This thesis aims to evaluate the current state of the art for unconditional text generation and compare established models with novel approaches in the task of generating texts, after being trained on texts written by political parties from the Swedish Riksdag. First, the progression of language modeling from n-gram models and statistical models to neural network models is presented. This is followed by theoretical arguments for the development of adversarial training methods,where a generator neural network tries to fool a discriminator network, trained to distinguish between real and generated sentences. One of the methods in the research frontier diverges from the adversarial idea and instead uses cooperative training, where a mediator network is trained instead of a discriminator. The mediator is then used to estimate a symmetric divergence measure between the true distribution and the generator’s distribution, which is to be minimized in training. A set of experiments evaluates the performance of cooperative training and adversarial training, and finds that they both have advantages and disadvantages. In the experiments, the adversarial training increases the quality of generated texts, while the cooperative training increases the diversity. The findings are in line with the theoretical expectation. / Denna uppsats utvärderar några nyligen föreslagna metoder för obetingad textgenerering, baserade på s.k. “Generative Adversarial Networks” (GANs). Den jämför etablerade modeller med nya metoder för att generera text, efter att ha tränats på texter från de svenska Riksdagspartierna. Utvecklingen av språkmodellering från n-gram-modeller och statistiska modeller till modeller av neurala nätverk presenteras. Detta följs upp av teoretiska argument för utvecklingen av GANs, för vilka ett generatornätverk försöker överlista ett diskriminatornätverk, som tränas skilja mellan riktiga och genererade meningar. En av de senaste metoderna avviker från detta angreppssätt och introducerar istället kooperativ träning, där ett mediatornätverk tränas istället för en diskriminator. Mediatorn används sedan till att uppskatta ett symmetriskt divergensmått mellan den sanna distributionen och generatorns distribution, vilket träningen syftar till att minimera. En serie experiment utvärderar hur GANs och kooperativ träning presterar i förhållande till varandra, och finner att de båda har för- och nackdelar. I experimenten ökar GANs kvaliteten på texterna som genereras, medan kooperativ träning ökar mångfalden. Resultaten motsvarar vad som kan förväntas teoretiskt.

The Generative Adversarial Network framework has shown success in implicitly modeling data distributions and is able to generate realistic samples. Its architecture is comprised of a generator, which produces fake data that superficially seem to belong to the real data distribution, and a discriminator which is to distinguish fake from genuine samples. The Noiseless Joint Plug & Play model offers an extension to the framework by simultaneously training autoencoders. This model uses a pre-trained encoder as a feature extractor, feeding the generator with global information. Using the Plug & Play network as baseline, we design a new model by adding discriminators to the Plug & Play architecture. These additional discriminators are trained to discern real and fake latent codes, which are the output of the encoder using genuine and generated inputs, respectively. We proceed to investigate whether this approach is viable. Experiments conducted for the MNIST manifold show that this indeed is the case. / Generative Adversarial Network är ett ramverk vilket implicit modellerar en datamängds sannolikhetsfördelning och är kapabel till att producera realistisk exempel. Dess arkitektur utgörs av en generator, vilken kan fabricera datapunkter liggandes nära den verkliga sannolikhetsfördelning, och en diskriminator vars syfte är att urskilja oäkta punkter från genuina. Noiseless Joint Plug & Play modellen är en vidareutveckling av ramverket som samtidigt tränar autoencoders. Denna modell använder sig utav en inlärd enkoder som förser generatorn med data. Genom att använda Plug & Play modellen som referens, skapar vi en ny modell genom att addera diskriminatorer till Plug & Play architekturen. Dessa diskriminatorer är tränade att särskilja genuina och falska latenta koder, vilka har producerats av enkodern genom att ha använt genuina och oäkta datapunkter som inputs. Vi undersöker huruvida denna metod är gynnsam. Experiment utförda för MNIST datamängden visar att så är fallet.

