Detecting Rare Cell Populations in Flow Cytometry Data Using UMAP

Lisa Weijler, Markus Diem, Michael Reiter

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Auto-TLDR; Unsupervised Manifold Approximation and Projection for Small Cell Population Detection in Flow cytometry Data

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We present an approach for detecting small cell populations in flow cytometry (FCM) samples based on the combination of unsupervised manifold embedding and supervised random forest classification. Each sample consists of hundred thousands to a few million cells where each cell typically corresponds to a measurement vector with 10 to 50 dimensions. The difficulty of the task is that clusters of measurement vectors formed in the data space according to standard clustering criteria often do not correspond to biologically meaningful sub-populations of cells, due to strong variations in shape and size of their distributions. In many cases the relevant population consists of less than 100 scattered events out of millions of events, where supervised approaches perform better than unsupervised clustering. The aim of this paper is to demonstrate that the performance of the standard supervised classifier can be improved significantly by combining it with a preceding unsupervised learning step involving the Uniform Manifold Approximation and Projection (UMAP). We present an experimental evaluation on FCM data from children suffering from Acute Lymphoblastic Leukemia (ALL) showing that the improvement particularly occurs in difficult samples where the size of the relevant population of leukemic cells is low in relation to other sub-populations. Further, the experiments indicate that on such samples the algorithm also outperforms other baseline methods based on Gaussian Mixture Models.

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N2D: (Not Too) Deep Clustering Via Clustering the Local Manifold of an Autoencoded Embedding

Ryan Mcconville, Raul Santos-Rodriguez, Robert Piechocki, Ian Craddock

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Auto-TLDR; Local Manifold Learning for Deep Clustering on Autoencoded Embeddings

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Deep clustering has increasingly been demonstrating superiority over conventional shallow clustering algorithms. Deep clustering algorithms usually combine representation learning with deep neural networks to achieve this performance, typically optimizing a clustering and non-clustering loss. In such cases, an autoencoder is typically connected with a clustering network, and the final clustering is jointly learned by both the autoencoder and clustering network. Instead, we propose to learn an autoencoded embedding and then search this further for the underlying manifold. For simplicity, we then cluster this with a shallow clustering algorithm, rather than a deeper network. We study a number of local and global manifold learning methods on both the raw data and autoencoded embedding, concluding that UMAP in our framework is able to find the best clusterable manifold of the embedding. This suggests that local manifold learning on an autoencoded embedding is effective for discovering higher quality clusters. We quantitatively show across a range of image and time-series datasets that our method has competitive performance against the latest deep clustering algorithms, including out-performing current state-of-the-art on several. We postulate that these results show a promising research direction for deep clustering. The code can be found at https://github.com/rymc/n2d.

Q-SNE: Visualizing Data Using Q-Gaussian Distributed Stochastic Neighbor Embedding

Motoshi Abe, Junichi Miyao, Takio Kurita

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Auto-TLDR; Q-Gaussian distributed stochastic neighbor embedding for 2-dimensional mapping and classification

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The dimensionality reduction has been widely introduced to use the high-dimensional data for regression, classification, feature analysis, and visualization. As the one technique of dimensionality reduction, a stochastic neighbor embedding (SNE) was introduced. The SNE leads powerful results to visualize high-dimensional data by considering the similarity between the local Gaussian distributions of high and low-dimensional space. To improve the SNE, a t-distributed stochastic neighbor embedding (t-SNE) was also introduced. To visualize high-dimensional data, the t-SNE leads to more powerful and flexible visualization on 2 or 3-dimensional mapping than the SNE by using a t-distribution as the distribution of low-dimensional data. Recently, Uniform manifold approximation and projection (UMAP) is proposed as a dimensionality reduction technique. We present a novel technique called a q-Gaussian distributed stochastic neighbor embedding (q-SNE). The q-SNE leads to more powerful and flexible visualization on 2 or 3-dimensional mapping than the t-SNE and the SNE by using a q-Gaussian distribution as the distribution of low-dimensional data. The q-Gaussian distribution includes the Gaussian distribution and the t-distribution as the special cases with q=1.0 and q=2.0. Therefore, the q-SNE can also express the t-SNE and the SNE by changing the parameter q, and this makes it possible to find the best visualization by choosing the parameter q. We show the performance of q-SNE as visualization on 2-dimensional mapping and classification by k-Nearest Neighbors (k-NN) classifier in embedded space compared with SNE, t-SNE, and UMAP by using the datasets MNIST, COIL-20, OlivettiFaces, FashionMNIST, and Glove.

Automatic Classification of Human Granulosa Cells in Assisted Reproductive Technology Using Vibrational Spectroscopy Imaging

Marina Paolanti, Emanuele Frontoni, Giorgia Gioacchini, Giorgini Elisabetta, Notarstefano Valentina, Zacà Carlotta, Carnevali Oliana, Andrea Borini, Marco Mameli

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Auto-TLDR; Predicting Oocyte Quality in Assisted Reproductive Technology Using Machine Learning Techniques

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In the field of reproductive technology, the biochemical composition of female gametes has been successfully investigated with the use of vibrational spectroscopy. Currently, in assistive reproductive technology (ART), there are no shared criteria for the choice of oocyte, and automatic classification methods for the best quality oocytes have not yet been applied. In this paper, considering the lack of criteria in Assisted Reproductive Technology (ART), we use Machine Learning (ML) techniques to predict oocyte quality for a successful pregnancy. To improve the chances of successful implantation and minimize any complications during the pregnancy, Fourier transform infrared microspectroscopy (FTIRM) analysis has been applied on granulosa cells (GCs) collected along with the oocytes during oocyte aspiration, as it is routinely done in ART, and specific spectral biomarkers were selected by multivariate statistical analysis. A proprietary biological reference dataset (BRD) was successfully collected to predict the best oocyte for a successful pregnancy. Personal health information are stored, maintained and backed up using a cloud computing service. Using a user-friendly interface, the user will evaluate whether or not the selected oocyte will have a positive result. This interface includes a dashboard for retrospective analysis, reporting, real-time processing, and statistical analysis. The experimental results are promising and confirm the efficiency of the method in terms of classification metrics: precision, recall, and F1-score (F1) measures.

Improved Time-Series Clustering with UMAP Dimension Reduction Method

Clément Pealat, Vincent Cheutet, Guillaume Bouleux

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Auto-TLDR; Time Series Clustering with UMAP as a Pre-processing Step

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Clustering is an unsupervised machine learning method giving insights on data without early knowledge. Classes of data are return by assembling similar elements together. Giving the increasing of the available data, this method is now applied in a lot of fields with various data types. Here, we propose to explore the case of time series clustering. Indeed, time series are one of the most classic data type, and are present in various fields such as medical or finance. This kind of data can be pre-processed by of dimension reduction methods, such as the recent UMAP algorithm. In this paper, a benchmark of time series clustering is created, comparing the results with and without UMAP as a pre-processing step. UMAP is used to enhance clustering results. For completeness, three different clustering algorithms and two different geometric representation for the time series (Classic Euclidean geometry, and Riemannian geometry on the Stiefel Manifold) are applied. The results are compared with and without UMAP as a pre-processing step on the databases available at UCR Time Series Classification Archive www.cs.ucr.edu/~eamonn/time_series_data/.

