Graph Networks for Molecular Design

Deep learning methods applied to chemistry can be used to accelerate the discovery of new molecules. This work introduces GraphINVENT, a platform developed for graph-based molecular design using graph neural networks (GNNs). GraphINVENT uses a tiered deep neural network architecture to probabilistically generate new molecules a single bond at a time. All models implemented in GraphINVENT can quickly learn to build molecules resembling the training set molecules without any explicit programming of chemical rules. The models have been benchmarked using the MOSES distribution-based metrics, showing how GraphINVENT models compare well with state-of-the-art generative models. This work is one of the first thorough graph-based molecular design studies, and illustrates how GNN-based models are promising tools for molecular discovery.

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Deep Neural Network Architecture Search for Wearable Heart Rate Estimations

Studies in Health Technology and Informatics - Public Health and Informatics ◽

10.3233/shti210366 ◽

2021 ◽

Author(s):

Daniel Ray ◽

Tim Collins ◽

Prasad Ponnapalli

Keyword(s):

Neural Network ◽

Heart Rate ◽

Deep Learning ◽

Network Architecture ◽

Deep Neural Network ◽

State Of The Art ◽

Data Driven ◽

Network Architectures ◽

Learning Approaches ◽

Neural Network Architecture

Extracting accurate heart rate estimations from wrist-worn photoplethysmography (PPG) devices is challenging due to the signal containing artifacts from several sources. Deep Learning approaches have shown very promising results outperforming classical methods with improvements of 21% and 31% on two state-of-the-art datasets. This paper provides an analysis of several data-driven methods for creating deep neural network architectures with hopes of further improvements.

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Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks

10.26434/chemrxiv.8427776.v1 ◽

2019 ◽

Author(s):

Shuangjia Zheng ◽

Jiahua Rao ◽

Zhongyue Zhang ◽

Jun Xu ◽

Yuedong Yang

Keyword(s):

Neural Network ◽

Network Architecture ◽

State Of The Art ◽

Neural Network Architecture ◽

Training Set ◽

Computer Aided ◽

Synthesis Planning ◽

Target Molecules ◽

Template Free ◽

Synthetic Routes

<a>Synthesis planning is the process of recursively decomposing target molecules into available precursors. Computer-aided retrosynthesis can potentially assist chemists in designing synthetic routes, but at present it is cumbersome and provides results of dissatisfactory quality. In this study, we develop a template-free self-corrected retrosynthesis predictor (SCROP) to perform a retrosynthesis prediction task trained by using the Transformer neural network architecture. In the method, the retrosynthesis planning is converted as a machine translation problem between molecular linear notations of reactants and the products. Coupled with a neural network-based syntax corrector, our method achieves an accuracy of 59.0% on a standard benchmark dataset, which increases >21% over other deep learning methods, and >6% over template-based methods. More importantly, our method shows an accuracy 1.7 times higher than other state-of-the-art methods for compounds not appearing in the training set.</a>

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Predicting Retrosynthetic Reaction using Self-Corrected Transformer Neural Networks

10.26434/chemrxiv.8427776 ◽

2019 ◽

Author(s):

Shuangjia Zheng ◽

Jiahua Rao ◽

Zhongyue Zhang ◽

Jun Xu ◽

Yuedong Yang

Keyword(s):

Neural Network ◽

Network Architecture ◽

State Of The Art ◽

Neural Network Architecture ◽

Training Set ◽

Computer Aided ◽

Synthesis Planning ◽

Target Molecules ◽

Template Free ◽

Synthetic Routes

<a>Synthesis planning is the process of recursively decomposing target molecules into available precursors. Computer-aided retrosynthesis can potentially assist chemists in designing synthetic routes, but at present it is cumbersome and provides results of dissatisfactory quality. In this study, we develop a template-free self-corrected retrosynthesis predictor (SCROP) to perform a retrosynthesis prediction task trained by using the Transformer neural network architecture. In the method, the retrosynthesis planning is converted as a machine translation problem between molecular linear notations of reactants and the products. Coupled with a neural network-based syntax corrector, our method achieves an accuracy of 59.0% on a standard benchmark dataset, which increases >21% over other deep learning methods, and >6% over template-based methods. More importantly, our method shows an accuracy 1.7 times higher than other state-of-the-art methods for compounds not appearing in the training set.</a>

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SketchGNN: Semantic Sketch Segmentation with Graph Neural Networks

ACM Transactions on Graphics ◽

10.1145/3450284 ◽

2021 ◽

Vol 40 (3) ◽

pp. 1-13

Author(s):

Lumin Yang ◽

Jiajie Zhuang ◽

Hongbo Fu ◽

Xiangzhi Wei ◽

Kun Zhou ◽

...