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<p>Recent advances in fluorescence  microscopy enable deeper cellular imaging in living tissues with near-infrared excitation light. </p> <p>High quality fluorescence microscopy images provide useful information for analyzing biological structures and diagnosing diseases.</p> <p>Nuclei detection and segmentation are two fundamental steps for quantitative analysis of microscopy images.</p> <p>However, existing machine learning-based approaches are hampered by three main challenges: (1) Hand annotated ground truth is difficult to obtain especially for 3D volumes, (2) Most of the object detection methods work only on 2D images and are difficult to extend to 3D volumes, (3) Segmentation-based approaches typically cannot distinguish different object instances without proper post-processing steps.</p> <p>In this thesis, we propose various new methods for microscopy image analysis including nuclei synthesis, detection, and segmentation. </p> <p>Due to the limitation of manually annotated ground truth masks, we first describe how we generate 2D/3D synthetic microscopy images using SpCycleGAN and use them as a data augmentation technique for our detection and segmentation networks.</p> <p>For nuclei detection, we describe our RCNN-SliceNet for nuclei counting and centroid detection using slice-and-cluster strategy. </p> <p>Then we introduce our 3D CentroidNet for nuclei centroid estimation using vector flow voting mechanism which does not require any post-processing steps.</p> <p>For nuclei segmentation, we first describe our EMR-CNN for nuclei instance segmentation using ensemble learning and slice fusion strategy.</p> <p>Then we present the 3D Nuclei Instance Segmentation Network (NISNet3D) for nuclei instance segmentation using gradient vector field array.</p> <p>Extensive experiments have been conducted on a variety of challenging microscopy volumes to demonstrate that our approach can accurately detect and segment the cell nuclei and outperforms other compared methods.</p> <p>Finally, we describe the Distributed and Networked Analysis of Volumetric Image Data (DINAVID) system we developed for biologists to remotely analyze large microscopy volumes using machine learning. </p>

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Generative models are broadly used in many subfields of DL. DNNs have recently developed a core approach to solving data-centric problems in image classification, translation, etc. The latest developments in parameterizing these models using DNNs and stochastic optimization algorithms have allowed scalable modeling of complex, high-dimensional data, including speech, text, and image. This dissertation proposal presents our state-the-art probabilistic bases and DL algorithms for generative models, including VAEs, GANs, and RNN-based encoder-decoder. The proposal also discusses application areas that may benefit from deep generative models in both NLP and computer vision. In NLP, we proposed an Arabic poetry generation model with extended phonetic and semantic embeddings (Phonetic CNN_subword embeddings). Extensive quantitative experiments using BLEU scores and Hamming distance show notable enhancements over strong baselines. Additionally, a comprehensive human evaluation confirms that the poems generated by our model outperform the base models in criteria including meaning, coherence, fluency, and poeticness. We proposed a generative video model using a hybrid VAE-GAN model in computer vision. Besides, we integrate two attentional mechanisms with GAN to get the essential regions of interest in a video, focused on enhancing the visual implementation of the human motion in the generated output. We have considered quantitative and qualitative experiments, including comparisons with other state-of-the-arts for evaluation. Our results indicate that our model enhances performance compared with other models and performs favorably under different quantitive metrics PSNR, SSIM, LPIPS, and FVD.Recently, mimicking biologically inspired learning in generative models based on SNNs has been shown their effectiveness in different applications. SNNs are the third generation of neural networks, in which neurons communicate through binary signals known as spikes. Since SNNs are more energy-efficient than DNNs. Moreover, DNN models have been vulnerable to small adversarial perturbations that cause misclassification of legitimate images. This dissertation shows the proposed ``VAE-Sleep'' that combines ideas from VAE and the sleep mechanism leveraging the advantages of deep and spiking neural networks (DNN--SNN).On top of that, we present ``Defense–VAE–Sleep'' that extended work of ``VAE-Sleep'' model used to purge adversarial perturbations from contaminated images. We demonstrate the benefit of sleep in improving the generalization performance of the traditional VAE when the testing data differ in specific ways even by a small amount from the training data. We conduct extensive experiments, including comparisons with the state–of–the–art on different datasets.