A Novel Random Forest Dissimilarity Measure for Multi-View Learning

Hongliu Cao, Simon Bernard, Robert Sabourin, Laurent Heutte

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Auto-TLDR; Multi-view Learning with Random Forest Relation Measure and Instance Hardness

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Multi-view learning is a learning task in which data is described by several concurrent representations. Its main challenge is most often to exploit the complementarities between these representations to help solve a classification/regression task. This is a challenge that can be met nowadays if there is a large amount of data available for learning. However, this is not necessarily true for all real-world problems, where data are sometimes scarce (e.g. problems related to the medical environment). In these situations, an effective strategy is to use intermediate representations based on the dissimilarities between instances. This work presents new ways of constructing these dissimilarity representations, learning them from data with Random Forest classifiers. More precisely, two methods are proposed, which modify the Random Forest proximity measure, to adapt it to the context of High Dimension Low Sample Size (HDLSS) multi-view classification problems. The second method, based on an Instance Hardness measurement, is significantly more accurate than other state-of-the-art measurements including the original RF Proximity measurement and the Large Margin Nearest Neighbor (LMNN) metric learning measurement.

On Learning Random Forests for Random Forest Clustering

Manuele Bicego, Francisco Escolano

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Auto-TLDR; Learning Random Forests for Clustering

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In this paper we study the poorly investigated problem of learning Random Forests for distance-based Random Forest clustering. We studied both classic schemes as well as alternative approaches, novel in this context. In particular, we investigated the suitability of Gaussian Density Forests, Random Forests specifically designed for density estimation. Further, we introduce a novel variant of Random Forest, based on an effective non parametric by-pass estimator of the Renyi entropy, which can be useful when the parametric assumption is too strict. An empirical evaluation involving different datasets and different RF-clustering strategies confirms that the learning step is crucial for RF-clustering. We also present a set of practical guidelines useful to determine the most suitable variant of RF-clustering according to the problem under examination.

Tensor Factorization of Brain Structural Graph for Unsupervised Classification in Multiple Sclerosis

Berardino Barile, Marzullo Aldo, Claudio Stamile, Françoise Durand-Dubief, Dominique Sappey-Marinier

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Auto-TLDR; A Fully Automated Tensor-based Algorithm for Multiple Sclerosis Classification based on Structural Connectivity Graph of the White Matter Network

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Analysis of longitudinal changes in brain diseases is essential for a better characterization of pathological processes and evaluation of the prognosis. This is particularly important in Multiple Sclerosis (MS) which is the first traumatic disease in young adults, with unknown etiology and characterized by complex inflammatory and degenerative processes leading to different clinical courses. In this work, we propose a fully automated tensor-based algorithm for the classification of MS clinical forms based on the structural connectivity graph of the white matter (WM) network. Using non-negative tensor factorization (NTF), we first focused on the detection of pathological patterns of the brain WM network affected by significant longitudinal variations. Second, we performed unsupervised classification of different MS phenotypes based on these longitudinal patterns, and finally, we used the latent factors obtained by the factorization algorithm to identify the most affected brain regions.

Deep Learning Based Sepsis Intervention: The Modelling and Prediction of Severe Sepsis Onset

Gavin Tsang, Xianghua Xie

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Auto-TLDR; Predicting Sepsis onset by up to six hours prior using a boosted cascading training methodology and adjustable margin hinge loss function

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Sepsis presents a significant challenge to healthcare providers during critical care scenarios such as within an intensive care unit. The prognosis of the onset of severe septic shock results in significant increases in mortality rate, length of stay and readmission rates. Continual advancements in health informatics data allows for applications within the machine learning field to predict sepsis onset in a timely manner, allowing for effective preventative intervention of severe septic shock. A novel deep learning application is proposed to provide effective prediction of sepsis onset by up to six hours prior, involving the use of novel concepts such as a boosted cascading training methodology and adjustable margin hinge loss function. The proposed methodology provides statistically significant improvements to that of current machine learning based modelling applications based off the Physionet Computing in Cardiology 2019 challenge. Results show test F1 scores of 0.420, a significant improvement of 0.281 as compared to the next best challenger results.

Supervised Feature Embedding for Classification by Learning Rank-Based Neighborhoods

Ghazaal Sheikhi, Hakan Altincay

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Auto-TLDR; Supervised Feature Embedding with Representation Learning of Rank-based Neighborhoods

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In feature embedding, the recovery of associated discriminative information in the reduced subspace is critical for downstream classifiers. In this study, a supervised feature embedding method is proposed inspired by the well-known word embedding technique, word2vec. Proposed embedding method is implemented as representative learning of rank-based neighborhoods. The notion of context words in word2vec is extended into neighboring instances within a given window. Neighborship is defined using ranks of instances rather than their values so that regions with different densities are captured properly. Each sample is represented by a unique one-hot vector whereas its neighbors are encoded by several two-hot vectors. The two-hot vectors are identical for neighboring samples of the same class. A feed-forward neural network with a continuous projection layer, then learns the mapping from one-hot vectors to multiple two-hot vectors. The hidden layer determines the reduced subspace for the train samples. The obtained transformation is then applied on test data to find a lower-dimensional representation. Proposed method is tested in classification problems on 10 UCI data sets. Experimental results confirm that the proposed method is effective in finding a discriminative representation of the features and outperforms several supervised embedding approaches in terms of classification performance.

Deep Convolutional Embedding for Digitized Painting Clustering

Giovanna Castellano, Gennaro Vessio

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Auto-TLDR; A Deep Convolutional Embedding Model for Clustering Artworks

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Clustering artworks is difficult because of several reasons. On one hand, recognizing meaningful patterns in accordance with domain knowledge and visual perception is extremely hard. On the other hand, the application of traditional clustering and feature reduction techniques to the highly dimensional pixel space can be ineffective. To address these issues, we propose to use a deep convolutional embedding model for digitized painting clustering, in which the task of mapping the input raw data to an abstract, latent space is jointly optimized with the task of finding a set of cluster centroids in this latent feature space. Quantitative and qualitative experimental results show the effectiveness of the proposed method. The model is also able to outperform other state-of-the-art deep clustering approaches to the same problem. The proposed method may be beneficial to several art-related tasks, particularly visual link retrieval and historical knowledge discovery in painting datasets.

Video Anomaly Detection by Estimating Likelihood of Representations

Yuqi Ouyang, Victor Sanchez

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Auto-TLDR; Video Anomaly Detection in the latent feature space using a deep probabilistic model

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Video anomaly detection is a challenging task not only because it involves solving many sub-tasks such as motion representation, object localization and action recognition, but also because it is commonly considered as an unsupervised learning problem that involves detecting outliers. Traditionally, solutions to this task have focused on the mapping between video frames and their low-dimensional features, while ignoring the spatial connections of those features. Recent solutions focus on analyzing these spatial connections by using hard clustering techniques, such as K-Means, or applying neural networks to map latent features to a general understanding, such as action attributes. In order to solve video anomaly in the latent feature space, we propose a deep probabilistic model to transfer this task into a density estimation problem where latent manifolds are generated by a deep denoising autoencoder and clustered by expectation maximization. Evaluations on several benchmarks datasets show the strengths of our model, achieving outstanding performance on challenging datasets.

