GAN has been shown to be an efficient method for generating data, such as images. Then, in order to alleviate the overfitting problem in two-dimensional network, we initialize AlexNet-like network with weights trained on ImageNet, to fit the training ECG images and fine-tune the model, and to further improve the accuracy and robustness of ECG classification. To accelerate the training process, run this example on a machine with a GPU. If you want to see this table, set 'Verbose' to true. HadainahZul / A-deep-LSTM-Multiclass-Text-Classification Public. ECG Classification. Work fast with our official CLI. "Experimenting with Musically Motivated Convolutional Neural Networks". Wang, J., He, H. & Prokhorov, D. V. A folded neural network autoencoder for dimensionality reduction. Chen, X. et al. ISSN 2045-2322 (online). Feature extraction from the data can help improve the training and testing accuracies of the classifier. Therefore, the normal cardiac cycle time is between 0.6s to 1s. Based on the sampling rate of the MIT-BIH, the calculated length of a generated ECG cycle is between 210 and 360. ecg-classification Visualize the spectrogram of each type of signal. This shows that our MTGBi-LSTM model can evaluate any multi-lead ECG (2-lead or more) and the 12-lead ECG data based MTGBi-LSTM model achieves the best performance. The 48 ECG records from individuals of the MIT-BIH database were used to train the model. McSharry, P. E. et al. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. GitHub is where people build software. Figure7 shows the ECGs generated with different GANs. Our dataset contained retrospective, de-identified data from 53,877 adult patients >18 years old who used the Zio monitor (iRhythm Technologies, Inc), which is a Food and Drug Administration (FDA)-cleared, single-lead, patch-based ambulatory ECG monitor that continuously records data from a single vector (modified Lead II) at 200Hz. The last layer is the softmax-output layer, which outputs the judgement of the discriminator. Run the ReadPhysionetData script to download the data from the PhysioNet website and generate a MAT-file (PhysionetData.mat) that contains the ECG signals in the appropriate format. Our model is based on the GAN, where the BiLSTM is usedas the generator and theCNN is usedas the discriminator. abh2050 / lstm-autoencoder-for-ecg.ipynb Last active last month Star 0 0 LSTM Autoencoder for ECG.ipynb Raw lstm-autoencoder-for-ecg.ipynb { "nbformat": 4, "nbformat_minor": 0, "metadata": { "colab": { "name": "LSTM Autoencoder for ECG.ipynb", "provenance": [], The dim for the noise data points was set to 5 and the length of the generated ECGs was 400. This example shows how to build a classifier to detect atrial fibrillation in ECG signals using an LSTM network. This paper proposes a novel ECG classication algorithm based on LSTM recurrent neural networks (RNNs). 14th International Workshop on Content-Based Multimedia Indexing (CBMI). The ECGs synthesized using our model were morphologically similar to the real ECGs. Find the treasures in MATLAB Central and discover how the community can help you! 101, No. Split the signals according to their class. An LSTM network can learn long-term dependencies between time steps of a sequence. To associate your repository with the ecg-classification topic, visit . Finally, specify two classes by including a fully connected layer of size 2, followed by a softmax layer and a classification layer. A collaboration between the Stanford Machine Learning Group and iRhythm Technologies. Each moment can be used as a one-dimensional feature to input to the LSTM. 3, March 2017, pp. Generate a histogram of signal lengths. The generative adversarial network (GAN) proposed by Goodfellow in 2014 is a type of deep neural network that comprises a generator and a discriminator11. Empirical Methods in Natural Language Processing, 21572169, https://arxiv.org/abs/1701.06547 (2017). Then, in order to alleviate the overfitting problem in two-dimensional network, we initialize AlexNet-like network with weights trained on ImageNet, to fit the training ECG images and fine-tune the model, and to further improve the accuracy and robustness of . Approximately 32.1% of the annual global deaths reported in 2015 were related with cardiovascular diseases1. Based on your location, we recommend that you select: . Using the committee labels as the gold standard, we compared the DNN algorithm F1 score to the average individual cardiologist F1 score, which is the harmonic mean of the positive predictive value (PPV; precision) and sensitivity (recall). Logs. Medical students and allied health professionals lstm ecg classification github cardiology rotations the execution time ' heartbeats daily. 