Personalized Automatic Estimation of Self-reported Pain Intensity from Facial Expressions

Pain is a personal, subjective experience that is commonly evaluated through visual analog scales (VAS). While this is often convenient and useful, automatic pain detection systems can reduce pain score acquisition efforts in large-scale studies by estimating it directly from the participants' facial expressions. In this paper, we propose a novel two-stage learning approach for VAS estimation: first, our algorithm employs Recurrent Neural Networks (RNNs) to automatically estimate Prkachin and Solomon Pain Intensity (PSPI) levels from face images. The estimated scores are then fed into the personalized Hidden Conditional Random Fields (HCRFs), used to estimate the VAS, provided by each person. Personalization of the model is performed using a newly introduced facial expressiveness score, unique for each person. To the best of our knowledge, this is the first approach to automatically estimate VAS from face images. We show the benefits of the proposed personalized over traditional non-personalized approach on a benchmark dataset for pain analysis from face images.Comment: Computer Vision and Pattern Recognition Conference, The 1st International Workshop on Deep Affective Learning and Context Modelin

Synthetic Observational Health Data with GANs: from slow adoption to a boom in medical research and ultimately digital twins?

After being collected for patient care, Observational Health Data (OHD) can further benefit patient well-being by sustaining the development of health informatics and medical research. Vast potential is unexploited because of the fiercely private nature of patient-related data and regulations to protect it. Generative Adversarial Networks (GANs) have recently emerged as a groundbreaking way to learn generative models that produce realistic synthetic data. They have revolutionized practices in multiple domains such as self-driving cars, fraud detection, digital twin simulations in industrial sectors, and medical imaging. The digital twin concept could readily apply to modelling and quantifying disease progression. In addition, GANs posses many capabilities relevant to common problems in healthcare: lack of data, class imbalance, rare diseases, and preserving privacy. Unlocking open access to privacy-preserving OHD could be transformative for scientific research. In the midst of COVID-19, the healthcare system is facing unprecedented challenges, many of which of are data related for the reasons stated above. Considering these facts, publications concerning GAN applied to OHD seemed to be severely lacking. To uncover the reasons for this slow adoption, we broadly reviewed the published literature on the subject. Our findings show that the properties of OHD were initially challenging for the existing GAN algorithms (unlike medical imaging, for which state-of-the-art model were directly transferable) and the evaluation synthetic data lacked clear metrics. We find more publications on the subject than expected, starting slowly in 2017, and since then at an increasing rate. The difficulties of OHD remain, and we discuss issues relating to evaluation, consistency, benchmarking, data modelling, and reproducibility.Comment: 31 pages (10 in previous version), not including references and glossary, 51 in total. Inclusion of a large number of recent publications and expansion of the discussion accordingl

Development of a probabilistic perception system for camera-lidar sensor fusion

La estimación de profundidad usando diferentes sensores es uno de los desafíos clave para dotar a las máquinas autónomas de sólidas capacidades de percepción robótica. Ha habido un avance sobresaliente en el desarrollo de técnicas de estimación de profundidad unimodales basadas en cámaras monoculares, debido a su alta resolución o sensores LiDAR, debido a los datos geométricos precisos que proporcionan. Sin embargo, cada uno de ellos presenta inconvenientes inherentes, como la alta sensibilidad a los cambios en las condiciones de iluminación en el caso delas cámaras y la resolución limitada de los sensores LiDAR. La fusión de sensores se puede utilizar para combinar los méritos y compensar las desventajas de estos dos tipos de sensores. Sin embargo, los métodos de fusión actuales funcionan a un alto nivel. Procesan los flujos de datos de los sensores de forma independiente y combinan las estimaciones de alto nivel obtenidas para cada sensor. En este proyecto, abordamos el problema en un nivel bajo, fusionando los flujos de sensores sin procesar, obteniendo así estimaciones de profundidad que son densas y precisas, y pueden usarse como una fuente de datos multimodal unificada para problemas de estimación de nivel superior. Este trabajo propone un modelo de campo aleatorio condicional (CRF) con múltiples potenciales de geometría y apariencia que representa a la perfección el problema de estimar mapas de profundidad densos a partir de datos de cámara y LiDAR. El modelo se puede optimizar de manera eficiente utilizando el algoritmo Conjúgate Gradient Squared (CGS). El método propuesto se evalúa y compara utilizando el conjunto de datos proporcionado por KITTI Datset. Adicionalmente, se evalúa cualitativamente el modelo, usando datos adquiridos por el autor de esté trabajoMulti-modal depth estimation is one of the key challenges for endowing autonomous machines with robust robotic perception capabilities. There has been an outstanding advance in the development of uni-modal depth estimation techniques based on either monocular cameras, because of their rich resolution or LiDAR sensors due to the precise geometric data they provide. However, each of them suffers from some inherent drawbacks like high sensitivity to changes in illumination conditions in the case of cameras and limited resolution for the LiDARs. Sensor fusion can be used to combine the merits and compensate the downsides of these two kinds of sensors. Nevertheless, current fusion methods work at a high level. They processes sensor data streams independently and combine the high level estimates obtained for each sensor. In this thesis, I tackle the problem at a low level, fusing the raw sensor streams, thus obtaining depth estimates which are both dense and precise, and can be used as a unified multi-modal data source for higher level estimation problems. This work proposes a Conditional Random Field (CRF) model with multiple geometry and appearance potentials that seamlessly represents the problem of estimating dense depth maps from camera and LiDAR data. The model can be optimized efficiently using the Conjugate Gradient Squared (CGS) algorithm. The proposed method was evaluated and compared with the state-of-the-art using the commonly used KITTI benchmark dataset. In addition, the model is qualitatively evaluated using data acquired by the author of this work.MaestríaMagíster en Ingeniería de Desarrollo de Producto