The eXPose Approach to Crosslier Detection

Antonio Barata, Frank Takes, Hendrik Van Den Herik, Cor Veenman

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Auto-TLDR; EXPose: Crosslier Detection Based on Supervised Category Modeling

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Transit of wasteful materials within the European Union is highly regulated through a system of permits. Waste processing costs vary greatly depending on the waste category of a permit. Therefore, companies may have a financial incentive to allege transporting waste with erroneous categorisation. Our goal is to assist inspectors in selecting potentially manipulated permits for further investigation, making their task more effective and efficient. Due to data limitations, a supervised learning approach based on historical cases is not possible. Standard unsupervised approaches, such as outlier detection and data quality-assurance techniques, are not suited since we are interested in targeting non-random modifications in both category and category-correlated features. For this purpose we (1) introduce the concept of crosslier: an anomalous instance of a category which lies across other categories; (2) propose eXPose: a novel approach to crosslier detection based on supervised category modelling; and (3) present the crosslier diagram: a visualisation tool specifically designed for domain experts to easily assess crossliers. We compare eXPose against traditional outlier detection methods in various benchmark datasets with synthetic crossliers and show the superior performance of our method in targeting these instances.

How to Define a Rejection Class Based on Model Learning?

Sarah Laroui, Xavier Descombes, Aurelia Vernay, Florent Villiers, Francois Villalba, Eric Debreuve

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Auto-TLDR; An innovative learning strategy for supervised classification that is able, by design, to reject a sample as not belonging to any of the known classes

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In supervised classification, the learning process typically trains a classifier to optimize the accuracy of classifying data into the classes that appear in the learning set, and only them. While this framework fits many use cases, there are situations where the learning process is knowingly performed using a learning set that only represents the data that have been observed so far among a virtually unconstrained variety of possible samples. It is then crucial to define a classifier which has the ability to reject a sample, i.e., to classify it into a rejection class that has not been yet defined. Although obvious solutions can add this ability a posteriori to a classifier that has been learned classically, a better approach seems to directly account for this requirement in the classifier design. In this paper, we propose an innovative learning strategy for supervised classification that is able, by design, to reject a sample as not belonging to any of the known classes. For that, we rely on modeling each class as the combination of a probability density function (PDF) and a threshold that is computed with respect to the other classes. Several alternatives are proposed and compared in this framework. A comparison with straightforward approaches is also provided.

Dependently Coupled Principal Component Analysis for Bivariate Inversion Problems

Navdeep Dahiya, Yifei Fan, Samuel Bignardi, Tony Yezzi, Romeil Sandhu

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Auto-TLDR; Asymmetric Principal Component Analysis between Paired Data in an Asymmetric manner

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Principal Component Analysis (PCA) is a widely used technique for dimensionality reduction in various problem domains including data compression, image processing, visualization, exploratory data analysis, pattern recognition, time series prediction and machine learning. Often, data is presented in a correlated paired manner such there exists observable and correlated unobservable measurements. Unfortunately, traditional PCA techniques generally fail to optimally capture the leverageable correlations between such paired data as it does not yield a maximally correlated basis between the observable and unobservable counterparts. This instead is the objective of Canonical Correlation Analysis (and the more general Partial Least Squares methods); however, such techniques are still symmetric in maximizing correlation (covariance for PLSR) over all choices of basis for both datasets without differentiating between observable and unobservable variables (except for the regression phase of PLSR). Further, these methods deviate from PCA's formulation objective to minimize approximation error, seeking instead to maximize correlation or covariance. While these are sensible optimization objectives, they are not equivalent to error minimization. We therefore introduce a new method of leveraging PCA between paired datasets in an asymmetric manner which is optimal with respect to approximation error during training. We generate an asymmetrically paired basis for which we relax orthogonality constraints on the orthogonality in decomposing unreliable unobservable measurements. In doing so, this allows us to optimally capture the variations of the observable data while conditionally minimizing the expected prediction error for the unobservable component. We show preliminary results that demonstrate improved learning of our proposed method compared to that of traditional techniques.

GazeMAE: General Representations of Eye Movements Using a Micro-Macro Autoencoder

Louise Gillian C. Bautista, Prospero Naval

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Auto-TLDR; Fast and Slow Eye Movement Representations for Sentiment-agnostic Eye Tracking

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Eye movements are intricate and dynamic events that contain a wealth of information about the subject and the stimuli. We propose an abstract representation of eye movements that preserve the important nuances in gaze behavior while being stimuli-agnostic. We consider eye movements as raw position and velocity signals and train a deep temporal convolutional autoencoder to learn micro-scale and macro-scale representations corresponding to the fast and slow features of eye movements. These joint representations are evaluated by fitting a linear classifier on various tasks and outperform other works in biometrics and stimuli classification. Further experiments highlight the validity and generalizability of this method, bringing eye tracking research closer to real-world applications.

Automatic Tuberculosis Detection Using Chest X-Ray Analysis with Position Enhanced Structural Information

Hermann Jepdjio Nkouanga, Szilard Vajda

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Auto-TLDR; Automatic Chest X-ray Screening for Tuberculosis in Rural Population using Localized Region on Interest

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For Tuberculosis (TB) detection beside the more expensive diagnosis solutions such as culture or sputum smear analysis one could consider the automatic analysis of the chest X-ray (CXR). This could mimic the lung region reading by the radiologist and it could provide a cheap solution to analyze and diagnose pulmonary abnormalities such as TB which often co- occurs with HIV. This software based pulmonary screening can be a reliable and affordable solution for rural population in different parts of the world such as India, Africa, etc. Our fully automatic system is processing the incoming CXR image by applying image processing techniques to detect the region on interest (ROI) followed by a computationally cheap feature extraction involving edge detection using Laplacian of Gaussian which we enrich by counting the local distribution of the intensities. The choice to ”zoom in” the ROI and look for abnormalities locally is motivated by the fact that some pulmonary abnormalities are localized in specific regions of the lungs. Later on the classifiers can decide about the normal or abnormal nature of each lung X-ray. Our goal is to find a simple feature, instead of a combination of several ones, -proposed and promoted in recent years’ literature, which can properly describe the different pathological alterations in the lungs. Our experiments report results on two publicly available data collections1, namely the Shenzhen and the Montgomery collection. For performance evaluation, measures such as area under the curve (AUC), and accuracy (ACC) were considered, achieving AUC = 0.81 (ACC = 83.33%) and AUC = 0.96 (ACC = 96.35%) for the Montgomery and Schenzen collections, respectively. Several comparisons are also provided to other state- of-the-art systems reported recently in the field.

Fused 3-Stage Image Segmentation for Pleural Effusion Cell Clusters

Sike Ma, Meng Zhao, Hao Wang, Fan Shi, Xuguo Sun, Shengyong Chen, Hong-Ning Dai

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Auto-TLDR; Coarse Segmentation of Stained and Stained Unstained Cell Clusters in pleural effusion using 3-stage segmentation method

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The appearance of tumor cell clusters in pleural effusion is usually a vital sign of cancer metastasis. Segmentation, as an indispensable basis, is of crucial importance for diagnosing, chemical treatment, and prognosis in patients. However, accurate segmentation of unstained cell clusters containing more detailed features than the fluorescent staining images remains to be a challenging problem due to the complex background and the unclear boundary. Therefore, in this paper, we propose a fused 3-stage image segmentation algorithm, namely Coarse segmentation-Mapping-Fine segmentation (CMF) to achieve unstained cell clusters from whole slide images. Firstly, we establish a tumor cell cluster dataset consisting of 107 sets of images, with each set containing one unstained image, one stained image, and one ground-truth image. Then, according to the features of the unstained and stained cell clusters, we propose a three-stage segmentation method: 1) Coarse segmentation on stained images to extract suspicious cell regions-Region of Interest (ROI); 2) Mapping this ROI to the corresponding unstained image to get the ROI of the unstained image (UI-ROI); 3) Fine Segmentation using improved automatic fuzzy clustering framework (AFCF) on the UI-ROI to get precise cell cluster boundaries. Experimental results on 107 sets of images demonstrate that the proposed algorithm can achieve better performance on unstained cell clusters with an F1 score of 90.40%.