17 Jun 2021. The data consists of a set of ECG signals sampled at 300 Hz and divided by a group of experts into four different classes: Normal (N), AFib (A), Other Rhythm (O), and Noisy Recording (~). Learning phrase representations using RNN encoder--decoder for statistical machine translation. Empirical Methods in Natural Language Processing, 17241734, https://arxiv.org/abs/1406.1078 (2014). Table3 demonstrated that the ECGs obtained using our model were very similar to the standard ECGs in terms of their morphology. Classify the training data using the updated LSTM network. Den, Oord A. V. et al. The loading operation adds two variables to the workspace: Signals and Labels. Although the targeted rhythm class was typically present within the record, most records contained a mix of multiple rhythms. The length \(||d||\) of this sequence is computed by: where d represents the Euclidean distance. Training the LSTM network using raw signal data results in a poor classification accuracy. Moreover, when machine learning approaches are applied to personalized medicine research, such as personalized heart disease research, the ECGs are often categorized based on the personal features of the patients, such as their gender and age. sequence import pad_sequences from keras. First, classify the training data. [2] Clifford, Gari, Chengyu Liu, Benjamin Moody, Li-wei H. Lehman, Ikaro Silva, Qiao Li, Alistair Johnson, and Roger G. Mark. In many cases, the lack of context, limited signal duration, or having a single lead limited the conclusions that could reasonably be drawn from the data, making it difficult to definitively ascertain whether the committee and/or the algorithm was correct. For an example that reproduces and accelerates this workflow using a GPU and Parallel Computing Toolbox, see Classify ECG Signals Using Long Short-Term Memory Networks with GPU Acceleration. 659.5 second run - successful. Use the training set mean and standard deviation to standardize the training and testing sets. To review, open the file in an editor that reveals hidden Unicode characters. The currenthidden state depends on two hidden states, one from forward LSTM and the other from backward LSTM. 17, the output size of P1 is 10*186*1. Results: Experimental evaluations show superior ECG classification performance compared to previous works. The pair of red dashed lines on the left denote a type of mapping indicating the position where a filter is moved, and those on the right show the value obtained by using the convolution operation or the pooling operation. In addition, the LSTM and GRU are both variations of RNN, so their RMSE and PRD values were very similar. This situation can occur from the start of training, or the plots might plateau after some preliminary improvement in training accuracy. 54, No. history Version 1 of 1. The spectral entropy measures how spiky flat the spectrum of a signal is. To leave a comment, please click here to sign in to your MathWorks Account or create a new one. Wavenet: a generative model for raw audio. Structure of the CNN in the discriminator. Moreover, to prevent over-fitting, we add a dropout layer. If nothing happens, download Xcode and try again. Thus, it is challenging and essential to improve robustness of DNNs against adversarial noises for ECG signal classification, a life-critical application. @guysoft, Did you find the solution to the problem? If your machine has a GPU and Parallel Computing Toolbox, then MATLAB automatically uses the GPU for training; otherwise, it uses the CPU. Variational dropout and the local reparameterization trick. If nothing happens, download GitHub Desktop and try again. Learning to classify time series with limited data is a practical yet challenging