Tensorflow implementation of paper: Learning to Diagnose with LSTM Recurrent Neural Networks.

Overview

Multilabel time series classification with LSTM

Tensorflow implementation of model discussed in the following paper: Learning to Diagnose with LSTM Recurrent Neural Networks.

Tools Required

Python 3.5 is used during development and following libraries are required to run the code provided in the notebook:

  • Tensorflow
  • Numpy
  • Pandas

Dataset

Cleaned version of MIMIC-III dataset and accompanying paper

MIMIC-III dataset can possibly be use to train and test the model. Beware this is not the data set used by the authors of the paper.

Note: If you see mistakes, want to suggest changes or have dataset that can be use to train/test the model, please submit a pull request.

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Comments
  • multilabel classification ?

    multilabel classification ?

    excuse me,the original is a multi-label classification problem, I did not get to know how your label is processed, after study your code I think your label is a single multi-label classification problem, am i wrong? would you help me to explain the label question? very very thank you!!

    opened by queyanaimao 3
  • Clarification regarding the data shape illustration

    Clarification regarding the data shape illustration

    Hello, Regarding the illustration of the shape of the data: "Each training example will be a sequence of shape [1, time_steps, number_of_features]" However, in the code: "segments=segments.reshape([len(segments),(win_size + 1),1])" If I understand correctly, win_size = number_of_features + 1 (because an extra feature of the tims step) and len(segments)=time_steps So it seems there is a mismatch between the order of dimensions in the illustration and the code

    Could you please clearify this issue? Thank you!

    opened by BY-hash 1
  • Data format

    Data format

    First of all, thank you for the code!

    I know it has already been discussed, but it is not clear to me the data format in the csv file needed to run your code. Does it have to be two coloumns, first coloumn with the full time series and in the second coloum the label associated with each time step? or what else?

    Thank you!

    opened by AnconaAndrea 1
  • error in creating multilayer lstm

    error in creating multilayer lstm

    hi,

    Thank you for sharing the code. I got the following error when constructing the multilayer LSTM:

    InvalidArgumentError: Dimensions must be equal, but are 128 and 65 for 'rnn/while/rnn/multi_rnn_cell/cell_0/lstm_cell/MatMul_1' (op: 'MatMul') with input shapes: [?,128], [65,256].

    I am using tensorflow 1.12 on Windows 10.

    I believe the issue is on how the multiple LSTM cells are in created. Specifically, this line multi_layer_cell = tf.nn.rnn_cell.MultiRNNCell([cell] * 2) likely creates two cell pointing to the same object. I was able to get rid of this issue by changing it to: multi_layer_cell = tf.nn.rnn_cell.MultiRNNCell[rnn_cell.LSTMCell(n_hidden, state_is_tuple=True) for _ in range(2)])

    opened by shopeth 0
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Aaqib
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