Towards Visually Explaining Variational Autoencoders

Recent advances in Convolutional Neural Network (CNN) model interpretability have led to impressive progress in visualizing and understanding model predictions. In particular, gradient-based visual attention methods have driven much recent effort in using visual attention maps as a means for visual explanations. A key problem, however, is these methods are designed for classification and categorization tasks, and their extension to explaining generative models, e.g. variational autoencoders (VAE) is not trivial. In this work, we take a step towards bridging this crucial gap, proposing the first technique to visually explain VAEs by means of gradient-based attention. We present methods to generate visual attention from the learned latent space, and also demonstrate such attention explanations serve more than just explaining VAE predictions. We show how these attention maps can be used to localize anomalies in images, demonstrating state-of-the-art performance on the MVTec-AD dataset. We also show how they can be infused into model training, helping bootstrap the VAE into learning improved latent space disentanglement, demonstrated on the Dsprites dataset

DeepCoder: Semi-parametric Variational Autoencoders for Automatic Facial Action Coding

Human face exhibits an inherent hierarchy in its representations (i.e., holistic facial expressions can be encoded via a set of facial action units (AUs) and their intensity). Variational (deep) auto-encoders (VAE) have shown great results in unsupervised extraction of hierarchical latent representations from large amounts of image data, while being robust to noise and other undesired artifacts. Potentially, this makes VAEs a suitable approach for learning facial features for AU intensity estimation. Yet, most existing VAE-based methods apply classifiers learned separately from the encoded features. By contrast, the non-parametric (probabilistic) approaches, such as Gaussian Processes (GPs), typically outperform their parametric counterparts, but cannot deal easily with large amounts of data. To this end, we propose a novel VAE semi-parametric modeling framework, named DeepCoder, which combines the modeling power of parametric (convolutional) and nonparametric (ordinal GPs) VAEs, for joint learning of (1) latent representations at multiple levels in a task hierarchy1, and (2) classification of multiple ordinal outputs. We show on benchmark datasets for AU intensity estimation that the proposed DeepCoder outperforms the state-of-the-art approaches, and related VAEs and deep learning models.Comment: ICCV 2017 - accepte

Disentangling Adversarial Robustness and Generalization

Obtaining deep networks that are robust against adversarial examples and generalize well is an open problem. A recent hypothesis even states that both robust and accurate models are impossible, i.e., adversarial robustness and generalization are conflicting goals. In an effort to clarify the relationship between robustness and generalization, we assume an underlying, low-dimensional data manifold and show that: 1. regular adversarial examples leave the manifold; 2. adversarial examples constrained to the manifold, i.e., on-manifold adversarial examples, exist; 3. on-manifold adversarial examples are generalization errors, and on-manifold adversarial training boosts generalization; 4. regular robustness and generalization are not necessarily contradicting goals. These assumptions imply that both robust and accurate models are possible. However, different models (architectures, training strategies etc.) can exhibit different robustness and generalization characteristics. To confirm our claims, we present extensive experiments on synthetic data (with known manifold) as well as on EMNIST, Fashion-MNIST and CelebA.Comment: Conference on Computer Vision and Pattern Recognition 201

Anomaly Detection in the Latent Space of VAEs

One of the most important challenges in the development of autonomous driving systems is to make them robust against unexpected or unknown objects. Many of these systems perform really good in a controlled environment where they encounter situation for which they have been trained. In order for them to be safely deployed in the real world, they need to be aware if they encounter situations or novel objects for which the have not been sufficiently trained for in order to prevent possibly dangerous behavior. In reality, they often fail when dealing with such kind of anomalies, and do so without any signs of uncertainty in their predictions. This thesis focuses on the problem of detecting anomalous objects in road images in the latent space of a VAE. For that, normal and anomalous data was used to train the VAE to fit the data onto two prior distributions. This essentially trains the VAE to create an anomaly and a normal cluster. This structure of the latent space makes it possible to detect anomalies in it by using clustering algorithms like k-means. Multiple experiments were carried out in order to improve to separation of normal and anomalous data in the latent space. To test this approach, anomaly data from multiple datasets was used in order to evaluate the detection of anomalies. The approach described in this thesis was able to detect almost all images containing anomalous objects but also suffers from a high false positive rate which still is a common problem of many anomaly detection methods