Development of a probabilistic perception system for camera-lidar sensor fusion

La estimación de profundidad usando diferentes sensores es uno de los desafíos clave para dotar a las máquinas autónomas de sólidas capacidades de percepción robótica. Ha habido un avance sobresaliente en el desarrollo de técnicas de estimación de profundidad unimodales basadas en cámaras monoculares, debido a su alta resolución o sensores LiDAR, debido a los datos geométricos precisos que proporcionan. Sin embargo, cada uno de ellos presenta inconvenientes inherentes, como la alta sensibilidad a los cambios en las condiciones de iluminación en el caso delas cámaras y la resolución limitada de los sensores LiDAR. La fusión de sensores se puede utilizar para combinar los méritos y compensar las desventajas de estos dos tipos de sensores. Sin embargo, los métodos de fusión actuales funcionan a un alto nivel. Procesan los flujos de datos de los sensores de forma independiente y combinan las estimaciones de alto nivel obtenidas para cada sensor. En este proyecto, abordamos el problema en un nivel bajo, fusionando los flujos de sensores sin procesar, obteniendo así estimaciones de profundidad que son densas y precisas, y pueden usarse como una fuente de datos multimodal unificada para problemas de estimación de nivel superior. Este trabajo propone un modelo de campo aleatorio condicional (CRF) con múltiples potenciales de geometría y apariencia que representa a la perfección el problema de estimar mapas de profundidad densos a partir de datos de cámara y LiDAR. El modelo se puede optimizar de manera eficiente utilizando el algoritmo Conjúgate Gradient Squared (CGS). El método propuesto se evalúa y compara utilizando el conjunto de datos proporcionado por KITTI Datset. Adicionalmente, se evalúa cualitativamente el modelo, usando datos adquiridos por el autor de esté trabajoMulti-modal depth estimation is one of the key challenges for endowing autonomous machines with robust robotic perception capabilities. There has been an outstanding advance in the development of uni-modal depth estimation techniques based on either monocular cameras, because of their rich resolution or LiDAR sensors due to the precise geometric data they provide. However, each of them suffers from some inherent drawbacks like high sensitivity to changes in illumination conditions in the case of cameras and limited resolution for the LiDARs. Sensor fusion can be used to combine the merits and compensate the downsides of these two kinds of sensors. Nevertheless, current fusion methods work at a high level. They processes sensor data streams independently and combine the high level estimates obtained for each sensor. In this thesis, I tackle the problem at a low level, fusing the raw sensor streams, thus obtaining depth estimates which are both dense and precise, and can be used as a unified multi-modal data source for higher level estimation problems. This work proposes a Conditional Random Field (CRF) model with multiple geometry and appearance potentials that seamlessly represents the problem of estimating dense depth maps from camera and LiDAR data. The model can be optimized efficiently using the Conjugate Gradient Squared (CGS) algorithm. The proposed method was evaluated and compared with the state-of-the-art using the commonly used KITTI benchmark dataset. In addition, the model is qualitatively evaluated using data acquired by the author of this work.MaestríaMagíster en Ingeniería de Desarrollo de Producto

autoTICI: Automatic Brain Tissue Reperfusion Scoring on 2D DSA Images of Acute Ischemic Stroke Patients

