A Topological Machine Learning Pipeline for Classification

In this work, we develop a pipeline that associates Persistence Diagrams to digital data via the most appropriate filtration for the type of data considered. Using a grid search approach, this pipeline determines optimal representation methods and parameters. The development of such a topological pipeline for Machine Learning involves two crucial steps that strongly affect its performance: firstly, digital data must be represented as an algebraic object with a proper associated filtration in order to compute its topological summary, the Persistence Diagram. Secondly, the persistence diagram must be transformed with suitable representation methods in order to be introduced in a Machine Learning algorithm. We assess the performance of our pipeline, and in parallel, we compare the different representation methods on popular benchmark datasets. This work is a first step toward both an easy and ready-to-use pipeline for data classification using persistent homology and Machine Learning, and to understand the theoretical reasons why, given a dataset and a task to be performed, a pair (filtration, topological representation) is better than another.

Alzheimer Disease Detection from Raman Spectroscopy of the Cerebrospinal Fluid via Topological Machine Learning

The cerebrospinal fluid (CSF) of 19 subjects who received a clinical diagnosis of Alzheimer's disease (AD) as well as of 5 pathological controls have been collected and analysed by Raman spectroscopy (RS). We investigated whether the raw and preprocessed Raman spectra could be used to distinguish AD from controls. First, we applied standard Machine Learning (ML) methods obtaining unsatisfactory results. Then, we applied ML to a set of topological descriptors extracted from raw spectra, achieving a very good classification accuracy (>87%). Although our results are preliminary, they indicate that RS and topological analysis together may provide an effective combination to confirm or disprove a clinical diagnosis of AD. The next steps will include enlarging the dataset of CSF samples to validate the proposed method better and, possibly, to understand if topological data analysis could support the characterization of AD subtypes.

Are We Using Autoencoders in a Wrong Way?

Autoencoders are certainly among the most studied and used Deep Learning models: the idea behind them is to train a model in order to reconstruct the same input data. The peculiarity of these models is to compress the information through a bottleneck, creating what is called Latent Space. Autoencoders are generally used for dimensionality reduction, anomaly detection and feature extraction. These models have been extensively studied and updated, given their high simplicity and power. Examples are (i) the Denoising Autoencoder, where the model is trained to reconstruct an image from a noisy one; (ii) Sparse Autoencoder, where the bottleneck is created by a regularization term in the loss function; (iii) Variational Autoencoder, where the latent space is used to generate new consistent data. In this article, we revisited the standard training for the undercomplete Autoencoder modifying the shape of the latent space without using any explicit regularization term in the loss function. We forced the model to reconstruct not the same observation in input, but another one sampled from the same class distribution. We also explored the behaviour of the latent space in the case of reconstruction of a random sample from the whole dataset.

High Dynamic Range Imaging via Visual Attention Modules

Thanks to High Dynamic Range (HDR) imaging methods, the scope of photography has seen profound changes recently. To be more specific, such methods try to reconstruct the lost luminosity of the real world caused by the limitation of regular cameras from the Low Dynamic Range (LDR) images. Additionally, although the State-Of-The-Art methods in this topic perform well, they mainly concentrate on combining different exposures and have less attention to extracting the informative parts of the images. Thus, this paper aims to introduce a new model capable of incorporating information from the most visible areas of each image extracted by a visual attention module (VAM), which is a result of a segmentation strategy. In particular, the model, based on a deep learning architecture, utilizes the extracted areas to produce the final HDR image. The results demonstrate that our method outperformed most of the State-Of-The-Art algorithms.

Supervised Image Segmentation for High Dynamic Range Imaging

Regular cameras and cell phones are able to capture limited luminosity. Thus, in terms of quality, most of the produced images from such devices are not similar to the real world. They are overly dark or too bright, and the details are not perfectly visible. Various methods, which fall under the name of High Dynamic Range (HDR) Imaging, can be utilised to cope with this problem. Their objective is to produce an image with more details. However, unfortunately, most methods for generating an HDR image from Multi-Exposure images only concentrate on how to combine different exposures and do not have any focus on choosing the best details of each image. Therefore, it is strived in this research to extract the most visible areas of each image with the help of image segmentation. Two methods of producing the Ground Truth were considered, as manual threshold and Otsu threshold, and a neural network will be used to train segment these areas. Finally, it will be shown that the neural network is able to segment the visible parts of pictures acceptably.

Efficient Adaptive Ensembling for Image Classification

In recent times, except for sporadic cases, the trend in Computer Vision is to achieve minor improvements over considerable increases in complexity. To reverse this tendency, we propose a novel method to boost image classification performances without an increase in complexity. To this end, we revisited ensembling, a powerful approach, not often adequately used due to its nature of increased complexity and training time, making it viable by specific design choices. First, we trained end-to-end two EfficientNet-b0 models (known to be the architecture with the best overall accuracy/complexity trade-off in image classification) on disjoint subsets of data (i.e. bagging). Then, we made an efficient adaptive ensemble by performing fine-tuning of a trainable combination layer. In this way, we were able to outperform the state-of-the-art by an average of 0.5\% on the accuracy with restrained complexity both in terms of number of parameters (by 5-60 times), and FLoating point Operations Per Second (by 10-100 times) on several major benchmark datasets, fully embracing the green AI.

From Human Mesenchymal Stromal Cells to Osteosarcoma Cells Classification by Deep Learning

Early diagnosis of cancer often allows for a more vast choice of therapy opportunities. After a cancer diagnosis, staging provides essential information about the extent of disease in the body and the expected response to a particular treatment. The leading importance of classifying cancer patients at the early stage into high or low-risk groups has led many research teams, both from the biomedical and bioinformatics field, to study the application of Deep Learning (DL) methods. The ability of DL to detect critical features from complex datasets is a significant achievement in early diagnosis and cell cancer progression. In this paper, we focus the attention on osteosarcoma. Osteosarcoma is one of the primary malignant bone tumors which usually afflicts people in adolescence. Our contribution to the classification of osteosarcoma cells is made as follows: a DL approach is applied to discriminate human Mesenchymal Stromal Cells (MSCs) from osteosarcoma cells and to classify the different cell populations under investigation. Glass slides of differ-ent cell populations were cultured including MSCs, differentiated in healthy bone cells (osteoblasts) and osteosarcoma cells, both single cell populations or mixed. Images of such samples of isolated cells (single-type of mixed) are recorded with traditional optical microscopy. DL is then applied to identify and classify single cells. Proper data augmentation techniques and cross-fold validation are used to appreciate the capabilities of a convolutional neural network to address the cell detection and classification problem. Based on the results obtained on individual cells, and to the versatility and scalability of our DL approach, the next step will be its application to discriminate and classify healthy or cancer tissues to advance digital pathology.