Adversarial Encoder-Multi-Task-Decoder for Multi-Stage Processes

Andre Mendes, Julian Togelius, Leandro Dos Santos Coelho

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Auto-TLDR; Multi-Task Learning and Semi-Supervised Learning for Multi-Stage Processes

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In multi-stage processes, decisions occur in an ordered sequence of stages. Early stages usually have more observations with general information (easier/cheaper to collect), while later stages have fewer observations but more specific data. This situation can be represented by a dual funnel structure, in which the sample size decreases from one stage to the other while the information increases. Training classifiers in this scenario is challenging since information in the early stages may not contain distinct patterns to learn (underfitting). In contrast, the small sample size in later stages can cause overfitting. We address both cases by introducing a framework that combines adversarial autoencoders (AAE), multi-task learning (MTL), and multi-label semi-supervised learning (MLSSL). We improve the decoder of the AAE with an MTL component so it can jointly reconstruct the original input and use feature nets to predict the features for the next stages. We also introduce a sequence constraint in the output of an MLSSL classifier to guarantee the sequential pattern in the predictions. Using real-world data from different domains (selection process, medical diagnosis), we show that our approach outperforms other state-of-the-art methods.

Hierarchical Routing Mixture of Experts

Wenbo Zhao, Yang Gao, Shahan Ali Memon, Bhiksha Raj, Rita Singh

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Auto-TLDR; A Binary Tree-structured Hierarchical Routing Mixture of Experts for Regression

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In regression tasks the distribution of the data is often too complex to be fitted by a single model. In contrast, partition-based models are developed where data is divided and fitted by local models. These models partition the input space and do not leverage the input-output dependency of multimodal-distributed data, and strong local models are needed to make good predictions. Addressing these problems, we propose a binary tree-structured hierarchical routing mixture of experts (HRME) model that has classifiers as non-leaf node experts and simple regression models as leaf node experts. The classifier nodes jointly soft-partition the input-output space based on the natural separateness of multimodal data. This enables simple leaf experts to be effective for prediction. Further, we develop a probabilistic framework for the HRME model, and propose a recursive Expectation-Maximization (EM) based algorithm to learn both the tree structure and the expert models. Experiments on a collection of regression tasks validate the effectiveness of our method compared to a variety of other regression models.

Attack-Agnostic Adversarial Detection on Medical Data Using Explainable Machine Learning

Matthew Watson, Noura Al Moubayed

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Auto-TLDR; Explainability-based Detection of Adversarial Samples on EHR and Chest X-Ray Data

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Explainable machine learning has become increasingly prevalent, especially in healthcare where explainable models are vital for ethical and trusted automated decision making. Work on the susceptibility of deep learning models to adversarial attacks has shown the ease of designing samples to mislead a model into making incorrect predictions. In this work, we propose an explainability-based method for the accurate detection of adversarial samples on two datasets with different complexity and properties: Electronic Health Record (EHR) and chest X-ray (CXR) data. On the MIMIC-III and Henan-Renmin EHR datasets, we report a detection accuracy of 77% against the Longitudinal Adversarial Attack. On the MIMIC-CXR dataset, we achieve an accuracy of 88%; significantly improving on the state of the art of adversarial detection in both datasets by over 10% in all settings. We propose an anomaly detection based method using explainability techniques to detect adversarial samples which is able to generalise to different attack methods without a need for retraining.

Inferring Functional Properties from Fluid Dynamics Features

Andrea Schillaci, Maurizio Quadrio, Carlotta Pipolo, Marcello Restelli, Giacomo Boracchi

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Auto-TLDR; Exploiting Convective Properties of Computational Fluid Dynamics for Medical Diagnosis

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In a wide range of applied problems involving fluid flows, Computational Fluid Dynamics (CFD) provides detailed quantitative information on the flow field, at various levels of fidelity and computational cost. However, CFD alone cannot predict high-level functional properties of the system that are not easily obtained from the equations of fluid motion. In this work, we present a data-driven framework to extract additional information, such as medical diagnostic output, from CFD solutions. The task is made difficult by the huge data dimensionality of CFD, together with the limited amount of training data implied by its high computational cost. By pursuing a traditional ML pipeline of pre-processing, feature extraction, and model training, we demonstrate that informative features can be extracted from CFD data. Two experiments, pertaining to different application domains, support the claim that the convective properties implicit into a CFD solution can be leveraged to retrieve functional information for which an analytical definition is missing. Despite the preliminary nature of our study and the relative simplicity of both the geometrical and CFD models, for the first time we demonstrate that the combination of ML and CFD can diagnose a complex system in terms of high-level functional information.

Generative Deep-Neural-Network Mixture Modeling with Semi-Supervised MinMax+EM Learning

Nilay Pande, Suyash Awate

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Auto-TLDR; Semi-supervised Deep Neural Networks for Generative Mixture Modeling and Clustering

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Deep neural networks (DNNs) for generative mixture modeling typically rely on unsupervised learning that employs hard clustering schemes, or variational learning with loose / approximate bounds, or under-regularized modeling. We propose a novel statistical framework for a DNN mixture model using a single generative adversarial network. Our learning formulation proposes a novel data-likelihood term relying on a well-regularized / constrained Gaussian mixture model in the latent space along with a prior term on the DNN weights. Our min-max learning increases the data likelihood using a tight variational lower bound using expectation maximization (EM). We leverage our min-max EM learning scheme for semi-supervised learning. Results on three real-world datasets demonstrate the benefits of our compact modeling and learning formulation over the state of the art for mixture modeling and clustering.

Using Machine Learning to Refer Patients with Chronic Kidney Disease to Secondary Care

Lee Au-Yeung, Xianghua Xie, Timothy Marcus Scale, James Anthony Chess

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Auto-TLDR; A Machine Learning Approach for Chronic Kidney Disease Prediction using Blood Test Data

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There has been growing interest recently in using machine learning techniques as an aid in clinical medicine. Machine learning offers a range of classification algorithms which can be applied to medical data to aid in making clinical predictions. Recent studies have demonstrated the high predictive accuracy of various classification algorithms applied to clinical data. Several studies have already been conducted in diagnosing or predicting chronic kidney disease at various stages using different sets of variables. In this study we are investigating the use machine learning techniques with blood test data. Such a system could aid renal teams in making recommendations to primary care general practitioners to refer patients to secondary care where patients may benefit from earlier specialist assessment and medical intervention. We are able to achieve an overall accuracy of 88.48\% using logistic regression, 87.12\% using ANN and 85.29\% using SVM. ANNs performed with the highest sensitivity at 89.74\% compared to 86.67\% for logistic regression and 85.51\% for SVM.