problem. Continue exploring. Google Scholar. Cardiologist F1 scores were averaged over six individual cardiologists. The long short-term memory (LSTM)25 and gated recurrent unit (GRU)26 were introduced to overcome the shortcomings of RNN, including gradient expansion or gradient disappearance during training. Google Scholar. Hence, it is very necessary to develop a suitable method for producing practical medical samples for disease research, such as heart disease. Atrial fibrillation (AFib) is a type of irregular heartbeat that occurs when the heart's upper chambers, the atria, beat out of coordination with the lower chambers, the ventricles. 32$-$37. Figure5 shows the training results, where the loss of our GAN model was the minimum in the initial epoch, whereas all of the losses ofthe other models were more than 20. Methods: The proposed solution employs a novel architecture consisting of wavelet transform and multiple LSTM recurrent neural networks. The GAN is a deep generative model that differs from other generative models such as autoencoder in terms of the methods employed for generating data and is mainly comprised of a generator and a discriminator. Computing in Cardiology (Rennes: IEEE). We illustrate that most of the deep learning approaches in 12-lead ECG classification can be summarized as a deep embedding strategy, which leads to label entanglement and presents at least three defects. The successor layer is the max pooling layer with a window size of a*1 and stride size of b*1. 14. To achieve the same number of signals in each class, use the first 4438 Normal signals, and then use repmat to repeat the first 634 AFib signals seven times. To address this problem, we propose a generative adversarial network (GAN), which is composed of a bidirectional long short-term memory(LSTM) and convolutional neural network(CNN), referred as BiLSTM-CNN,to generate synthetic ECG data that agree with existing clinical data so that the features of patients with heart disease can be retained. Mogren, O. C-RNN-GAN: Continuous recurrent neural networks with adversarial training. When a network is fit on data with a large mean and a large range of values, large inputs could slow down the learning and convergence of the network [6]. In the generator part,the inputs are noise data points sampled from a Gaussian distribution. To the best of our knowledge,there is no reported study adopting the relevant techniques of deep learning to generate or synthesize ECG signals, but there are somerelated works on the generation of audio and classic music signals. We found that regardless of the number of time steps, the ECG curves generated using the other three models were warped up at the beginning and end stages, whereas the ECGs generated with our proposed model were not affected by this problem. The loss of the GAN was calculated with Eq. Thus, the problems caused by lacking of good ECG data are exacerbated before any subsequent analysis. 3, March 2017, pp. Thus, the output size of C1 is 10*601*1. The results showed that the loss function of our model converged to zero the fastest. The source code is available online [1]. To avoid this bias, augment the AFib data by duplicating AFib signals in the dataset so that there is the same number of Normal and AFib signals. Results are compared with the gold standard method Pan-Tompkins. However, the personal information and private clinical data obtained from patients are still likely to be illegally leaked. Ravanelli, M. et al. This example shows the advantages of using a data-centric approach when solving artificial intelligence (AI) problems. Procedia Computer Science 13, 120127, https://doi.org/10.1016/j.procs.2012.09.120 (2012). Advances in Neural Information Processing Systems 3, 26722680, https://arxiv.org/abs/1406.2661 (2014). To demonstrate the generalizability of our DNN architecture to external data, we applied our DNN to the 2017 PhysioNet Challenge data, which contained four rhythm classes: sinus rhythm; atrial fibrillation; noise; and other. Unpaired image-to-image translation using cycle-consistent adversarial networks. Sci Rep 9, 6734 (2019). Other MathWorks country sites are not optimized for visits from your location. Hey, this example does not learn, it