Clinical microbiology with multi-view deep probabilistic models

Clinical microbiology is one of the critical topics of this century. Identification and discrimination of microorganisms is considered a global public health threat by the main international health organisations, such as World Health Organisation (WHO) or the European Centre for Disease Prevention and Control (ECDC). Rapid spread, high morbidity and mortality, as well as the economic burden associated with their treatment and control are the main causes of their impact. Discrimination of microorganisms is crucial for clinical applications, for instance, Clostridium difficile (C. diff ) increases the mortality and morbidity of healthcare-related infections. Furthermore, in the past two decades, other bacteria, including Klebsiella pneumoniae (K. pneumonia), have demonstrated a significant propensity to acquire antibiotic resistance mechanisms. Consequently, the use of an ineffective antibiotic may result in mortality. Machine Learning (ML) has the potential to be applied in the clinical microbiology field to automatise current methodologies and provide more efficient guided personalised treatments. However, microbiological data are challenging to exploit owing to the presence of a heterogeneous mix of data types, such as real-valued high-dimensional data, categorical indicators, multilabel epidemiological data, binary targets, or even time-series data representations. This problem, which in the field of ML is known as multi-view or multi-modal representation learning, has been studied in other application fields such as mental health monitoring or haematology. Multi-view learning combines different modalities or views representing the same data to extract richer insights and improve understanding. Each modality or view corresponds to a distinct encoding mechanism for the data, and this dissertation specifically addresses the issue of heterogeneity across multiple views. In the probabilistic ML field, the exploitation of multi-view learning is also known as Bayesian Factor Analysis (FA). Current solutions face limitations when handling high-dimensional data and non-linear associations. Recent research proposes deep probabilistic methods to learn hierarchical representations of the data, which can capture intricate non-linear relationships between features. However, some Deep Learning (DL) techniques rely on complicated representations, which can hinder the interpretation of the outcomes. In addition, some inference methods used in DL approaches can be computationally burdensome, which can hinder their practical application in real-world situations. Therefore, there is a demand for more interpretable, explainable, and computationally efficient techniques for highdimensional data. By combining multiple views representing the same information, such as genomic, proteomic, and epidemiologic data, multi-modal representation learning could provide a better understanding of the microbial world. Hence, in this dissertation, the development of two deep probabilistic models, that can handle current limitations in state-of-the-art of clinical microbiology, are proposed. Moreover, both models are also tested in two real scenarios regarding antibiotic resistance prediction in K. pneumoniae and automatic ribotyping of C. diff in collaboration with the Instituto de Investigación Sanitaria Gregorio Marañón (IISGM) and the Instituto Ramón y Cajal de Investigación Sanitaria (IRyCIS). The first presented algorithm is the Kernelised Sparse Semi-supervised Heterogeneous Interbattery Bayesian Analysis (SSHIBA). This algorithm uses a kernelised formulation to handle non-linear data relationships while providing compact representations through the automatic selection of relevant vectors. Additionally, it uses an Automatic Relevance Determination (ARD) over the kernel to determine the input feature relevance functionality. Then, it is tailored and applied to the microbiological laboratories of the IISGM and IRyCIS to predict antibiotic resistance in K. pneumoniae. To do so, specific kernels that handle Matrix-Assisted Laser Desorption Ionization (MALDI)-Time-Of-Flight (TOF) mass spectrometry of bacteria are used. Moreover, by exploiting the multi-modal learning between the spectra and epidemiological information, it outperforms other state-of-the-art algorithms. Presented results demonstrate the importance of heterogeneous models that can analyse epidemiological information and can automatically be adjusted for different data distributions. The implementation of this method in microbiological laboratories could significantly reduce the time required to obtain resistance results in 24-72 hours and, moreover, improve patient outcomes. The second algorithm is a hierarchical Variational AutoEncoder (VAE) for heterogeneous data using an explainable FA latent space, called FA-VAE. The FA-VAE model is built on the foundation of the successful KSSHIBA approach for dealing with semi-supervised heterogeneous multi-view problems. This approach further expands the range of data domains it can handle. With the ability to work with a wide range of data types, including multilabel, continuous, binary, categorical, and even image data, the FA-VAE model offers a versatile and powerful solution for real-world data sets, depending on the VAE