The Thrombolysis in Cerebral Infarction (TICI) score is an important metric for reperfusion therapy assessment in acute ischemic stroke. It is commonly used as a technical outcome measure after endovascular treatment (EVT). Existing TICI scores are defined in coarse ordinal grades based on visual inspection, leading to inter- and intra-observer variation. In this work, we present autoTICI, an automatic and quantitative TICI scoring method. First, each digital subtraction angiography (DSA) sequence is separated into four phases (non-contrast, arterial, parenchymal and venous phase) using a multi-path convolutional neural network (CNN), which exploits spatio-temporal features. The network also incorporates sequence level label dependencies in the form of a state-transition matrix. Next, a minimum intensity map (MINIP) is computed using the motion corrected arterial and parenchymal frames. On the MINIP image, vessel, perfusion and background pixels are segmented. Finally, we quantify the autoTICI score as the ratio of reperfused pixels after EVT. On a routinely acquired multi-center dataset, the proposed autoTICI shows good correlation with the extended TICI (eTICI) reference with an average area under the curve (AUC) score of 0.81. The AUC score is 0.90 with respect to the dichotomized eTICI. In terms of clinical outcome prediction, we demonstrate that autoTICI is overall comparable to eTICI.Comment: 10 pages; submitted to IEEE TM

CLADAG 2021 BOOK OF ABSTRACTS AND SHORT PAPERS

The book collects the short papers presented at the 13th Scientific Meeting of the Classification and Data Analysis Group (CLADAG) of the Italian Statistical Society (SIS). The meeting has been organized by the Department of Statistics, Computer Science and Applications of the University of Florence, under the auspices of the Italian Statistical Society and the International Federation of Classification Societies (IFCS). CLADAG is a member of the IFCS, a federation of national, regional, and linguistically-based classification societies. It is a non-profit, non-political scientific organization, whose aims are to further classification research

Affective Music Information Retrieval

Much of the appeal of music lies in its power to convey emotions/moods and to evoke them in listeners. In consequence, the past decade witnessed a growing interest in modeling emotions from musical signals in the music information retrieval (MIR) community. In this article, we present a novel generative approach to music emotion modeling, with a specific focus on the valence-arousal (VA) dimension model of emotion. The presented generative model, called \emph{acoustic emotion Gaussians} (AEG), better accounts for the subjectivity of emotion perception by the use of probability distributions. Specifically, it learns from the emotion annotations of multiple subjects a Gaussian mixture model in the VA space with prior constraints on the corresponding acoustic features of the training music pieces. Such a computational framework is technically sound, capable of learning in an online fashion, and thus applicable to a variety of applications, including user-independent (general) and user-dependent (personalized) emotion recognition and emotion-based music retrieval. We report evaluations of the aforementioned applications of AEG on a larger-scale emotion-annotated corpora, AMG1608, to demonstrate the effectiveness of AEG and to showcase how evaluations are conducted for research on emotion-based MIR. Directions of future work are also discussed.Comment: 40 pages, 18 figures, 5 tables, author versio

Multilevel mixed-type data analysis for validating partitions of scrapie isolates

The dissertation arises from a joint study with the Department of Food Safety and Veterinary Public Health of the Istituto Superiore di Sanità. The aim is to investigate and validate the existence of distinct strains of the scrapie disease taking into account the availability of a priori benchmark partition formulated by researchers. Scrapie of small ruminants is caused by prions, which are unconventional infectious agents of proteinaceous nature a ecting humans and animals. Due to the absence of nucleic acids, which precludes direct analysis of strain variation by molecular methods, the presence of di erent sheep scrapie strains is usually investigated by bioassay in laboratory rodents. Data are collected by an experimental study on scrapie conducted at the Istituto Superiore di Sanità by experimental transmission of scrapie isolates to bank voles. We aim to discuss the validation of a given partition in a statistical classification framework using a multi-step procedure. Firstly, we use unsupervised classification to see how alternative clustering results match researchers’ understanding of the heterogeneity of the isolates. We discuss whether and how clustering results can be eventually exploited to extend the preliminary partition elicited by researchers. Then we motivate the subsequent partition validation based on the predictive performance of several supervised classifiers. Our data-driven approach contains two main methodological original contributions. We advocate the use of partition validation measures to investigate a given benchmark partition: firstly we discuss the issue of how the data can be used to evaluate a preliminary benchmark partition and eventually modify it with statistical results to find a conclusive partition that could be used as a “gold standard” in future studies. Moreover, collected data have a multilevel structure and for each lower-level unit, mixed-type data are available. Each step in the procedure is then adapted to deal with multilevel mixed-type data. We extend distance-based clustering algorithms to deal with multilevel mixed-type data. Whereas in supervised classification we propose a two-step approach to classify the higher-level units starting from the lower-level observations. In this framework, we also need to define an ad-hoc cross validation algorithm