A Comparison of Neural Network Approaches for Melanoma Classification

Maria Frasca, Michele Nappi, Michele Risi, Genoveffa Tortora, Alessia Auriemma Citarella

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Auto-TLDR; Classification of Melanoma Using Deep Neural Network Methodologies

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Melanoma is the deadliest form of skin cancer and it is diagnosed mainly visually, starting from initial clinical screening and followed by dermoscopic analysis, biopsy and histopathological examination. A dermatologist’s recognition of melanoma may be subject to errors and may take some time to diagnose it. In this regard, deep learning can be useful in the study and classification of skin cancer. In particular, by classifying images with Deep Neural Network methodologies, it is possible to obtain comparable or even superior results compared to those of dermatologists. In this paper, we propose a methodology for the classification of melanoma by adopting different deep learning techniques applied to a common dataset, composed of images from the ISIC dataset and consisting of different types of skin diseases, including melanoma on which we applied a specific pre-processing phase. In particular, a comparison of the results is performed in order to select the best effective neural network to be applied to the problem of recognition and classification of melanoma. Moreover, we also evaluate the impact of the pre- processing phase on the final classification. Different metrics such as accuracy, sensitivity, and specificity have been selected to assess the goodness of the adopted neural networks and compare them also with the manual classification of dermatologists.

Dealing with Scarce Labelled Data: Semi-Supervised Deep Learning with Mix Match for Covid-19 Detection Using Chest X-Ray Images

Saúl Calderón Ramirez, Raghvendra Giri, Shengxiang Yang, Armaghan Moemeni, Mario Umaña, David Elizondo, Jordina Torrents-Barrena, Miguel A. Molina-Cabello

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Auto-TLDR; Semi-supervised Deep Learning for Covid-19 Detection using Chest X-rays

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Coronavirus (Covid-19) is spreading fast, infecting people through contact in various forms including droplets from sneezing and coughing. Therefore, the detection of infected subjects in an early, quick and cheap manner is urgent. Currently available tests are scarce and limited to people in danger of serious illness. The application of deep learning to chest X-ray images for Covid-19 detection is an attractive approach. However, this technology usually relies on the availability of large labelled datasets, a requirement hard to meet in the context of a virus outbreak. To overcome this challenge, a semi-supervised deep learning model using both labelled and unlabelled data is proposed. We developed and tested a semi-supervised deep learning framework based on the Mix Match architecture to classify chest X-rays into Covid-19, pneumonia and healthy cases. The presented approach was calibrated using two publicly available datasets. The results show an accuracy increase of around $15\%$ under low labelled / unlabelled data ratio. This indicates that our semi-supervised framework can help improve performance levels towards Covid-19 detection when the amount of high-quality labelled data is scarce. Also, we introduce a semi-supervised deep learning boost coefficient which is meant to ease the scalability of our approach and performance comparison.

A Novel Adaptive Minority Oversampling Technique for Improved Classification in Data Imbalanced Scenarios

Ayush Tripathi, Rupayan Chakraborty, Sunil Kumar Kopparapu

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Auto-TLDR; Synthetic Minority OverSampling Technique for Imbalanced Data

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Imbalance in the proportion of training samples belonging to different classes often poses performance degradation of conventional classifiers. This is primarily due to the tendency of the classifier to be biased towards the majority classes in the imbalanced dataset. In this paper, we propose a novel three step technique to address imbalanced data. As a first step we significantly oversample the minority class distribution by employing the traditional Synthetic Minority OverSampling Technique (SMOTE) algorithm using the neighborhood of the minority class samples and in the next step we partition the generated samples using a Gaussian-Mixture Model based clustering algorithm. In the final step synthetic data samples are chosen based on the weight associated with the cluster, the weight itself being determined by the distribution of the majority class samples. Extensive experiments on several standard datasets from diverse domains show the usefulness of the proposed technique in comparison with the original SMOTE and its state-of-the-art variants algorithms.

Supervised Domain Adaptation Using Graph Embedding

Lukas Hedegaard, Omar Ali Sheikh-Omar, Alexandros Iosifidis

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Auto-TLDR; Domain Adaptation from the Perspective of Multi-view Graph Embedding and Dimensionality Reduction

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Getting deep convolutional neural networks to perform well requires a large amount of training data. When the available labelled data is small, it is often beneficial to use transfer learning to leverage a related larger dataset (source) in order to improve the performance on the small dataset (target). Among the transfer learning approaches, domain adaptation methods assume that distributions between the two domains are shifted and attempt to realign them. In this paper, we consider the domain adaptation problem from the perspective of multi-view graph embedding and dimensionality reduction. Instead of solving the generalised eigenvalue problem to perform the embedding, we formulate the graph-preserving criterion as loss in the neural network and learn a domain-invariant feature transformation in an end-to-end fashion. We show that the proposed approach leads to a powerful Domain Adaptation framework which generalises the prior methods CCSA and d-SNE, and enables simple and effective loss designs; an LDA-inspired instantiation of the framework leads to performance on par with the state-of-the-art on the most widely used Domain Adaptation benchmarks, Office31 and MNIST to USPS datasets.

3D Facial Matching by Spiral Convolutional Metric Learning and a Biometric Fusion-Net of Demographic Properties

Soha Sadat Mahdi, Nele Nauwelaers, Philip Joris, Giorgos Bouritsas, Imperial London, Sergiy Bokhnyak, Susan Walsh, Mark Shriver, Michael Bronstein, Peter Claes

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Auto-TLDR; Multi-biometric Fusion for Biometric Verification using 3D Facial Mesures

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Face recognition is a widely accepted biometric verification tool, as the face contains a lot of information about the identity of a person. In this study, a 2-step neural-based pipeline is presented for matching 3D facial shape to multiple DNA-related properties (sex, age, BMI and genomic background). The first step consists of a triplet loss-based metric learner that compresses facial shape into a lower dimensional embedding while preserving information about the property of interest. Most studies in the field of metric learning have only focused on Euclidean data. In this work, geometric deep learning is employed to learn directly from 3D facial meshes. To this end, spiral convolutions are used along with a novel mesh-sampling scheme that retains uniformly sampled 3D points at different levels of resolution. The second step is a multi-biometric fusion by a fully connected neural network. The network takes an ensemble of embeddings and property labels as input and returns genuine and imposter scores. Since embeddings are accepted as an input, there is no need to train classifiers for the different properties and available data can be used more efficiently. Results obtained by a 10-fold cross-validation for biometric verification show that combining multiple properties leads to stronger biometric systems. Furthermore, the proposed neural-based pipeline outperforms a linear baseline, which consists of principal component analysis, followed by classification with linear support vector machines and a Naïve Bayes-based score-fuser.

Recursive Convolutional Neural Networks for Epigenomics

Aikaterini Symeonidi, Anguelos Nicolaou, Frank Johannes, Vincent Christlein

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Auto-TLDR; Recursive Convolutional Neural Networks for Epigenomic Data Analysis

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Deep learning for epigenomic data analysis has demonstrated to be very promising for analysis of genomic and epigenomic data. In this paper we introduce the use of Recursive Convolutional Neural Networks (RCNN) as tool for epigenomic data analysis. We focus on the task of predicting gene expression from the intensity of histone modifications. The proposed RCNN architecture can be applied on data of an arbitrary size and has a single meta-parameter that quantifies the models capacity making it flexible for experimenting. The proposed architecture outperforms state-of-the-art systems while having several orders of magnitude fewer parameters.

