference, we propose a graph neural network-based deconvolution method (i.e., GNNDeconvolver). Extensive experiments show that GNNDeconvolver often outperforms existing state-of-the-art methods by a substantial margin, without requiring scRNA-seq data. To enable comprehensive evaluations of spatial transcriptomics data from flexible protocols, we provide an online tool capable of converting spatial transcriptomic data from various platforms (e.g., 10× Visium, MERFISH, and sci-Space) into pseudo spots, featuring adjustable spot size. The SpatialCTD dataset and GNNDeconvolver implementation are available at https://github.com/OmicsML/SpatialCTD, and the online converter tool can be accessed at https://omicsml.github.io/SpatialCTD/.


Subject(s)
Transcriptome , Tumor Microenvironment , Tumor Microenvironment/genetics , Humans , Transcriptome/genetics , Gene Expression Profiling/methods , Computational Biology/methods , Single-Cell Analysis/methods , Mice , Animals , Neoplasms/genetics , Neoplasms/pathology , Algorithms , Software , Neural Networks, Computer
15.
Sci Bull (Beijing) ; 2024 Jul 15.
Article in English | MEDLINE | ID: mdl-39142945

ABSTRACT

We present a full space inverse materials design (FSIMD) approach that fully automates the materials design for target physical properties without the need to provide the atomic composition, chemical stoichiometry, and crystal structure in advance. Here, we used density functional theory reference data to train a universal machine learning potential (UPot) and transfer learning to train a universal bulk modulus model (UBmod). Both UPot and UBmod were able to cover materials systems composed of any element among 42 elements. Interfaced with optimization algorithm and enhanced sampling, the FSIMD approach is applied to find the materials with the largest cohesive energy and the largest bulk modulus, respectively. NaCl-type ZrC was found to be the material with the largest cohesive energy. For bulk modulus, diamond was identified to have the largest value. The FSIMD approach is also applied to design materials with other multi-objective properties with accuracy limited principally by the amount, reliability, and diversity of the training data. The FSIMD approach provides a new way for inverse materials design with other functional properties for practical applications.

16.
Front Neuroinform ; 18: 1392661, 2024.
Article in English | MEDLINE | ID: mdl-39006894

ABSTRACT

Decoding of cognitive states aims to identify individuals' brain states and brain fingerprints to predict behavior. Deep learning provides an important platform for analyzing brain signals at different developmental stages to understand brain dynamics. Due to their internal architecture and feature extraction techniques, existing machine-learning and deep-learning approaches are suffering from low classification performance and explainability issues that must be improved. In the current study, we hypothesized that even at the early childhood stage (as early as 3-years), connectivity between brain regions could decode brain states and predict behavioral performance in false-belief tasks. To this end, we proposed an explainable deep learning framework to decode brain states (Theory of Mind and Pain states) and predict individual performance on ToM-related false-belief tasks in a developmental dataset. We proposed an explainable spatiotemporal connectivity-based Graph Convolutional Neural Network (Ex-stGCNN) model for decoding brain states. Here, we consider a developmental dataset, N = 155 (122 children; 3-12 yrs and 33 adults; 18-39 yrs), in which participants watched a short, soundless animated movie, shown to activate Theory-of-Mind (ToM) and pain networs. After scanning, the participants underwent a ToM-related false-belief task, leading to categorization into the pass, fail, and inconsistent groups based on performance. We trained our proposed model using Functional Connectivity (FC) and Inter-Subject Functional Correlations (ISFC) matrices separately. We observed that the stimulus-driven feature set (ISFC) could capture ToM and Pain brain states more accurately with an average accuracy of 94%, whereas it achieved 85% accuracy using FC matrices. We also validated our results using five-fold cross-validation and achieved an average accuracy of 92%. Besides this study, we applied the SHapley Additive exPlanations (SHAP) approach to identify brain fingerprints that contributed the most to predictions. We hypothesized that ToM network brain connectivity could predict individual performance on false-belief tasks. We proposed an Explainable Convolutional Variational Auto-Encoder (Ex-Convolutional VAE) model to predict individual performance on false-belief tasks and trained the model using FC and ISFC matrices separately. ISFC matrices again outperformed the FC matrices in prediction of individual performance. We achieved 93.5% accuracy with an F1-score of 0.94 using ISFC matrices and achieved 90% accuracy with an F1-score of 0.91 using FC matrices.

17.
Brief Bioinform ; 25(4)2024 May 23.
Article in English | MEDLINE | ID: mdl-39007599

ABSTRACT

The interaction between T-cell receptors (TCRs) and peptides (epitopes) presented by major histocompatibility complex molecules (MHC) is fundamental to the immune response. Accurate prediction of TCR-epitope interactions is crucial for advancing the understanding of various diseases and their prevention and treatment. Existing methods primarily rely on sequence-based approaches, overlooking the inherent topology structure of TCR-epitope interaction networks. In this study, we present $GTE$, a novel heterogeneous Graph neural network model based on inductive learning to capture the topological structure between TCRs and Epitopes. Furthermore, we address the challenge of constructing negative samples within the graph by proposing a dynamic edge update strategy, enhancing model learning with the nonbinding TCR-epitope pairs. Additionally, to overcome data imbalance, we adapt the Deep AUC Maximization strategy to the graph domain. Extensive experiments are conducted on four public datasets to demonstrate the superiority of exploring underlying topological structures in predicting TCR-epitope interactions, illustrating the benefits of delving into complex molecular networks. The implementation code and data are available at https://github.com/uta-smile/GTE.


