Integrating Deep Neural Networks and Symbolic Inference for Organic Reactivity Prediction

2020 ◽  
Author(s):  
Wesley Wei Qian ◽  
Nathan T. Russell ◽  
Claire L. W. Simons ◽  
Yunan Luo ◽  
Martin D. Burke ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Probability Distribution ◽  
Deep Neural Networks ◽  
Machine Intelligence ◽  
Data Availability ◽  
Learning Models ◽  
Expert Performance ◽  
Covalent Bonds ◽  
Chemical Reasoning

<div>Accurate <i>in silico</i> models for the prediction of novel chemical reaction outcomes can be used to guide the rapid discovery of new reactivity and enable novel synthesis strategies for newly discovered lead compounds. Recent advances in machine learning, driven by deep learning models and data availability, have shown utility throughout synthetic organic chemistry as a data-driven method for reaction prediction. Here we present a machine-intelligence approach to predict the products of an organic reaction by integrating deep neural networks with a probabilistic and symbolic inference that flexibly enforces chemical constraints and accounts for prior chemical knowledge. We first train a graph convolutional neural network to estimate the likelihood of changes in covalent bonds, hydrogen counts, and formal charges. These estimated likelihoods govern a probability distribution over potential products. Integer Linear Programming is then used to infer the most probable products from the probability distribution subject to heuristic rules such as the octet rule and chemical constraints that reflect a user's prior knowledge. Our approach outperforms previous graph-based neural networks by predicting products with more than 90% accuracy, demonstrates intuitive chemical reasoning through a learned attention mechanism, and provides generalizability across various reaction types. Furthermore, we demonstrate the potential for even higher model accuracy when complemented by expert chemists contributing to the system, boosting both machine and expert performance. The results show the advantages of empowering deep learning models with chemical intuition and knowledge to expedite the drug discovery process.</div>

scholarly journals Integrating Deep Neural Networks and Symbolic Inference for Organic Reactivity Prediction

2020 ◽  
Author(s):  
Wesley Wei Qian ◽  
Nathan T. Russell ◽  
Claire L. W. Simons ◽  
Yunan Luo ◽  
Martin D. Burke ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Probability Distribution ◽  
Deep Neural Networks ◽  
Machine Intelligence ◽  
Data Availability ◽  
Learning Models ◽  
Expert Performance ◽  
Covalent Bonds ◽  
Chemical Reasoning

<div>Accurate <i>in silico</i> models for the prediction of novel chemical reaction outcomes can be used to guide the rapid discovery of new reactivity and enable novel synthesis strategies for newly discovered lead compounds. Recent advances in machine learning, driven by deep learning models and data availability, have shown utility throughout synthetic organic chemistry as a data-driven method for reaction prediction. Here we present a machine-intelligence approach to predict the products of an organic reaction by integrating deep neural networks with a probabilistic and symbolic inference that flexibly enforces chemical constraints and accounts for prior chemical knowledge. We first train a graph convolutional neural network to estimate the likelihood of changes in covalent bonds, hydrogen counts, and formal charges. These estimated likelihoods govern a probability distribution over potential products. Integer Linear Programming is then used to infer the most probable products from the probability distribution subject to heuristic rules such as the octet rule and chemical constraints that reflect a user's prior knowledge. Our approach outperforms previous graph-based neural networks by predicting products with more than 90% accuracy, demonstrates intuitive chemical reasoning through a learned attention mechanism, and provides generalizability across various reaction types. Furthermore, we demonstrate the potential for even higher model accuracy when complemented by expert chemists contributing to the system, boosting both machine and expert performance. The results show the advantages of empowering deep learning models with chemical intuition and knowledge to expedite the drug discovery process.</div>

A Review of Recent Deep Learning Models in COVID-19 Diagnosis

2021 ◽  
Vol 6 (5) ◽  
pp. 10-15
Author(s):  
Ela Bhattacharya ◽  
D. Bhattacharya
Keyword(s):  
Artificial Intelligence ◽  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Test Results ◽  
Learning Models ◽  
Future Directions ◽  
Human Contact ◽  
The World ◽  
Short Span

COVID-19 has emerged as the latest worrisome pandemic, which is reported to have its outbreak in Wuhan, China. The infection spreads by means of human contact, as a result, it has caused massive infections across 200 countries around the world. Artificial intelligence has likewise contributed to managing the COVID-19 pandemic in various aspects within a short span of time. Deep Neural Networks that are explored in this paper have contributed to the detection of COVID-19 from imaging sources. The datasets, pre-processing, segmentation, feature extraction, classification and test results which can be useful for discovering future directions in the domain of automatic diagnosis of the disease, utilizing artificial intelligence-based frameworks, have been investigated in this paper.