Supporting Skin Lesion Diagnosis with Content-Based Image Retrieval

Stefano Allegretti, Federico Bolelli, Federico Pollastri, Sabrina Longhitano, Giovanni Pellacani, Costantino Grana

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Auto-TLDR; Skin Images Retrieval Using Convolutional Neural Networks for Skin Lesion Classification and Segmentation

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Given the relevance of skin cancer, many attempts have been dedicated to the creation of automated devices that could assist both expert and beginner dermatologists towards fast and early diagnosis of skin lesions. In recent years, tasks such as skin lesion classification and segmentation have been extensively addressed with deep learning algorithms, which in some cases reach a diagnostic accuracy comparable to that of expert physicians. However, the general lack of interpretability and reliability severely hinders the ability of those approaches to actually support dermatologists in the diagnosis process. In this paper a novel skin images retrieval system is presented, which exploits features extracted by Convolutional Neural Networks to gather similar images from a publicly available dataset, in order to assist the diagnosis process of both expert and novice practitioners. In the proposed framework, Resnet-50 is initially trained for the classification of dermoscopic images; then, the feature extraction part is isolated, and an embedding network is build on top of it. The embedding learns an alternative representation, which allows to check image similarity by means of a distance measure. Experimental results reveal that the proposed method is able to select meaningful images, which can effectively boost the classification accuracy of human dermatologists.

Modeling the Distribution of Normal Data in Pre-Trained Deep Features for Anomaly Detection

Oliver Rippel, Patrick Mertens, Dorit Merhof

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Auto-TLDR; Deep Feature Representations for Anomaly Detection in Images

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Anomaly Detection (AD) in images is a fundamental computer vision problem and refers to identifying images and/or image substructures that deviate significantly from the norm. Popular AD algorithms commonly try to learn a model of normality from scratch using task specific datasets, but are limited to semi-supervised approaches employing mostly normal data due to the inaccessibility of anomalies on a large scale combined with the ambiguous nature of anomaly appearance. We follow an alternative approach and demonstrate that deep feature representations learned by discriminative models on large natural image datasets are well suited to describe normality and detect even subtle anomalies. Our model of normality is established by fitting a multivariate Gaussian to deep feature representations of classification networks trained on ImageNet using normal data only in a transfer learning setting. By subsequently applying the Mahalanobis distance as the anomaly score we outperform the current state of the art on the public MVTec AD dataset, achieving an Area Under the Receiver Operating Characteristic curve of 95.8 +- 1.2 % (mean +- SEM) over all 15 classes. We further investigate why the learned representations are discriminative to the AD task using Principal Component Analysis. We find that the principal components containing little variance in normal data are the ones crucial for discriminating between normal and anomalous instances. This gives a possible explanation to the often sub-par performance of AD approaches trained from scratch using normal data only. By selectively fitting a multivariate Gaussian to these most relevant components only, we are able to further reduce model complexity while retaining AD performance. We also investigate setting the working point by selecting acceptable False Positive Rate thresholds based on the multivariate Gaussian assumption.

Detecting Marine Species in Echograms Via Traditional, Hybrid, and Deep Learning Frameworks

Porto Marques Tunai, Alireza Rezvanifar, Melissa Cote, Alexandra Branzan Albu, Kaan Ersahin, Todd Mudge, Stephane Gauthier

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Auto-TLDR; End-to-End Deep Learning for Echogram Interpretation of Marine Species in Echograms

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This paper provides a comprehensive comparative study of traditional, hybrid, and deep learning (DL) methods for detecting marine species in echograms. Acoustic backscatter data obtained from multi-frequency echosounders is visualized as echograms and typically interpreted by marine biologists via manual or semi-automatic methods, which are time-consuming. Challenges related to automatic echogram interpretation are the variable size and acoustic properties of the biological targets (marine life), along with significant inter-class similarities. Our study explores and compares three types of approaches that cover the entire range of machine learning methods. Based on our experimental results, we conclude that an end-to-end DL-based framework, that can be readily scaled to accommodate new species, is overall preferable to other learning approaches for echogram interpretation, even when only a limited number of annotated training samples is available.

A Systematic Investigation on Deep Architectures for Automatic Skin Lesions Classification

Pierluigi Carcagni, Marco Leo, Andrea Cuna, Giuseppe Celeste, Cosimo Distante

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Auto-TLDR; RegNet: Deep Investigation of Convolutional Neural Networks for Automatic Classification of Skin Lesions

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Computer vision-based techniques are more and more employed in healthcare and medical fields nowadays in order, principally, to be as a support to the experienced medical staff to help them to make a quick and correct diagnosis. One of the hot topics in this arena concerns the automatic classification of skin lesions. Several promising works exist about it, mainly leveraging Convolutional Neural Networks (CNN), but proposed pipeline mainly rely on complex data preprocessing and there is no systematic investigation about how available deep models can actually reach the accuracy needed for real applications. In order to overcome these drawbacks, in this work, an end-to-end pipeline is introduced and some of the most recent Convolutional Neural Networks (CNNs) architectures are included in it and compared on the largest common benchmark dataset recently introduced. To this aim, for the first time in this application context, a new network design paradigm, namely RegNet, has been exploited to get the best models among a population of configurations. The paper introduces a threefold level of contribution and novelty with respect the previous literature: the deep investigation of several CNN architectures driving to a consistent improvement of the lesions recognition accuracy, the exploitation of a new network design paradigm able to study the behavior of populations of models and a deep discussion about pro and cons of each analyzed method paving the path towards new research lines.

Generative Latent Implicit Conditional Optimization When Learning from Small Sample

Idan Azuri, Daphna Weinshall

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Auto-TLDR; GLICO: Generative Latent Implicit Conditional Optimization for Small Sample Learning

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We revisit the long-standing problem of learning from small sample. The generation of new samples from a small training set of labeled points has attracted increased attention in recent years. In this paper, we propose a novel such method called GLICO (Generative Latent Implicit Conditional Optimization). GLICO learns a mapping from the training examples to a latent space and a generator that generates images from vectors in the latent space. Unlike most recent work, which rely on access to large amounts of unlabeled data, GLICO does not require access to any additional data other than the small set of labeled points. In fact, GLICO learns to synthesize completely new samples for every class using as little as 5 or 10 examples per class, with as few as 10 such classes and no data from unknown classes. GLICO is then used to augment the small training set while training a classifier on the small sample. To this end, our proposed method samples the learned latent space using spherical interpolation (slerp) and generates new examples using the trained generator. Empirical results show that the new sampled set is diverse enough, leading to improvement in image classification in comparison with the state of the art when trained on small samples obtained from CIFAR-10, CIFAR-100, and CUB-200.

