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Papers by Moctard Oloulade

Graph neural architecture search has received a lot of attention as Graph Neural Networks (GNNs) ... more Graph neural architecture search has received a lot of attention as Graph Neural Networks (GNNs) has been successfully applied on the non-Euclidean data recently. However, exploring all possible GNNs architectures in the huge search space is too time-consuming or impossible for big graph data. In this paper, we propose a parallel graph architecture search (ℎ) framework for graph neural networks. In ℎ , we explore the search space in parallel by designing a sharing-based evolution learning, which can improve the search efficiency without losing the accuracy. Additionally, architecture information entropy is adopted dynamically for mutation selection probability, which can reduce space exploration. The experimental result shows that ℎ outperforms state-of-art models with efficiency and accuracy simultaneously. CCS CONCEPTS • Computing methodologies → Search methodologies.

Bioinformatics

Motivation Understanding drug–response differences in cancer treatments is one of the most challe... more Motivation Understanding drug–response differences in cancer treatments is one of the most challenging aspects of personalized medicine. Recently, graph neural networks (GNNs) have become state-of-the-art methods in many graph representation learning scenarios in bioinformatics. However, building an optimal handcrafted GNN model for a particular drug sensitivity dataset requires manual design and fine-tuning of the hyperparameters for the GNN model, which is time-consuming and requires expert knowledge. Results In this work, we propose AutoCDRP, a novel framework for automated cancer drug–response predictor using GNNs. Our approach leverages surrogate modeling to efficiently search for the most effective GNN architecture. AutoCDRP uses a surrogate model to predict the performance of GNN architectures sampled from a search space, allowing it to select the optimal architecture based on evaluation performance. Hence, AutoCDRP can efficiently identify the optimal GNN architecture by exp...

Knowledge and Information Systems

IEEE Transactions on Emerging Topics in Computing

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Sensors

Pneumonia is one of the main causes of child mortality in the world and has been reported by the ... more Pneumonia is one of the main causes of child mortality in the world and has been reported by the World Health Organization (WHO) to be the cause of one-third of child deaths in India. Designing an automated classification system to detect pneumonia has become a worthwhile research topic. Numerous deep learning models have attempted to detect pneumonia by applying convolutional neural networks (CNNs) to X-ray radiographs, as they are essentially images and have achieved great performances. However, they failed to capture higher-order feature information of all objects based on the X-ray images because the topology of the X-ray images’ dimensions does not always come with some spatially regular locality properties, which makes defining a spatial kernel filter in X-ray images non-trivial. This paper proposes a principal neighborhood aggregation-based graph convolutional network (PNA-GCN) for pneumonia detection. In PNA-GCN, we propose a new graph-based feature construction utilizing th...

Tsinghua Science and Technology, 2022

In academia and industries, graph neural networks (GNNs) have emerged as a powerful approach to g... more In academia and industries, graph neural networks (GNNs) have emerged as a powerful approach to graph data processing ranging from node classification and link prediction tasks to graph clustering tasks. GNN models are usually handcrafted. However, building handcrafted GNN models is difficult and requires expert experience because GNN model components are complex and sensitive to variations. The complexity of GNN model components has brought significant challenges to the existing efficiencies of GNNs. Hence, many studies have focused on building automated machine learning frameworks to search for the best GNN models for targeted tasks. In this work, we provide a comprehensive review of automatic GNN model building frameworks to summarize the status of the field to facilitate future progress. We categorize the components of automatic GNN model building frameworks into three dimensions according to the challenges of building them. After reviewing the representative works for each dimension, we discuss promising future research directions in this rapidly growing field.

IEEE Transactions on Parallel and Distributed Systems, 2022

Proceedings of the 44th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2021

2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

Understanding the relationship between molecular structure and metabolic pathway classes is signi... more Understanding the relationship between molecular structure and metabolic pathway classes is significant for optimizing drug metabolization. In bioinformatics, graph neural networks (GNNs) can effectively capture structural and semantic features for molecular representation. Graph neural networks have become an essential method to encode molecular structures for multi-label prediction of metabolic pathways. However, building a GNN model for a given molecular structure dataset requires the manual design of GNN structure and fine-tuning of the hyperparameters for the GNN model, which is time-consuming and relies on expert experience. In this paper, we design an automatic end-to-end molecular structure representation learning framework named Auto-MSR that can design a GNN model for molecular structure encoding with little manual intervention. For a given compound molecule structure dataset, Auto-MSR first uses an efficient pa rallel GNN structure search algorithm to identify the optimal GNN structure from the GNN structure subspace. Then, it adopts a tree-structured parzen estimator approach to obtain the best hyperparameters of the GNN model in the hyperparameters subspace. We test AutoMSR on the dataset KEGG based on the multi-label metabolic pathway prediction task. The comparing results show that AutoMSR outperforms state-of-art manual graph neural networks on performance.