1D-Convolutional transformer for Parkinson disease diagnosis from gait

This paper presents an efficient deep neural network model for diagnosing Parkinson's disease from gait. More specifically, we introduce a hybrid ConvNet-Transformer architecture to accurately diagnose the disease by detecting the severity stage. The proposed architecture exploits the strengths of both Convolutional Neural Networks and Transformers in a single end-to-end model, where the former is able to extract relevant local features from Vertical Ground Reaction Force (VGRF) signal, while the latter allows to capture long-term spatio-temporal dependencies in data. In this manner, our hybrid architecture achieves an improved performance compared to using either models individually. Our experimental results show that our approach is effective for detecting the different stages of Parkinson's disease from gait data, with a final accuracy of 88%, outperforming other state-of-the-art AI methods on the Physionet gait dataset. Moreover, our method can be generalized and adapted for other classification problems to jointly address the feature relevance and spatio-temporal dependency problems in 1D signals. Our source code and pre-trained models are publicly available at https://github.com/SafwenNaimi/1D-Convolutional-transformer-for-Parkinson-disease-diagnosis-from-gait.

Automating lichen monitoring in ecological studies using instance segmentation of time-lapse images

Lichens are symbiotic organisms composed of fungi, algae, and/or cyanobacteria that thrive in a variety of environments. They play important roles in carbon and nitrogen cycling, and contribute directly and indirectly to biodiversity. Ecologists typically monitor lichens by using them as indicators to assess air quality and habitat conditions. In particular, epiphytic lichens, which live on trees, are key markers of air quality and environmental health. A new method of monitoring epiphytic lichens involves using time-lapse cameras to gather images of lichen populations. These cameras are used by ecologists in Newfoundland and Labrador to subsequently analyze and manually segment the images to determine lichen thalli condition and change. These methods are time-consuming and susceptible to observer bias. In this work, we aim to automate the monitoring of lichens over extended periods and to estimate their biomass and condition to facilitate the task of ecologists. To accomplish this, our proposed framework uses semantic segmentation with an effective training approach to automate monitoring and biomass estimation of epiphytic lichens on time-lapse images. We show that our method has the potential to significantly improve the accuracy and efficiency of lichen population monitoring, making it a valuable tool for forest ecologists and environmental scientists to evaluate the impact of climate change on Canada's forests. To the best of our knowledge, this is the first time that such an approach has been used to assist ecologists in monitoring and analyzing epiphytic lichens.

HCT: Hybrid Convnet-Transformer for Parkinson's disease detection and severity prediction from gait

In this paper, we propose a novel deep learning method based on a new Hybrid ConvNet-Transformer architecture to detect and stage Parkinson's disease (PD) from gait data. We adopt a two-step approach by dividing the problem into two sub-problems. Our Hybrid ConvNet-Transformer model first distinguishes healthy versus parkinsonian patients. If the patient is parkinsonian, a multi-class Hybrid ConvNet-Transformer model determines the Hoehn and Yahr (H&Y) score to assess the PD severity stage. Our hybrid architecture exploits the strengths of both Convolutional Neural Networks (ConvNets) and Transformers to accurately detect PD and determine the severity stage. In particular, we take advantage of ConvNets to capture local patterns and correlations in the data, while we exploit Transformers for handling long-term dependencies in the input signal. We show that our hybrid method achieves superior performance when compared to other state-of-the-art methods, with a PD detection accuracy of 97% and a severity staging accuracy of 87%. Our source code is available at: https://github.com/SafwenNaimi

Hybrid BYOL-ViT: Efficient approach to deal with small datasets

Supervised learning can learn large representational spaces, which are crucial for handling difficult learning tasks. However, due to the design of the model, classical image classification approaches struggle to generalize to new problems and new situations when dealing with small datasets. In fact, supervised learning can lose the location of image features which leads to supervision collapse in very deep architectures. In this paper, we investigate how self-supervision with strong and sufficient augmentation of unlabeled data can train effectively the first layers of a neural network even better than supervised learning, with no need for millions of labeled data. The main goal is to disconnect pixel data from annotation by getting generic task-agnostic low-level features. Furthermore, we look into Vision Transformers (ViT) and show that the low-level features derived from a self-supervised architecture can improve the robustness and the overall performance of this emergent architecture. We evaluated our method on one of the smallest open-source datasets STL-10 and we obtained a significant boost of performance from 41.66% to 83.25% when inputting low-level features from a self-supervised learning architecture to the ViT instead of the raw images.

Hybrid BYOL-ViT: Efficient approach to deal with small Datasets

Supervised learning can learn large representational spaces, which are crucial for handling difficult learning tasks. However, due to the design of the model, classical image classification approaches struggle to generalize to new problems and new situations when dealing with small datasets. In fact, supervised learning can lose the location of image features which leads to supervision collapse in very deep architectures. In this paper, we investigate how self-supervision with strong and sufficient augmentation of unlabeled data can train effectively the first layers of a neural network even better than supervised learning, with no need for millions of labeled data. The main goal is to disconnect pixel data from annotation by getting generic task-agnostic low-level features. Furthermore, we look into Vision Transformers (ViT) and show that the low-level features derived from a self-supervised architecture can improve the robustness and the overall performance of this emergent architecture. We evaluated our method on one of the smallest open-source datasets STL-10 and we obtained a significant boost of performance from 41.66% to 83.25% when inputting low-level features from a self-supervised learning architecture to the ViT instead of the raw images.