Keyword(s):

Neural Network ◽

Neural Networks ◽

Network Architecture ◽

Large Scale ◽

State Of The Art ◽

Semantic Segmentation ◽

Structure Information ◽

Graph Neural Networks ◽

Node Labels ◽

Point Level

We introduce SketchGNN , a convolutional graph neural network for semantic segmentation and labeling of freehand vector sketches. We treat an input stroke-based sketch as a graph with nodes representing the sampled points along input strokes and edges encoding the stroke structure information. To predict the per-node labels, our SketchGNN uses graph convolution and a static-dynamic branching network architecture to extract the features at three levels, i.e., point-level, stroke-level, and sketch-level. SketchGNN significantly improves the accuracy of the state-of-the-art methods for semantic sketch segmentation (by 11.2% in the pixel-based metric and 18.2% in the component-based metric over a large-scale challenging SPG dataset) and has magnitudes fewer parameters than both image-based and sequence-based methods.

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Fighting Together against the Pandemic: Learning Multiple Models on Tomography Images for COVID-19 Diagnosis

AI ◽

10.3390/ai2020016 ◽

2021 ◽

Vol 2 (2) ◽

pp. 261-273

Author(s):

Mario Manzo ◽

Simone Pellino

Keyword(s):

Network Architecture ◽

State Of The Art ◽

Ensemble Classification ◽

Effective Vaccine ◽

Rt Pcr ◽

Neural Network Architecture ◽

Experimental Phase ◽

Different Types ◽

Polymerase Chain ◽

Better Than

COVID-19 has been a great challenge for humanity since the year 2020. The whole world has made a huge effort to find an effective vaccine in order to save those not yet infected. The alternative solution is early diagnosis, carried out through real-time polymerase chain reaction (RT-PCR) tests or thorax Computer Tomography (CT) scan images. Deep learning algorithms, specifically convolutional neural networks, represent a methodology for image analysis. They optimize the classification design task, which is essential for an automatic approach with different types of images, including medical. In this paper, we adopt a pretrained deep convolutional neural network architecture in order to diagnose COVID-19 disease from CT images. Our idea is inspired by what the whole of humanity is achieving, as the set of multiple contributions is better than any single one for the fight against the pandemic. First, we adapt, and subsequently retrain for our assumption, some neural architectures that have been adopted in other application domains. Secondly, we combine the knowledge extracted from images by the neural architectures in an ensemble classification context. Our experimental phase is performed on a CT image dataset, and the results obtained show the effectiveness of the proposed approach with respect to the state-of-the-art competitors.

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Hybrid Graph Neural Networks for Crowd Counting

Proceedings of the AAAI Conference on Artificial Intelligence ◽

10.1609/aaai.v34i07.6839 ◽

2020 ◽

Vol 34 (07) ◽

pp. 11693-11700 ◽

Cited By ~ 2

Author(s):

Ao Luo ◽

Fan Yang ◽

Xin Li ◽

Dong Nie ◽

Zhicheng Jiao ◽

...

Keyword(s):

Network Architecture ◽

Message Passing ◽

Large Scale ◽

State Of The Art ◽

Density Variation ◽

Feature Maps ◽

Crowd Counting ◽

Multi Scale ◽

Crowd Density ◽

Graph Neural Networks

Crowd counting is an important yet challenging task due to the large scale and density variation. Recent investigations have shown that distilling rich relations among multi-scale features and exploiting useful information from the auxiliary task, i.e., localization, are vital for this task. Nevertheless, how to comprehensively leverage these relations within a unified network architecture is still a challenging problem. In this paper, we present a novel network structure called Hybrid Graph Neural Network (HyGnn) which targets to relieve the problem by interweaving the multi-scale features for crowd density as well as its auxiliary task (localization) together and performing joint reasoning over a graph. Specifically, HyGnn integrates a hybrid graph to jointly represent the task-specific feature maps of different scales as nodes, and two types of relations as edges: (i) multi-scale relations capturing the feature dependencies across scales and (ii) mutual beneficial relations building bridges for the cooperation between counting and localization. Thus, through message passing, HyGnn can capture and distill richer relations between nodes to obtain more powerful representations, providing robust and accurate results. Our HyGnn performs significantly well on four challenging datasets: ShanghaiTech Part A, ShanghaiTech Part B, UCF_CC_50 and UCF_QNRF, outperforming the state-of-the-art algorithms by a large margin.

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