A Deep Learning Approach for the Segmentation of Myocardial Diseases

Khawala Brahim, Abdull Qayyum, Alain Lalande, Arnaud Boucher, Anis Sakly, Fabrice Meriaudeau

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Auto-TLDR; Segmentation of Myocardium Infarction Using Late GADEMRI and SegU-Net

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Cardiac left ventricular (LV) segmentation is of paramount essential step for both diagnosis and treatment of cardiac pathologies such as ischemia, myocardial infarction, arrhythmia and myocarditis. However, this segmentation is challenging due to high variability across patients and the potential lack of contrast between structures. In this work, we propose and evaluate a (2.5D) SegU-Net model based on the fusion of two deep learning techniques (U-Net and Seg-Net) for automated LGEMRI (Late gadolinium enhanced magnetic resonance imaging) myocardial disease (infarct core and no reflow region) quantification in a new multifield expert annotated dataset. Given that the scar tissue represents a small part of the whole MRI slices, we focused on myocardium area. Segmentation results show that this preprocessing step facilitate the learning procedure. In order to solve the class imbalance problem, we propose to apply the Jaccard loss and the Focal Loss as optimization loss function and to integrate a class weights strategy into the objective function. Late combination has been used to merge the output of the best trained models on a different set of hyperparameters. The final network segmentation performances will be useful for future comparison of new method to the current related work for this task. A total number of 2237 of slices (320 cases) were used for training/validation and 210 slices (35 cases) were used for testing. Experiments over our proposed dataset, using several evaluation metrics such Jaccard distance (IOU), Accuracy and Dice similarity coefficient (DSC), demonstrate efficiency performance in quantifying different zones of myocardium infarction across various patients. As compared to the second intra-observer study, our testing results showed that the SegUNet prediction model leads to these average dice coefficients over all segmented tissue classes, respectively : 'Background': 0.99999, 'Myocardium': 0.99434, 'Infarctus': 0.95587, 'Noreflow': 0.78187.

Low Dimensional State Representation Learning with Reward-Shaped Priors

Nicolò Botteghi, Ruben Obbink, Daan Geijs, Mannes Poel, Beril Sirmacek, Christoph Brune, Abeje Mersha, Stefano Stramigioli

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Auto-TLDR; Unsupervised Learning for Unsupervised Reinforcement Learning in Robotics

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Reinforcement Learning has been able to solve many complicated robotics tasks without any need of feature engineering in an end-to-end fashion. However, learning the optimal policy directly from the sensory inputs, i.e the observations, often requires processing and storage of huge amount of data. In the context of robotics, the cost of data from real robotics hardware is usually very high, thus solutions that achieves high sample-efficiency are needed. We propose a method that aims at learning a mapping from the observations into a lower dimensional state space. This mapping is learned with unsupervised learning using loss functions shaped to incorporate prior knowledge of the environment and the task. Using the samples from the state space, the optimal policy is quickly and efficiently learned. We test the method on several mobile robot navigation tasks in simulation environment and also on a real robot.

Confidence Calibration for Deep Renal Biopsy Immunofluorescence Image Classification

Federico Pollastri, Juan Maroñas, Federico Bolelli, Giulia Ligabue, Roberto Paredes, Riccardo Magistroni, Costantino Grana

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Auto-TLDR; A Probabilistic Convolutional Neural Network for Immunofluorescence Classification in Renal Biopsy

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With this work we tackle immunofluorescence classification in renal biopsy, employing state-of-the-art Convolutional Neural Networks. In this setting, the aim of the probabilistic model is to assist an expert practitioner towards identifying the location pattern of antibody deposits within a glomerulus. Since modern neural networks often provide overconfident outputs, we stress the importance of having a reliable prediction, demonstrating that Temperature Scaling, a recently introduced re-calibration technique, can be successfully applied to immunofluorescence classification in renal biopsy. Experimental results demonstrate that the designed model yields good accuracy on the specific task, and that Temperature Scaling is able to provide reliable probabilities, which are highly valuable for such a task given the low inter-rater agreement.

Feature Extraction by Joint Robust Discriminant Analysis and Inter-Class Sparsity

Fadi Dornaika, Ahmad Khoder

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Auto-TLDR; Robust Discriminant Analysis with Feature Selection and Inter-class Sparsity (RDA_FSIS)

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Feature extraction methods have been successfully applied to many real-world applications. The classical Linear Discriminant Analysis (LDA) and its variants are widely used as feature extraction methods. Although they have been used for different classification tasks, these methods have some shortcomings. The main one is that the projection axes obtained are not informative about the relevance of original features. In this paper, we propose a linear embedding method that merges two interesting properties: Robust LDA and inter-class sparsity. Furthermore, the targeted projection transformation focuses on the most discriminant original features. The proposed method is called Robust Discriminant Analysis with Feature Selection and Inter-class Sparsity (RDA_FSIS). Two kinds of sparsity are explicitly included in the proposed model. The first kind is obtained by imposing the $\ell_{2,1}$ constraint on the projection matrix in order to perform feature ranking. The second kind is obtained by imposing the inter-class sparsity constraint used for getting a common sparsity structure in each class. Comprehensive experiments on five real-world image datasets demonstrate the effectiveness and advantages of our framework over existing linear methods.

A Joint Representation Learning and Feature Modeling Approach for One-Class Recognition

Pramuditha Perera, Vishal Patel

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Auto-TLDR; Combining Generative Features and One-Class Classification for Effective One-class Recognition

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One-class recognition is traditionally approached either as a representation learning problem or a feature modelling problem. In this work, we argue that both of these approaches have their own limitations; and a more effective solution can be obtained by combining the two. The proposed approach is based on the combination of a generative framework and a one-class classification method. First, we learn generative features using the one-class data with a generative framework. We augment the learned features with the corresponding reconstruction errors to obtain augmented features. Then, we qualitatively identify a suitable feature distribution that reduces the redundancy in the chosen classifier space. Finally, we force the augmented features to take the form of this distribution using an adversarial framework. We test the effectiveness of the proposed method on three one-class classification tasks and obtain state-of-the-art results.

Categorizing the Feature Space for Two-Class Imbalance Learning

Rosa Sicilia, Ermanno Cordelli, Paolo Soda

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Auto-TLDR; Efficient Ensemble of Classifiers for Minority Class Inference

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Class imbalance limits the performance of most learning algorithms, resulting in a low recognition rate for samples belonging to the minority class. Although there are different strategies to address this problem, methods that generate ensemble of classifiers have proven to be effective in several applications. This paper presents a new strategy to construct the training set of each classifier in the ensemble by exploiting information in the feature space that can give rise to unreliable classifications, which are determined by a novel algorithm here introduced. The performance of our proposal is compared against multiple standard ensemble approaches on 25 publicly available datasets, showing promising results.

Dimensionality Reduction for Data Visualization and Linear Classification, and the Trade-Off between Robustness and Classification Accuracy

Martin Becker, Jens Lippel, Thomas Zielke

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Auto-TLDR; Robustness Assessment of Deep Autoencoder for Data Visualization using Scatter Plots

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This paper has three intertwined goals. The first is to introduce a new similarity measure for scatter plots. It uses Delaunay triangulations to compare two scatter plots regarding their relative positioning of clusters. The second is to apply this measure for the robustness assessment of a recent deep neural network (DNN) approach to dimensionality reduction (DR) for data visualization. It uses a nonlinear generalization of Fisher's linear discriminant analysis (LDA) as the encoder network of a deep autoencoder (DAE). The DAE's decoder network acts as a regularizer. The third goal is to look at different variants of the DNN: ones that promise robustness and ones that promise high classification accuracies. This is to study the trade-off between these two objectives -- our results support the recent claim that robustness may be at odds with accuracy; however, results that are balanced regarding both objectives are achievable. We see a restricted Boltzmann machine (RBM) pretraining and the DAE based regularization as important building blocks for achieving balanced results. As a means of assessing the robustness of DR methods, we propose a measure that is based on our similarity measure for scatter plots. The robustness measure comes with a superimposition view of Delaunay triangulations, which allows a fast comparison of results from multiple DR methods.