Identification of Thoracic Diseases by Exploiting Deep Neural Networks (Preprint)

2020 ◽  
Author(s):  
Albahli Saleh ◽  
Ali Alkhalifah
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Convolutional Neural Network ◽  
Deep Neural Networks ◽  
Medical Image Analysis ◽  
Medical Community ◽  
Learning Models ◽  
X Ray ◽  
Chest Disease

BACKGROUND To diagnose cardiothoracic diseases, a chest x-ray (CXR) is examined by a radiologist. As more people get affected, doctors are becoming scarce especially in developing countries. However, with the advent of image processing tools, the task of diagnosing these cardiothoracic diseases has seen great progress. A lot of researchers have put in work to see how the problems associated with medical images can be mitigated by using neural networks. OBJECTIVE Previous works used state-of-the-art techniques and got effective results with one or two cardiothoracic diseases but could lead to misclassification. In our work, we adopted GANs to synthesize the chest radiograph (CXR) to augment the training set on multiple cardiothoracic diseases to efficiently diagnose the chest diseases in different classes as shown in Figure 1. In this regard, our major contributions are classifying various cardiothoracic diseases to detect a specific chest disease based on CXR, use the advantage of GANs to overcome the shortages of small training datasets, address the problem of imbalanced data; and implementing optimal deep neural network architecture with different hyper-parameters to improve the model with the best accuracy. METHODS For this research, we are not building a model from scratch due to computational restraints as they require very high-end computers. Rather, we use a Convolutional Neural Network (CNN) as a class of deep neural networks to propose a generative adversarial network (GAN) -based model to generate synthetic data for training the data as the amount of the data is limited. We will use pre-trained models which are models that were trained on a large benchmark dataset to solve a problem similar to the one we want to solve. For example, the ResNet-152 model we used was initially trained on the ImageNet dataset. RESULTS After successful training and validation of the models we developed, ResNet-152 with image augmentation proved to be the best model for the automatic detection of cardiothoracic disease. However, one of the main problems associated with radiographic deep learning projects and research is the scarcity and unavailability of enough datasets which is a key component of all deep learning models as they require a lot of data for training. This is the reason why some of our models had image augmentation to increase the number of images without duplication. As more data are collected in the field of chest radiology, the models could be retrained to improve the accuracies of the models as deep learning models improve with more data. CONCLUSIONS This research employs the advantages of computer vision and medical image analysis to develop an automated model that has the clinical potential for early detection of the disease. Using deep learning models, the research aims to evaluate the effectiveness and accuracy of different convolutional neural network models in the automatic diagnosis of cardiothoracic diseases from x-ray images compared to diagnosis by experts in the medical community.

Exemplar models are useful and deep neural networks overcome their limitations: A commentary on Ambridge (2020)

2020 ◽  
Vol 40 (5-6) ◽  
pp. 612-615
Author(s):  
James L. McClelland
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Language Processing ◽  
Deep Neural Networks ◽  
Machine Intelligence ◽  
Human Language ◽  
Language Usage ◽  
Primitive Elements ◽  
Exemplar Models ◽  
Learning Architectures

Humans are sensitive to the properties of individual items, and exemplar models are useful for capturing this sensitivity. I am a proponent of an extension of exemplar-based architectures that I briefly describe. However, exemplar models are very shallow architectures in which it is necessary to stipulate a set of primitive elements that make up each example, and such architectures have not been as successful as deep neural networks in capturing language usage and meaning. More work is needed bringing contemporary deep learning architectures used in machine intelligence to the effort to understand human language processing.

Network attributes describe a similarity between deep neural networks and large scale brain networks

2019 ◽  
Author(s):  
Kosuke Takagi
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Human Brain ◽  
Large Scale ◽  
Deep Neural Networks ◽  
Distribution Model ◽  
Common Mechanism ◽  
Learning Models ◽  
Connection Weight ◽  
Wide Range