Subject(s)
Receptors, Antigen, T-Cell , Receptors, Antigen, T-Cell/chemistry , Receptors, Antigen, T-Cell/immunology , Receptors, Antigen, T-Cell/metabolism , Humans , Epitopes, T-Lymphocyte/immunology , Epitopes, T-Lymphocyte/chemistry , Neural Networks, Computer , Computational Biology/methods , Protein Binding , Epitopes/chemistry , Epitopes/immunology , Algorithms , Software
18.
Front Big Data ; 7: 1410424, 2024.
Article in English | MEDLINE | ID: mdl-39011466

ABSTRACT

With the increasing popularity of Graph Neural Networks (GNNs) for predictive tasks on graph structured data, research on their explainability is becoming more critical and achieving significant progress. Although many methods are proposed to explain the predictions of GNNs, their focus is mainly on "how to generate explanations." However, other important research questions like "whether the GNN explanations are inaccurate," "what if the explanations are inaccurate," and "how to adjust the model to generate more accurate explanations" have gained little attention. Our previous GNN Explanation Supervision (GNES) framework demonstrated effectiveness on improving the reasonability of the local explanation while still keep or even improve the backbone GNNs model performance. In many applications instead of per sample explanations, we need to find global explanations which are reasonable and faithful to the domain data. Simply learning to explain GNNs locally is not an optimal solution to a global understanding of the model. To improve the explainability power of the GNES framework, we propose the Global GNN Explanation Supervision (GGNES) technique which uses a basic trained GNN and a global extension of the loss function used in the GNES framework. This GNN creates local explanations which are fed to a Global Logic-based GNN Explainer, an existing technique that can learn the global Explanation in terms of a logic formula. These two frameworks are then trained iteratively to generate reasonable global explanations. Extensive experiments demonstrate the effectiveness of the proposed model on improving the global explanations while keeping the performance similar or even increase the model prediction power.

19.
Article in English | MEDLINE | ID: mdl-38985412

ABSTRACT

PURPOSE: Decision support systems and context-aware assistance in the operating room have emerged as the key clinical applications supporting surgeons in their daily work and are generally based on single modalities. The model- and knowledge-based integration of multimodal data as a basis for decision support systems that can dynamically adapt to the surgical workflow has not yet been established. Therefore, we propose a knowledge-enhanced method for fusing multimodal data for anticipation tasks. METHODS: We developed a holistic, multimodal graph-based approach combining imaging and non-imaging information in a knowledge graph representing the intraoperative scene of a surgery. Node and edge features of the knowledge graph are extracted from suitable data sources in the operating room using machine learning. A spatiotemporal graph neural network architecture subsequently allows for interpretation of relational and temporal patterns within the knowledge graph. We apply our approach to the downstream task of instrument anticipation while presenting a suitable modeling and evaluation strategy for this task. RESULTS: Our approach achieves an F1 score of 66.86% in terms of instrument anticipation, allowing for a seamless surgical workflow and adding a valuable impact for surgical decision support systems. A resting recall of 63.33% indicates the non-prematurity of the anticipations. CONCLUSION: This work shows how multimodal data can be combined with the topological properties of an operating room in a graph-based approach. Our multimodal graph architecture serves as a basis for context-sensitive decision support systems in laparoscopic surgery considering a comprehensive intraoperative operating scene.

20.
Sensors (Basel) ; 24(13)2024 Jul 04.
Article in English | MEDLINE | ID: mdl-39001135

ABSTRACT

Mechanical equipment is composed of several parts, and the interaction between parts exists throughout the whole life cycle, leading to the widespread phenomenon of fault coupling. The diagnosis of independent faults cannot meet the requirements of the health management of mechanical equipment under actual working conditions. In this paper, the dynamic vertex interpretable graph neural network (DIGNN) is proposed to solve the problem of coupling fault diagnosis, in which dynamic vertices are defined in the data topology. First, in the date preprocessing phase, wavelet transform is utilized to make input features interpretable and reduce the uncertainty of model training. In the fault topology, edge connections are made between nodes according to the fault coupling information, and edge connections are established between dynamic nodes and all other nodes. Second the data topology with dynamic vertices is used in the training phase and in the testing phase, the time series data are only fed into dynamic vertices for classification and analysis, which makes it possible to realize coupling fault diagnosis in an industrial production environment. The features extracted in different layers of DIGNN interpret how the model works. The method proposed in this paper can realize the accurate diagnosis of independent faults in the dataset with an accuracy of 100%, and can effectively judge the coupling mode of coupling faults with a comprehensive accuracy of 88.3%.

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