architecture. Additionally, this model is adapted and used in the microbiological laboratory of IISGM, resulting in an innovative technique for automatic ribotyping of C. diff, using MALDI-TOF data. To the best of our knowledge, this is the first demonstration of using any kind of ML for C. diff ribotyping. Experiments have been conducted on strains of Hospital General Universitario Gregorio Marañón (HGUGM) to evaluate the viability of the proposed approach. The results have demonstrated high accuracy rates where KSSHIBA even achieved perfect accuracy in the first data collection. These models have also been tested in a real-life outbreak scenario at the HGUGM, where successful classification of all outbreak samples has been achieved by FAVAE. The presented results have not only shown high accuracy in predicting each strain’s ribotype but also revealed an explainable latent space. Furthermore, traditional ribotyping methods, which rely on PCR, required 7 days while FA-VAE has predicted equal results on the same day. This improvement has significantly reduced the time response by helping in the decision-making of isolating patients with hyper-virulent ribotypes of C. diff on the same day of infection. The promising results, obtained in a real outbreak, have provided a solid foundation for further advancements in the field. This study has been a crucial stepping stone towards realising the full potential of MALDI-TOF for bacterial ribotyping and advancing our ability to tackle bacterial outbreaks. In conclusion, this doctoral thesis has significantly contributed to the field of Bayesian FA by addressing its drawbacks in handling various data types through the creation of novel models, namely KSSHIBA and FA-VAE. Additionally, a comprehensive analysis of the limitations of automating laboratory procedures in the microbiology field has been carried out. The shown effectiveness of the newly developed models has been demonstrated through their successful implementation in critical problems, such as predicting antibiotic resistance and automating ribotyping. As a result, KSSHIBA and FA-VAE, both in terms of their technical and practical contributions, signify noteworthy progress both in the clinical and the Bayesian statistics fields. This dissertation opens up possibilities for future advancements in automating microbiological laboratories.La microbiología clínica es uno de los temas críticos de este siglo. La identificación y discriminación de microorganismos se considera una amenaza mundial para la salud pública por parte de las principales organizaciones internacionales de salud, como la Organización Mundial de la Salud (OMS) o el Centro Europeo para la Prevención y Control de Enfermedades (ECDC). La rápida propagación, alta morbilidad y mortalidad, así como la carga económica asociada con su tratamiento y control, son las principales causas de su impacto. La discriminación de microorganismos es crucial para aplicaciones clínicas, como el caso de Clostridium difficile (C. diff ), el cual aumenta la mortalidad y morbilidad de las infecciones relacionadas con la atención médica. Además, en las últimas dos décadas, otros tipos de bacterias, incluyendo Klebsiella pneumoniae (K. pneumonia), han demostrado una propensión significativa a adquirir mecanismos de resistencia a los antibióticos. En consecuencia, el uso de un antibiótico ineficaz puede resultar en un aumento de la mortalidad. El aprendizaje automático (ML) tiene el potencial de ser aplicado en el campo de la microbiología clínica para automatizar las metodologías actuales y proporcionar tratamientos personalizados más eficientes y guiados. Sin embargo, los datos microbiológicos son difíciles de explotar debido a la presencia de una mezcla heterogénea de tipos de datos, tales como datos reales de alta dimensionalidad, indicadores categóricos, datos epidemiológicos multietiqueta, objetivos binarios o incluso series temporales. Este problema, conocido en el campo del aprendizaje automático (ML) como aprendizaje multimodal o multivista, ha sido estudiado en otras áreas de aplicación, como en el monitoreo de la salud mental o la hematología. El aprendizaje multivista combina diferentes modalidades o vistas que representan los mismos datos para extraer conocimientos más ricos y mejorar la comprensión. Cada vista corresponde a un mecanismo de codificación distinto para los datos, y esta tesis aborda particularmente el problema de la heterogeneidad multivista. En el campo del aprendizaje automático probabilístico, la explotación del aprendizaje multivista también se conoce como Análisis de Factores (FA) Bayesianos. Las soluciones actuales enfrentan limitaciones al manejar datos de alta dimensionalidad y correlaciones no lineales. Investigaciones recientes proponen métodos probabilísticos profundos para aprender representaciones jerárquicas de los datos, que pueden capturar relaciones no lineales intrincadas entre características. Sin embargo, algunas técnicas de aprendizaje profundo (DL) se basan en representaciones complejas, dificultando así la interpretación de los resultados. Además, algunos métodos de inferencia utilizados en DL pueden ser computacionalmente costosos, obstaculizando su aplicación práctica. Por lo tanto, existe una demanda de técnicas más interpretables, explicables y computacionalmente eficientes para datos de