Abstract Despite the recent success of deep learning models in solving various problems, their ability is still limited compared with human intelligence, which has the flexibility to adapt to a changing environment. To obtain a model which achieves adaptability to a wide range of problems and tasks is a challenging problem. To achieve this, an issue that must be addressed is identification of the similarities and differences between the human brain and deep neural networks. In this article, inspired by the human flexibility which might suggest the existence of a common mechanism allowing solution of different kinds of tasks, we consider a general learning process in neural networks, on which no specific conditions and constraints are imposed. Subsequently, we theoretically show that, according to the learning progress, the network structure converges to the state, which is characterized by a unique distribution model with respect to network quantities such as the connection weight and node strength. Noting that the empirical data indicate that this state emerges in the large scale network in the human brain, we show that the same state can be reproduced in a simple example of deep learning models. Although further research is needed, our findings provide an insight into the common inherent mechanism underlying the human brain and deep learning. Thus, our findings provide suggestions for designing efficient learning algorithms for solving a wide variety of tasks in the future.

scholarly journals Exploring deep neural networks via layer-peeled model: Minority collapse in imbalanced training

2021 ◽  
Vol 118 (43) ◽  
pp. e2103091118
Author(s):  
Cong Fang ◽  
Hangfeng He ◽  
Qi Long ◽  
Weijie J. Su
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Model Minority ◽  
Tight Frame ◽  
Learning Models ◽  
The Neural Network ◽  
Long Time ◽  
Topmost Layer

In this paper, we introduce the Layer-Peeled Model, a nonconvex, yet analytically tractable, optimization program, in a quest to better understand deep neural networks that are trained for a sufficiently long time. As the name suggests, this model is derived by isolating the topmost layer from the remainder of the neural network, followed by imposing certain constraints separately on the two parts of the network. We demonstrate that the Layer-Peeled Model, albeit simple, inherits many characteristics of well-trained neural networks, thereby offering an effective tool for explaining and predicting common empirical patterns of deep-learning training. First, when working on class-balanced datasets, we prove that any solution to this model forms a simplex equiangular tight frame, which, in part, explains the recently discovered phenomenon of neural collapse [V. Papyan, X. Y. Han, D. L. Donoho, Proc. Natl. Acad. Sci. U.S.A. 117, 24652–24663 (2020)]. More importantly, when moving to the imbalanced case, our analysis of the Layer-Peeled Model reveals a hitherto-unknown phenomenon that we term Minority Collapse, which fundamentally limits the performance of deep-learning models on the minority classes. In addition, we use the Layer-Peeled Model to gain insights into how to mitigate Minority Collapse. Interestingly, this phenomenon is first predicted by the Layer-Peeled Model before being confirmed by our computational experiments.

scholarly journals An Experimental Analysis of Deep Learning Architectures for Supervised Speech Enhancement

Electronics ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 17
Author(s):  
Soha A. Nossier ◽  
Julie Wall ◽  
Mansour Moniri ◽  
Cornelius Glackin ◽  
Nigel Cannings
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Speech Enhancement ◽  
Network Architecture ◽  
Deep Neural Networks ◽  
Subjective Evaluation ◽  
Objective Evaluation ◽  
Learning Models ◽  
Factors Affecting ◽  
General Evaluation

Recent speech enhancement research has shown that deep learning techniques are very effective in removing background noise. Many deep neural networks are being proposed, showing promising results for improving overall speech perception. The Deep Multilayer Perceptron, Convolutional Neural Networks, and the Denoising Autoencoder are well-established architectures for speech enhancement; however, choosing between different deep learning models has been mainly empirical. Consequently, a comparative analysis is needed between these three architecture types in order to show the factors affecting their performance. In this paper, this analysis is presented by comparing seven deep learning models that belong to these three categories. The comparison includes evaluating the performance in terms of the overall quality of the output speech using five objective evaluation metrics and a subjective evaluation with 23 listeners; the ability to deal with challenging noise conditions; generalization ability; complexity; and, processing time. Further analysis is then provided while using two different approaches. The first approach investigates how the performance is affected by changing network hyperparameters and the structure of the data, including the Lombard effect. While the second approach interprets the results by visualizing the spectrogram of the output layer of all the investigated models, and the spectrograms of the hidden layers of the convolutional neural network architecture. Finally, a general evaluation is performed for supervised deep learning-based speech enhancement while using SWOC analysis, to discuss the technique’s Strengths, Weaknesses, Opportunities, and Challenges. The results of this paper contribute to the understanding of how different deep neural networks perform the speech enhancement task, highlight the strengths and weaknesses of each architecture, and provide recommendations for achieving better performance. This work facilitates the development of better deep neural networks for speech enhancement in the future.

scholarly journals Zero-Keep Filter Pruning for Energy/Power Efficient Deep Neural Networks