Influence of Event Duration on Automatic Wheeze Classification

Bruno M Rocha, Diogo Pessoa, Alda Marques, Paulo Carvalho, Rui Pedro Paiva

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Auto-TLDR; Experimental Design of the Non-wheeze Class for Wheeze Classification

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Patients with respiratory conditions typically exhibit adventitious respiratory sounds, such as wheezes. Wheeze events have variable duration. In this work we studied the influence of event duration on wheeze classification, namely how the creation of the non-wheeze class affected the classifiers' performance. First, we evaluated several classifiers on an open access respiratory sound database, with the best one reaching sensitivity and specificity values of 98% and 95%, respectively. Then, by changing one parameter in the design of the non-wheeze class, i.e., event duration, the best classifier only reached sensitivity and specificity values of 53% and 75%, respectively. These results demonstrate the importance of experimental design on the assessment of wheeze classification algorithms' performance.

Deep Transformation Models: Tackling Complex Regression Problems with Neural Network Based Transformation Models

Beate Sick, Torsten Hothorn, Oliver Dürr

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Auto-TLDR; A Deep Transformation Model for Probabilistic Regression

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We present a deep transformation model for probabilistic regression. Deep learning is known for outstandingly accurate predictions on complex data but in regression tasks it is predominantly used to just predict a single number. This ignores the non-deterministic character of most tasks. Especially if crucial decisions are based on the predictions, like in medical applications, it is essential to quantify the prediction uncertainty. The presented deep learning transformation model estimates the whole conditional probability distribution, which is the most thorough way to capture uncertainty about the outcome. We combine ideas from a statistical transformation model (most likely transformation) with recent transformation models from deep learning (normalizing flows) to predict complex outcome distributions. The core of the method is a parameterized transformation function which can be trained with the usual maximum likelihood framework using gradient descent. The method can be combined with existing deep learning architectures. For small machine learning benchmark datasets, we report state of the art performance for most dataset and partly even outperform it. Our method works for complex input data, which we demonstrate by employing a CNN architecture on image data.

Local Clustering with Mean Teacher for Semi-Supervised Learning

Zexi Chen, Benjamin Dutton, Bharathkumar Ramachandra, Tianfu Wu, Ranga Raju Vatsavai

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Auto-TLDR; Local Clustering for Semi-supervised Learning

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The Mean Teacher (MT) model of Tarvainen and Valpola has shown favorable performance on several semi-supervised benchmark datasets. MT maintains a teacher model's weights as the exponential moving average of a student model's weights and minimizes the divergence between their probability predictions under diverse perturbations of the inputs. However, MT is known to suffer from confirmation bias, that is, reinforcing incorrect teacher model predictions. In this work, we propose a simple yet effective method called Local Clustering (LC) to mitigate the effect of confirmation bias. In MT, each data point is considered independent of other points during training; however, data points are likely to be close to each other in feature space if they share similar features. Motivated by this, we cluster data points locally by minimizing the pairwise distance between neighboring data points in feature space. Combined with a standard classification cross-entropy objective on labeled data points, the misclassified unlabeled data points are pulled towards high-density regions of their correct class with the help of their neighbors, thus improving model performance. We demonstrate on semi-supervised benchmark datasets SVHN and CIFAR-10 that adding our LC loss to MT yields significant improvements compared to MT and performance comparable to the state of the art in semi-supervised learning.

SAGE: Sequential Attribute Generator for Analyzing Glioblastomas Using Limited Dataset

Padmaja Jonnalagedda, Brent Weinberg, Jason Allen, Taejin Min, Shiv Bhanu, Bir Bhanu

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Auto-TLDR; SAGE: Generative Adversarial Networks for Imaging Biomarker Detection and Prediction

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While deep learning approaches have shown remarkable performance in many imaging tasks, most of these methods rely on availability of large quantities of data. Medical image data, however, is scarce and fragmented. Generative Adversarial Networks (GANs) have recently been very effective in handling such datasets by generating more data. If the datasets are very small, however, GANs cannot learn the data distribution properly, resulting in less diverse or low-quality results. One such limited dataset is that for the concurrent gain of 19/20 chromosomes (19/20 co-gain), a mutation with positive prognostic value in Glioblastomas (GBM). In this paper, we detect imaging biomarkers for the mutation to streamline the extensive and invasive prognosis pipeline. Since this mutation is relatively rare, i.e. small dataset, we propose a novel generative framework – the Sequential Attribute GEnerator (SAGE), that generates detailed tumor imaging features while learning from a limited dataset. Experiments show that not only does SAGE generate high quality tumors when compared to standard Deep Convolutional GAN (DC-GAN) and Wasserstein GAN with Gradient Penalty (WGAN-GP), it also captures the imaging biomarkers accurately.

Separation of Aleatoric and Epistemic Uncertainty in Deterministic Deep Neural Networks

Denis Huseljic, Bernhard Sick, Marek Herde, Daniel Kottke

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Auto-TLDR; AE-DNN: Modeling Uncertainty in Deep Neural Networks

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Despite the success of deep neural networks (DNN) in many applications, their ability to model uncertainty is still significantly limited. For example, in safety-critical applications such as autonomous driving, it is crucial to obtain a prediction that reflects different types of uncertainty to address life-threatening situations appropriately. In such cases, it is essential to be aware of the risk (i.e., aleatoric uncertainty) and the reliability (i.e., epistemic uncertainty) that comes with a prediction. We present AE-DNN, a model allowing the separation of aleatoric and epistemic uncertainty while maintaining a proper generalization capability. AE-DNN is based on deterministic DNN, which can determine the respective uncertainty measures in a single forward pass. In analyses with synthetic and image data, we show that our method improves the modeling of epistemic uncertainty while providing an intuitively understandable separation of risk and reliability.

Soft Label and Discriminant Embedding Estimation for Semi-Supervised Classification

Fadi Dornaika, Abdullah Baradaaji, Youssof El Traboulsi

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Auto-TLDR; Semi-supervised Semi-Supervised Learning for Linear Feature Extraction and Label Propagation

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In recent times, graph-based semi-supervised learning proved to be a powerful paradigm for processing and mining large datasets. The main advantage relies on the fact that these methods can be useful in propagating a small set of known labels to a large set of unlabeled data. The scarcity of labeled data may affect the performance of the semi-learning. This paper introduces a new semi-supervised framework for simultaneous linear feature extraction and label propagation. The proposed method simultaneously estimates a discriminant transformation and the unknown label by exploiting both labeled and unlabeled data. In addition, the unknowns of the learning model are estimated by integrating two types of graph-based smoothness constraints. The resulting semi-supervised model is expected to learn more discriminative information. Experiments are conducted on six public image datasets. These experimental results show that the performance of the proposed method can be better than that of many state-of-the-art graph-based semi-supervised algorithms.

Learning Embeddings for Image Clustering: An Empirical Study of Triplet Loss Approaches

Kalun Ho, Janis Keuper, Franz-Josef Pfreundt, Margret Keuper

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Auto-TLDR; Clustering Objectives for K-means and Correlation Clustering Using Triplet Loss

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In this work, we evaluate two different image clustering objectives, k-means clustering and correlation clustering, in the context of Triplet Loss induced feature space embeddings. Specifically, we train a convolutional neural network to learn discriminative features by optimizing two popular versions of the Triplet Loss in order to study their clustering properties under the assumption of noisy labels. Additionally, we propose a new, simple Triplet Loss formulation, which shows desirable properties with respect to formal clustering objectives and outperforms the existing methods. We evaluate all three Triplet loss formulations for K-means and correlation clustering on the CIFAR-10 image classification dataset.