LiPCoT: Linear Predictive Coding based Tokenizer for Self-Supervised Learning of Time Series Data via BERT

LiPCoT (Linear Predictive Coding based Tokenizer for time series) is a novel tokenizer that encodes time series data into a sequence of tokens, enabling self-supervised learning of time series using existing Language model architectures such as BERT.

Main Article: LiPCoT: Linear Predictive Coding based Tokenizer for Self-supervised Learning of Time Series Data via Language Models

Unlike traditional time series tokenizers that rely heavily on CNN encoder for time series feature generation, LiPCoT employs stochastic modeling through linear predictive coding to create a latent space for time series providing a compact yet rich representation of the inherent stochastic nature of the data.
LiPCoT is computationally efficient and can effectively handle time series data with varying sampling rates and lengths, overcoming common limitations of existing time series tokenizers.

Citation

If you use this dataset or code in your research, please cite the following paper:

    @misc{anjum2024lipcot,
        title={LiPCoT: Linear Predictive Coding based Tokenizer for Self-supervised Learning of Time Series Data via Language Models},
        author={Md Fahim Anjum},
        year={2024},
        eprint={2408.07292},
        archivePrefix={arXiv},
        primaryClass={cs.LG}
    }

Dataset

We use EEG dataset of 28 PD and 28 control participants.

Original dataset can be found at link. The data are in .mat formats and you need Matlab to load them. (No need for this unless you are interested into the original EEG data)
Raw CSV dataset used for this repo can be found at link. Download this for running all steps in this repo.

How to run

If you want to run all steps:
- Download raw CSV dataset and place them in the data/raw folder
- Run Step 1-7
If you want to run only the BERT models, run Step 4-6. No need to download raw data as the processed dataset is included in this repo.

Steps

1. Data Preparation

First, the data must be processed. data_processing notebook loads raw data and prepares training,validation and test dataset.

2. Tokenization via LiPCoT

data_tokenizer notebook tokenizes the data using LiPCoT model

3. Prepare tokenized dataset for BERT

data_prepare notebook prepares datasets for BERT models. If you are downloading from GitHub, up to this step is done for you.

4. Self-supervised learning via BERT

pretrain_bert notebook conducts pretraining of BERT model.

If you are running code with data from GitHub, start with this step.

5. Classification task: with pretrained BERT

finetune_bert notebook conducts fine-tune of BERT model for binary classification

6. Classification task: without pretraining

finetune_bert_without_pretrain notebook uses a randomly initialized BERT model and fine tunes it for classification

7. Classification task: CNN-based architectures

cnn_classifier notebook uses CNN model as described in Oh et. al. (2018)
deepnet_classifier notebook uses Deep Convolutional Network as described in Schirrmeister et. al. (2017)
shallownet_classifier notebook uses Shallow Convolutional Network as described in Schirrmeister et. al. (2017)
eegnet_classifier notebook uses EEGNet as described in here

MDFahimAnjum/LiPCoT