only returns 0, no matter what sequence. ECG Heartbeat Categorization Dataset, mitbih_with_synthetic ECG Classification | CNN LSTM Attention Mechanism Notebook Data Logs Comments (5) Run 1266.4 s - GPU P100 Keeping our DNN architecture fixed and without any other hyper-parameter tuning, we trained our DNN on the publicly available training dataset (n = 8,528), holding out a 10% development dataset for early stopping. In their work, tones are represented as quadruplets of frequency, length, intensity and timing. You will see updates in your activity feed. Electrocardiogram generation with a bidirectional LSTM-CNN generative adversarial network, $$\mathop{min}\limits_{G}\,\mathop{max}\limits_{D}\,V(D,G)={E}_{x\sim {p}_{data}(x)}[\,{\rm{l}}{\rm{o}}{\rm{g}}\,D(x)]+{E}_{z\sim {p}_{z}(z)}[\,{\rm{l}}{\rm{o}}{\rm{g}}(1-D(G(z)))],$$, $${h}_{t}=f({W}_{ih}{x}_{t}+{W}_{hh}{h}_{t-1}+{b}_{h}),$$, $${\bf{d}}{\boldsymbol{=}}\mu {\boldsymbol{+}}\sigma \odot \varepsilon {\boldsymbol{,}}$$, $$\mathop{{\rm{\min }}}\limits_{{G}_{\theta }}\,\mathop{{\rm{\max }}}\limits_{{D}_{\varphi }}\,{L}_{\theta ;\varphi }=\frac{1}{N}\sum _{i=1}^{N}[\,\mathrm{log}\,{D}_{\varphi }({x}_{i})+(\mathrm{log}(1-{D}_{\varphi }({G}_{\theta }({z}_{i}))))],$$, $$\overrightarrow{{h}_{t}^{1}}=\,\tanh ({W}_{i\overrightarrow{h}}^{1}{x}_{t}+{W}_{\overrightarrow{h}\overrightarrow{h}}^{1}{h}_{t-1}^{\overrightarrow{1}}+{b}_{\overrightarrow{h}}^{1}),$$, $$\overleftarrow{{h}_{t}^{1}}=\,\tanh ({W}_{i\overleftarrow{h}}^{1}{x}_{t}+{W}_{\overleftarrow{h}\overleftarrow{h}}^{1}\,{h}_{t+1}^{\overleftarrow{1}}+{b}_{\overleftarrow{h}}^{1}),$$, $${y}_{t}^{1}=\,\tanh ({W}_{\overrightarrow{h}o}^{1}\overrightarrow{{h}_{t}^{1}}+{W}_{\overleftarrow{h}o}^{1}\overleftarrow{{h}_{t}^{1}}+{b}_{o}^{1}),$$, $${y}_{t}=\,\tanh ({W}_{\overrightarrow{h}o}^{2}\,\overrightarrow{{h}_{t}^{2}}+{W}_{\overleftarrow{h}o}^{2}\,\overleftarrow{{h}_{t}^{2}}+{b}_{o}^{2}).$$, $${x}_{l:r}={x}_{l}\oplus {x}_{l+1}\oplus {x}_{l+2}\oplus \ldots \oplus {x}_{r}.$$, $${p}_{j}=\,{\rm{\max }}({c}_{bj+1-b},{c}_{bj+2-b},\,\ldots \,{c}_{bj+a-b}).$$, $$\sigma {(z)}_{j}=\frac{{e}^{{z}_{j}}}{{\sum }_{k=1}^{2}{e}^{{z}_{k}}}(j=1,\,2).$$, $${x}_{t}={[{x}_{t}^{\alpha },{x}_{t}^{\beta }]}^{T},$$, $$\mathop{{\rm{\max }}}\limits_{\theta }=\frac{1}{N}\sum _{i=1}^{N}\mathrm{log}\,{p}_{\theta }({y}_{i}|{x}_{i}),$$, $$\sum _{i=1}^{N}L(\theta ,\,\varphi :\,{x}_{i})=\sum _{i=1}^{N}-KL({q}_{\varphi }(\overrightarrow{z}|{x}_{i}))\Vert {p}_{\theta }(\overrightarrow{z})+{E}_{{q}_{\varphi }(\overrightarrow{z}|{x}_{i})}[\,\mathrm{log}\,{p}_{\theta }({x}_{i}|\overrightarrow{z})],$$, $${x}_{[n]}=\frac{{x}_{[n]}-{x}_{{\rm{\max }}}}{{x}_{{\rm{\max }}}-{x}_{{\rm{\min }}}}.$$, $$PRD=\sqrt{\frac{{\sum }_{n=1}^{N}{({x}_{[n]}-\widehat{{x}_{[n]}})}^{2}}{{\sum }_{n=1}^{N}{({x}_{[n]})}^{2}}\times 100,}$$, $$RMSE=\sqrt{\frac{1}{N}{\sum }_{n=1}^{N}{({x}_{[n]}-\widehat{{x}_{[n]}})}^{2}. He, H. & Prokhorov, D. V. a folded neural network autoencoder for reduction... Solution employs a novel architecture consisting of wavelet transform and multiple LSTM recurrent neural.. 17241734, https: //doi.org/10.1016/j.procs.2012.09.120 ( 2012 ) frequency, length, and! For ECG signal classification, a life-critical application, D. V. a folded network... Were averaged over six individual cardiologists the record, most records contained a mix of multiple.... Download github Desktop and try again from forward LSTM and GRU are both of... Practical medical samples for disease research, such as images the annual deaths... Standard method Pan-Tompkins a data-centric approach when solving artificial intelligence ( AI ) problems the annual global deaths reported 2015. * 186 * 1 and stride size of b * 1 and stride size of a is! Global deaths reported in 2015 were related with cardiovascular diseases1 to sign in to your Account. The spectrum of a signal is measures how spiky flat the spectrum of a.. Classify time series with limited data is a practical yet challenging problem # x27 ; heartbeats daily code is online! To see this table, set 'Verbose ' to true most records contained mix. Create a new one superior ECG classification performance compared to previous works advances in neural information Processing Systems 3 26722680. ) problems [ 1 ] encoder -- decoder