Electronics ◽  
2021 ◽  
Vol 10 (11) ◽  
pp. 1238
Author(s):  
Yunhee Woo ◽  
Dongyoung Kim ◽  
Jaemin Jeong ◽  
Young-Woong Ko ◽  
Jeong-Gun Lee
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
High Performance ◽  
Deep Neural Networks ◽  
Learning Models ◽  
Power Efficient ◽  
Number Of Zeros ◽  
Iot Devices ◽  
Deep Learning Model ◽  
Performance Computing

Recent deep learning models succeed in achieving high accuracy and fast inference time, but they require high-performance computing resources because they have a large number of parameters. However, not all systems have high-performance hardware. Sometimes, a deep learning model needs to be run on edge devices such as IoT devices or smartphones. On edge devices, however, limited computing resources are available and the amount of computation must be reduced to launch the deep learning models. Pruning is one of the well-known approaches for deriving light-weight models by eliminating weights, channels or filters. In this work, we propose “zero-keep filter pruning” for energy-efficient deep neural networks. The proposed method maximizes the number of zero elements in filters by replacing small values with zero and pruning the filter that has the lowest number of zeros. In the conventional approach, the filters that have the highest number of zeros are generally pruned. As a result, through this zero-keep filter pruning, we can have the filters that have many zeros in a model. We compared the results of the proposed method with the random filter pruning and proved that our method shows better performance with many fewer non-zero elements with a marginal drop in accuracy. Finally, we discuss a possible multiplier architecture, zero-skip multiplier circuit, which skips the multiplications with zero to accelerate and reduce energy consumption.

scholarly journals Benchmarking Attention-Based Interpretability of Deep Learning in Multivariate Time Series Predictions

Entropy ◽  
2021 ◽  
Vol 23 (2) ◽  
pp. 143
Author(s):  
Domjan Barić ◽  
Petar Fumić ◽  
Davor Horvatić ◽  
Tomislav Lipic
Keyword(s):  
Neural Networks ◽  
Time Series ◽  
Deep Learning ◽  
Deep Neural Networks ◽  
Prediction Performance ◽  
Good Prediction ◽  
Multiple Time ◽  
Multiple Time Series ◽  
Learning Models ◽  
Performance Score

The adaptation of deep learning models within safety-critical systems cannot rely only on good prediction performance but needs to provide interpretable and robust explanations for their decisions. When modeling complex sequences, attention mechanisms are regarded as the established approach to support deep neural networks with intrinsic interpretability. This paper focuses on the emerging trend of specifically designing diagnostic datasets for understanding the inner workings of attention mechanism based deep learning models for multivariate forecasting tasks. We design a novel benchmark of synthetically designed datasets with the transparent underlying generating process of multiple time series interactions with increasing complexity. The benchmark enables empirical evaluation of the performance of attention based deep neural networks in three different aspects: (i) prediction performance score, (ii) interpretability correctness, (iii) sensitivity analysis. Our analysis shows that although most models have satisfying and stable prediction performance results, they often fail to give correct interpretability. The only model with both a satisfying performance score and correct interpretability is IMV-LSTM, capturing both autocorrelations and crosscorrelations between multiple time series. Interestingly, while evaluating IMV-LSTM on simulated data from statistical and mechanistic models, the correctness of interpretability increases with more complex datasets.

scholarly journals MIOpen: An Open Source Library For Deep Learning Primitives

2020 ◽  
pp. invited2-1-invited2-12
Author(s):  
Jehandad Khan ◽  
Paul Fultz ◽  
Artem Tamazov ◽  
Daniel Lowell ◽  
Chao Liu ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Open Source ◽  
Deep Neural Networks ◽  
Design Space ◽  
Data Type ◽  
Data Availability ◽  
Memory Bandwidth ◽  
Common Occurrence ◽  
Auto Tuning

Deep Learning has established itself to be a common occurrence in the business lexicon. The unprecedented success of deep learning in recent years can be attributed to: an abundance of data, availability of gargantuan compute capabilities offered by GPUs, and adoption of open-source philosophy by the researchers and industry. Deep neural networks can be decomposed into a series of different operators. MIOpen, AMD's open-source deep learning primitives library for GPUs, provides highly optimized implementations of such operators, shielding researchers from internal implementation details and hence, accelerating the time to discovery. This paper introduces MIOpen and provides details about the internal workings of the library and supported features. MIOpen innovates on several fronts, such as implementing fusion to optimize for memory bandwidth and GPU launch overheads, providing an auto-tuning infrastructure to overcome the large design space of problem configurations, and implementing different algorithms to optimize convolutions for different filter and input sizes. MIOpen is one of the first libraries to publicly support the bfloat16 data-type for convolutions, allowing efficient training at lower precision without the loss of accuracy.

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