Time Series Classification of Autism Spectrum Disorder Using the Light-Adapted Electroretinogram
Abstract
1. Introduction
- To the best of the authors’ knowledge, this is the first application of SHAP explanation to the TSC algorithms’ results for an ERG signal classification task.
- SHAP methods were applied on the TSC models to provide a domain-agnostic explanation, highlighting the important regions of the signals for classification.
2. Materials and Methods
2.1. Dataset
2.2. Time Series Classification Models
- Word extraction for TSC (WEASEL) is a dictionary-based classifier for time-series data. The algorithm is based on the bag-of-patterns representation, which consists of extracting sub-sequences of different lengths from the time series, discretizing each sub-sequence into a coarsely discrete-valued word, then building a histogram from word counts and training a logistic regression classifier on this bag [41]. In the WEASEL case, it was expected that explainability allowed for highlighting which symbolic patterns (e.g., specific wave chunks) or sub-sequences contributed most to class classification.
- Time Series Forest (TSF) is an ensemble method for TSC that builds multiple decision trees. The algorithm selects each tree in the forest through random selection of several intervals with randomized lengths and positional offsets. For each sampled interval, three statistical features are computed: the mean, the standard deviation, and the slope. The features of each interval are then aggregated into a composite feature vector that subsequently serves as the input feature space for the construction of a decision tree. The resulting trees are then integrated into the ensemble model. The random forest-like classifier algorithm is applied to all trees [42]. In the TSF case, it was expected that explainability would allow the identification of the critical intervals that corresponded to a clinically relevant interpretation of ERG signals for classification.
- KNeighborsTimeSeriesClassifier (TS-KNN) is an implementation of the k-nearest neighbors algorithm specifically designed for time series with Dynamic Time Wrapping Distance (DTW). DTW is an elastic distance measure that optimally compares two sequences by warping them non-linearly in time. DTW was applied instead of the traditional Euclidean distance due to the robustness of signal delays (latency) and other distortions in the time domain [43]. In the TS-KNN case, it was expected that explainability would allow for the identification of waveform intervals that corresponded to important patterns of behavior in the ERG signal for classification.
- Random Convolutional Kernel Transform (ROCKET) is a method for TSC based on 1D convolution kernels with random parameter selection. It works by generating a large variety of kernels, each containing different parameters (length, weight, dilation, etc.), and applies these kernels to the data through convolution. Each convolution results in two features, the positive value amount and the maximum value [44]. In this work a random forest was applied to the vector of features obtained for 3000 kernels. In the ROCKET case, it was expected that explainability would identify regions and points (e.g., a-wave amplitude) emphasized by the kernel emphasis, which correspond to differences in retinal signaling between the groups for classification.
2.3. Hyperparameter Selection
- If there was no variation in hyperparameters in the algorithm, then it was run once and the classification metrics values were saved to memory.
- If the algorithm had variations of hyperparameters, then it was run in the amount of these variations and all of the obtained classification metrics were saved to memory.
- —112, 1231, 42, 990, 2500, 467, 777, 89, 258, 24;
- of the TSF algorithm—10, 50, 100, 200, 300, 400, 500;
- of the TS-KNN algorithm—1, 2, 3, 4, 5, 6, 7;
- of the ROCKET algorithm—100, 1000, 10,000, 20,000, 30,000.
- F1-score (separately for control and ASD individuals;
- Balanced accuracy;
- Time for training.
2.4. Explaining TSC Models Using the SHAP Library
- Train a time-series model using sktime.
- Use the trained model to make predictions on the test data.
- Apply SHAP to the model to obtain feature importance values.
3. Results
3.1. Visual Inspection of the Signals
3.2. Model Evaluation
- of the TSF algorithm was 10.
- of the TS-KNN algorithm was 3.
- of the ROCKET algorithm was 20,000.
3.3. Analysis of Algorithm Errors
- If was equal to 1 and was equal to 0, then mark the array element as Falsely ASD (or false positive).
- If was 0 and was 1, then mark the array element as Falsely control (or false negative).
- If was 0 and was 0, then mark the array element Correct control (or True Negative).
- If was equal to 1 and was equal to 1, then mark the array element Correct ASD (or true positive).
3.4. Explanation of the Signals
- ROCKET results (see Figure A1, Figure A2 and Figure A3). The explanations of this algorithm were the most sparse and not spread along the whole time series. Similar to the TS-KNN algorithm, the ROCKET algorithm largely ignored the initial baseline part of the signal. The most indicative parts for the predication were associated with the 35 ms and 45 ms time steps, as well as spread throughout the final part of the signal.
- TS-KNN results (see Figure A4, Figure A5 and Figure A6). The first 25 ms of the signal was mostly ignored by the algorithm. The most significant parts of the signals for positive class prediction were associated with the 35–45 ms interval, as well as with the end part of the signal. The significant part for negative class prediction was mostly located in the 35–45 ms region.
- WEASEL results (see Figure A7, Figure A8 and Figure A9). Throughout the entire signal, there were significant deviations for both control and ASD individuals. The SHAP coefficients were associated with the first part of the signal baseline (from 0 to 25 ms), as well as significant contribution of the middle part (around 50 ms), and the end of the signal (around 85 ms and 100 ms). In general, the WEASEL algorithm failed to highlight the significant parts of the signal associated with the b-wave.
- TSF results (see Figure A10, Figure A11 and Figure A12). Similar to the WEASEL algorithm throughout the entire signal, there were significant deviations for both control and ASD individuals. The most significant signals parts associated with importance for classifications were related to the 50 ms, 60 ms, 75 ms, and 100 ms marks. Overall, the TSF algorithm used the whole signal for prediction but failed to identify specific local significant regions of the signal.
3.5. Discussion
4. Conclusions
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
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TSC | F1 Control | F1 ASD | Balanced Accuracy |
---|---|---|---|
WEASEL | |||
TSF | |||
TS-KNN | |||
ROCKET |
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Chistiakov, S.; Dolganov, A.; Constable, P.A.; Zhdanov, A.; Kulyabin, M.; Thompson, D.A.; Lee, I.O.; Albasu, F.; Borisov, V.; Ronkin, M. Time Series Classification of Autism Spectrum Disorder Using the Light-Adapted Electroretinogram. Bioengineering 2025, 12, 951. https://doi.org/10.3390/bioengineering12090951
Chistiakov S, Dolganov A, Constable PA, Zhdanov A, Kulyabin M, Thompson DA, Lee IO, Albasu F, Borisov V, Ronkin M. Time Series Classification of Autism Spectrum Disorder Using the Light-Adapted Electroretinogram. Bioengineering. 2025; 12(9):951. https://doi.org/10.3390/bioengineering12090951
Chicago/Turabian StyleChistiakov, Sergey, Anton Dolganov, Paul A. Constable, Aleksei Zhdanov, Mikhail Kulyabin, Dorothy A. Thompson, Irene O. Lee, Faisal Albasu, Vasilii Borisov, and Mikhail Ronkin. 2025. "Time Series Classification of Autism Spectrum Disorder Using the Light-Adapted Electroretinogram" Bioengineering 12, no. 9: 951. https://doi.org/10.3390/bioengineering12090951
APA StyleChistiakov, S., Dolganov, A., Constable, P. A., Zhdanov, A., Kulyabin, M., Thompson, D. A., Lee, I. O., Albasu, F., Borisov, V., & Ronkin, M. (2025). Time Series Classification of Autism Spectrum Disorder Using the Light-Adapted Electroretinogram. Bioengineering, 12(9), 951. https://doi.org/10.3390/bioengineering12090951