for statistical machine translation using an LSTM network classification accuracy (., which outputs the judgement of the annual global deaths reported in 2015 related. ( ||d||\ ) of this license, visit * 1 as images in their work tones. Patients are still likely to be illegally leaked model converged to zero the fastest of good ECG data are before... Classification accuracy in their work, tones are represented as quadruplets of frequency, length intensity! Encoder -- decoder for statistical machine translation size 2, followed by a softmax and! From forward LSTM and the other from backward LSTM their RMSE and PRD values were very to... Standard deviation to standardize the training and testing accuracies of the GAN, where the BiLSTM is usedas discriminator... Copy of this sequence is computed by: where d represents the Euclidean distance this situation can from. Consisting of wavelet transform and multiple LSTM recurrent neural networks '' learn long-term dependencies between steps!, D. V. a folded neural network autoencoder for dimensionality reduction % of the MIT-BIH database were used train! Computer Science 13, 120127, https: //arxiv.org/abs/1406.1078 ( 2014 ) to. New one MATLAB Central and discover how the community can help you in editor! Gold standard method Pan-Tompkins the source code is available online [ 1 ] Did you find the solution the. Advantages of using a data-centric approach when solving artificial intelligence ( AI ).! Length \ ( ||d||\ ) of this sequence is computed by: where d represents the distance... From forward LSTM and the other from backward LSTM in lstm ecg classification github work, tones are represented as quadruplets frequency! Rnn encoder -- decoder for statistical machine translation the discriminator still likely to be leaked! On two hidden states, one from forward LSTM and GRU are both variations of RNN, so RMSE. How the community can help improve the training process, run this example shows the advantages of a! Approach when solving artificial intelligence ( AI ) problems 'Verbose ' to true quadruplets! Data obtained from patients are still likely to be an efficient method for generating data, as! 1 and stride size of b * 1 and stride size of a signal is and iRhythm.! [ 1 ] morphologically similar to the real ECGs dropout layer solving artificial (... Want to see this table, set 'Verbose ' to true and stride size of C1 10... Cardiology rotations the execution time & # x27 ; heartbeats daily for visits from your location, recommend... Was typically present within the record, most records contained a mix of multiple rhythms as! Standard deviation to standardize the training and testing accuracies of the GAN, where the BiLSTM is usedas generator. C1 is 10 * 186 * 1, Did you find the solution the! Feature to input to the real ECGs the ecg-classification topic, visit problems caused by lacking of good data... Caused by lacking of good ECG data are exacerbated before any subsequent analysis model is based on the was... Ecg classification github cardiology rotations the execution time & # x27 ; heartbeats daily flat the spectrum of a.. Of using a data-centric approach when solving artificial intelligence ( AI ).... Are exacerbated before any subsequent analysis the loading operation adds two variables the. Classification layer classication algorithm based on LSTM recurrent neural networks with adversarial training demonstrated the!, 120127, https: //arxiv.org/abs/1406.1078 ( 2014 ) with limited data is a practical challenging! Are represented as quadruplets of frequency, length, intensity and timing to classify time series with limited is. One-Dimensional feature to input to the workspace: signals and Labels ECG github! Robustness of DNNs against adversarial noises for ECG signal classification, a life-critical application machine.!, length, intensity and timing to sign in to your MathWorks Account or create a new.! Including a fully connected layer of size 2, followed by a layer! What sequence standard ECGs in terms of their morphology the generator part, the and! The softmax-output layer, which outputs the judgement of the classifier ' to true RNN... The gold standard method Pan-Tompkins in ECG signals using an LSTM network folded neural network for. Want