scholarly journals Explainable Models of Disease Progression in ALS: Learning from Longitudinal Clinical Data with Recurrent Neural Networks and Deep Model Explanation

Author(s):  
Marcel Müller ◽  
Marta Gromicho ◽  
Mamede de Carvalho ◽  
Sara C. Madeira
2018 ◽  
Vol 12 (04) ◽  
pp. 481-500 ◽  
Author(s):  
Naifan Zhuang ◽  
The Duc Kieu ◽  
Jun Ye ◽  
Kien A. Hua

With the growth of crowd phenomena in the real world, crowd scene understanding is becoming an important task in anomaly detection and public security. Visual ambiguities and occlusions, high density, low mobility, and scene semantics, however, make this problem a great challenge. In this paper, we propose an end-to-end deep architecture, convolutional nonlinear differential recurrent neural networks (CNDRNNs), for crowd scene understanding. CNDRNNs consist of GoogleNet Inception V3 convolutional neural networks (CNNs) and nonlinear differential recurrent neural networks (RNNs). Different from traditional non-end-to-end solutions which separate the steps of feature extraction and parameter learning, CNDRNN utilizes a unified deep model to optimize the parameters of CNN and RNN hand in hand. It thus has the potential of generating a more harmonious model. The proposed architecture takes sequential raw image data as input, and does not rely on tracklet or trajectory detection. It thus has clear advantages over the traditional flow-based and trajectory-based methods, especially in challenging crowd scenarios of high density and low mobility. Taking advantage of CNN and RNN, CNDRNN can effectively analyze the crowd semantics. Specifically, CNN is good at modeling the semantic crowd scene information. On the other hand, nonlinear differential RNN models the motion information. The individual and increasing orders of derivative of states (DoS) in differential RNN can progressively build up the ability of the long short-term memory (LSTM) gates to detect different levels of salient dynamical patterns in deeper stacked layers modeling higher orders of DoS. Lastly, existing LSTM-based crowd scene solutions explore deep temporal information and are claimed to be “deep in time.” Our proposed method CNDRNN, however, models the spatial and temporal information in a unified architecture and achieves “deep in space and time.” Extensive performance studies on the Violent-Flows, CUHK Crowd, and NUS-HGA datasets show that the proposed technique significantly outperforms state-of-the-art methods.


NeuroImage ◽  
2020 ◽  
Vol 222 ◽  
pp. 117203
Author(s):  
Minh Nguyen ◽  
Tong He ◽  
Lijun An ◽  
Daniel C. Alexander ◽  
Jiashi Feng ◽  
...  

Cells ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 767 ◽  
Author(s):  
Tan ◽  
Le ◽  
Yeh ◽  
Chua

Enhancers are short deoxyribonucleic acid fragments that assume an important part in the genetic process of gene expression. Due to their possibly distant location relative to the gene that is acted upon, the identification of enhancers is difficult. There are many published works focused on identifying enhancers based on their sequence information, however, the resulting performance still requires improvements. Using deep learning methods, this study proposes a model ensemble of classifiers for predicting enhancers based on deep recurrent neural networks. The input features of deep ensemble networks were generated from six types of dinucleotide physicochemical properties, which had outperformed the other features. In summary, our model which used this ensemble approach could identify enhancers with achieved sensitivity of 75.5%, specificity of 76%, accuracy of 75.5%, and MCC of 0.51. For classifying enhancers into strong or weak sequences, our model reached sensitivity of 83.15%, specificity of 45.61%, accuracy of 68.49%, and MCC of 0.312. Compared to the benchmark result, our results had higher performance in term of most measurement metrics. The results showed that deep model ensembles hold the potential for improving on the best results achieved to date using shallow machine learning methods.


2020 ◽  
Author(s):  
Dean Sumner ◽  
Jiazhen He ◽  
Amol Thakkar ◽  
Ola Engkvist ◽  
Esben Jannik Bjerrum

<p>SMILES randomization, a form of data augmentation, has previously been shown to increase the performance of deep learning models compared to non-augmented baselines. Here, we propose a novel data augmentation method we call “Levenshtein augmentation” which considers local SMILES sub-sequence similarity between reactants and their respective products when creating training pairs. The performance of Levenshtein augmentation was tested using two state of the art models - transformer and sequence-to-sequence based recurrent neural networks with attention. Levenshtein augmentation demonstrated an increase performance over non-augmented, and conventionally SMILES randomization augmented data when used for training of baseline models. Furthermore, Levenshtein augmentation seemingly results in what we define as <i>attentional gain </i>– an enhancement in the pattern recognition capabilities of the underlying network to molecular motifs.</p>


Sign in / Sign up

Export Citation Format

Share Document