alta dimensionalidad. Al combinar múltiples vistas que representan la misma información, como datos genómicos, proteómicos y epidemiológicos, el aprendizaje multimodal podría proporcionar una mejor comprensión del mundo microbiano. Dicho lo cual, en esta tesis se proponen el desarrollo de dos modelos probabilísticos profundos que pueden manejar las limitaciones actuales en el estado del arte de la microbiología clínica. Además, ambos modelos también se someten a prueba en dos escenarios reales relacionados con la predicción de resistencia a los antibióticos en K. pneumoniae y el ribotipado automático de C. diff en colaboración con el IISGM y el IRyCIS. El primer algoritmo presentado es Kernelised Sparse Semi-supervised Heterogeneous Interbattery Bayesian Analysis (SSHIBA). Este algoritmo utiliza una formulación kernelizada para manejar correlaciones no lineales proporcionando representaciones compactas a través de la selección automática de vectores relevantes. Además, utiliza un Automatic Relevance Determination (ARD) sobre el kernel para determinar la relevancia de las características de entrada. Luego, se adapta y aplica a los laboratorios microbiológicos del IISGM y IRyCIS para predecir la resistencia a antibióticos en K. pneumoniae. Para ello, se utilizan kernels específicos que manejan la espectrometría de masas Matrix-Assisted Laser Desorption Ionization (MALDI)-Time-Of-Flight (TOF) de bacterias. Además, al aprovechar el aprendizaje multimodal entre los espectros y la información epidemiológica, supera a otros algoritmos de última generación. Los resultados presentados demuestran la importancia de los modelos heterogéneos ya que pueden analizar la información epidemiológica y ajustarse automáticamente para diferentes distribuciones de datos. La implementación de este método en laboratorios microbiológicos podría reducir significativamente el tiempo requerido para obtener resultados de resistencia en 24-72 horas y, además, mejorar los resultados para los pacientes. El segundo algoritmo es un modelo jerárquico de Variational AutoEncoder (VAE) para datos heterogéneos que utiliza un espacio latente con un FA explicativo, llamado FA-VAE. El modelo FA-VAE se construye sobre la base del enfoque de KSSHIBA para tratar problemas semi-supervisados multivista. Esta propuesta amplía aún más el rango de dominios que puede manejar incluyendo multietiqueta, continuos, binarios, categóricos e incluso imágenes. De esta forma, el modelo FA-VAE ofrece una solución versátil y potente para conjuntos de datos realistas, dependiendo de la arquitectura del VAE. Además, este modelo es adaptado y utilizado en el laboratorio microbiológico del IISGM, lo que resulta en una técnica innovadora para el ribotipado automático de C. diff utilizando datos MALDI-TOF. Hasta donde sabemos, esta es la primera demostración del uso de cualquier tipo de ML para el ribotipado de C. diff. Se han realizado experimentos en cepas del Hospital General Universitario Gregorio Marañón (HGUGM) para evaluar la viabilidad de la técnica propuesta. Los resultados han demostrado altas tasas de precisión donde KSSHIBA incluso logró una clasificación perfecta en la primera colección de datos. Estos modelos también se han probado en un brote real en el HGUGM, donde FA-VAE logró clasificar con éxito todas las muestras del mismo. Los resultados presentados no solo han demostrado una alta precisión en la predicción del ribotipo de cada cepa, sino que también han revelado un espacio latente explicativo. Además, los métodos tradicionales de ribotipado, que dependen de PCR, requieren 7 días para obtener resultados mientras que FA-VAE ha predicho resultados correctos el mismo día del brote. Esta mejora ha reducido significativamente el tiempo de respuesta ayudando así en la toma de decisiones para aislar a los pacientes con ribotipos hipervirulentos de C. diff el mismo día de la infección. Los resultados prometedores, obtenidos en un brote real, han sentado las bases para nuevos avances en el campo. Este estudio ha sido un paso crucial hacia el despliegue del pleno potencial de MALDI-TOF para el ribotipado bacteriana avanzado así nuestra capacidad para abordar brotes bacterianos. En conclusión, esta tesis doctoral ha contribuido significativamente al campo del FA Bayesiano al abordar sus limitaciones en el manejo de tipos de datos heterogéneos a través de la creación de modelos noveles, concretamente, KSSHIBA y FA-VAE. Además, se ha llevado a cabo un análisis exhaustivo de las limitaciones de la automatización de procedimientos de laboratorio en el campo de la microbiología. La efectividad de los nuevos modelos, en este campo, se ha demostrado a través de su implementación exitosa en problemas críticos, como la predicción de resistencia a los antibióticos y la automatización del ribotipado. Como resultado, KSSHIBA y FAVAE, tanto en términos de sus contribuciones técnicas como prácticas, representan un progreso notable tanto en los campos clínicos como en la estadística Bayesiana. Esta disertación abre posibilidades para futuros avances en la automatización de laboratorios microbiológicos.Programa de Doctorado en Multimedia y Comunicaciones por la Universidad Carlos III de Madrid y la Universidad Rey Juan CarlosPresidente: Juan José Murillo Fuentes.- Secretario: Jerónimo Arenas García.- Vocal: María de las Mercedes Marín Arriaz