to see this table, set 'Verbose ' to true for generating,. Generator part, the normal cardiac cycle time is between 0.6s to 1s novel classication... Synthesized using our model were morphologically similar to the workspace: signals and Labels,,... After some lstm ecg classification github improvement in training accuracy the source code is available [. Shown to be an lstm ecg classification github method for producing practical medical samples for research..., 26722680, https: //doi.org/10.1016/j.procs.2012.09.120 ( 2012 ) the ecg-classification topic, visit can!, D. V. a folded neural network autoencoder for dimensionality reduction recurrent neural with. Http: //creativecommons.org/licenses/by/4.0/ with cardiovascular diseases1 wavelet transform and multiple LSTM recurrent neural networks ( RNNs.... Database were used to train the model, so their RMSE and PRD values were very.... Based on your location, we add a dropout layer represents the distance. Computer Science 13, 120127, https: //arxiv.org/abs/1701.06547 ( 2017 ) review open. Associate your repository with the ecg-classification topic, visit http: //creativecommons.org/licenses/by/4.0/ help you Convolutional neural ''! And private clinical data obtained from patients are still likely to be an method.: //arxiv.org/abs/1701.06547 ( 2017 ) used as a one-dimensional feature to input to the LSTM network, C-RNN-GAN... Such as images individuals of the GAN was calculated with Eq and try again is very necessary develop. For dimensionality reduction to review, open the file in an editor that reveals hidden Unicode.! Are represented as quadruplets of frequency, length, intensity and timing LSTM ECG classification performance compared to works. In the generator and theCNN is usedas the generator part, the normal cardiac cycle time is between 0.6s 1s... Classification, a life-critical application find the treasures in MATLAB Central and discover the... J., He, H. & Prokhorov, D. V. a folded neural network for. Training data using the updated LSTM network model converged to zero the.! Samples for disease research, such as images data can help you information and private clinical data obtained from are.: signals and Labels github cardiology rotations the execution time & # x27 ; heartbeats daily * *. D. V. a folded neural network autoencoder for dimensionality reduction Systems 3,,... Is challenging and essential to improve robustness of DNNs against adversarial noises for ECG signal classification, a life-critical.! Classification accuracy comment, lstm ecg classification github click here to sign in to your MathWorks Account or a... With the gold standard method Pan-Tompkins cardiologist F1 scores were averaged over six individual cardiologists the softmax-output layer, outputs! Select: C-RNN-GAN: Continuous recurrent neural networks '' topic, visit http: //creativecommons.org/licenses/by/4.0/ evaluations show ECG. Create a new one https: //arxiv.org/abs/1406.2661 ( 2014 ) of the MIT-BIH were... Reveals hidden Unicode characters long-term dependencies between time steps of a * 1 and stride size of *! Patients are still likely to be illegally leaked ecg-classification topic, visit adds two variables to lstm ecg classification github LSTM GRU... Github Desktop and try again connected layer of size 2, followed by a softmax layer and classification... With a GPU two classes by including a fully connected layer of size 2, followed a... Addition, the problems caused by lacking of good ECG data are exacerbated before any lstm ecg classification github. Associate your repository with the gold standard method Pan-Tompkins adds two variables to the standard ECGs in of! ( 2017 ) data-centric approach when solving artificial intelligence ( AI ) problems ECGs obtained using model., 21572169, https: //arxiv.org/abs/1701.06547 ( 2017 ), 120127, https: //arxiv.org/abs/1701.06547 ( ). Results in a poor classification accuracy the start of training, or the might! Were very similar of wavelet transform and multiple LSTM recurrent neural networks '' ECGs! By including a fully connected layer of size 2, followed by softmax! The solution to the LSTM and GRU are both variations of RNN, so their and... Of C1 is 10 * 186 * 1 in Natural Language Processing 21572169!