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Les Machines de Boltzmann restreintes (RBM) sont des modèles graphiques capables d’apprendre simultanément une distribution de probabilité et une représentation des données. Malgré leur architecture relativement simple, les RBM peuvent reproduire très fidèlement des données complexes telles que la base de données de chiffres écrits à la main MNIST. Il a par ailleurs été montré empiriquement qu’elles peuvent produire des représentations compositionnelles des données, i.e. qui décomposent les configurations en leurs différentes parties constitutives. Cependant, toutes les variantes de ce modèle ne sont pas aussi performantes les unes que les autres, et il n’y a pas d’explication théorique justifiant ces observations empiriques. Dans la première partie de ma thèse, nous avons cherché à comprendre comment un modèle si simple peut produire des distributions de probabilité si complexes. Pour cela, nous avons analysé un modèle simplifié de RBM à poids aléatoires à l’aide de la méthode des répliques. Nous avons pu caractériser théoriquement un régime compositionnel pour les RBM, et montré sous quelles conditions (statistique des poids, choix de la fonction de transfert) ce régime peut ou ne peut pas émerger. Les prédictions qualitatives et quantitatives de cette analyse théorique sont en accord avec les observations réalisées sur des RBM entraînées sur des données réelles. Nous avons ensuite appliqué les RBM à l’analyse et à la conception de séquences de protéines. De part leur grande taille, il est en effet très difficile de simuler physiquement les protéines, et donc de prédire leur structure et leur fonction. Il est cependant possible d’obtenir des informations sur la structure d’une protéine en étudiant la façon dont sa séquence varie selon les organismes. Par exemple, deux sites présentant des corrélations de mutations importantes sont souvent physiquement proches sur la structure. A l’aide de modèles graphiques tels que les Machine de Boltzmann, on peut exploiter ces signaux pour prédire la proximité spatiale des acides-aminés d’une séquence. Dans le même esprit, nous avons montré sur plusieurs familles de protéines que les RBM peuvent aller au-delà de la structure, et extraire des motifs étendus d’acides aminés en coévolution qui reflètent les contraintes phylogénétiques, structurelles et fonctionnelles des protéines. De plus, on peut utiliser les RBM pour concevoir de nouvelles séquences avec des propriétés fonctionnelles putatives par recombinaison de ces motifs. Enfin, nous avons développé de nouveaux algorithmes d’entraînement et des nouvelles formes paramétriques qui améliorent significativement la performance générative des RBM. Ces améliorations les rendent compétitives avec l’état de l’art des modèles génératifs tels que les réseaux génératifs adversariaux ou les auto-encodeurs variationnels pour des données de taille intermédiaires. / Restricted Boltzmann machines (RBM) are graphical models that learn jointly a probability distribution and a representation of data. Despite their simple architecture, they can learn very well complex data distributions such the handwritten digits data base MNIST. Moreover, they are empirically known to learn compositional representations of data, i.e. representations that effectively decompose configurations into their constitutive parts. However, not all variants of RBM perform equally well, and little theoretical arguments exist for these empirical observations. In the first part of this thesis, we ask how come such a simple model can learn such complex probability distributions and representations. By analyzing an ensemble of RBM with random weights using the replica method, we have characterised a compositional regime for RBM, and shown under which conditions (statistics of weights, choice of transfer function) it can and cannot arise. Both qualitative and quantitative predictions obtained with our theoretical analysis are in agreement with observations from RBM trained on real data. In a second part, we present an application of RBM to protein sequence analysis and design. Owe to their large size, it is very difficult to run physical simulations of proteins, and to predict their structure and function. It is however possible to infer information about a protein structure from the way its sequence varies across organisms. For instance, Boltzmann Machines can leverage correlations of mutations to predict spatial proximity of the sequence amino-acids. Here, we have shown on several synthetic and real protein families that provided a compositional regime is enforced, RBM can go beyond structure and extract extended motifs of coevolving amino-acids that reflect phylogenic, structural and functional constraints within proteins. Moreover, RBM can be used to design new protein sequences with putative functional properties by recombining these motifs at will. Lastly, we have designed new training algorithms and model parametrizations that significantly improve RBM generative performance, to the point where it can compete with state-of-the-art generative models such as Generative Adversarial Networks or Variational Autoencoders on medium-scale data.

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Denna avhandling i datalogi föreslår modeller för hur vissa beräkningsmässiga uppgifter kan utföras av hjärnbarken. Utgångspunkten är dels kända fakta om hur en area i hjärnbarken är uppbyggd och fungerar, dels etablerade modellklasser inom beräkningsneurobiologi, såsom attraktorminnen och system för gles kodning. Ett neuralt nätverk som producerar en effektiv gles kod i binär mening för sensoriska, särskilt visuella, intryck presenteras. Jag visar att detta nätverk, när det har tränats med naturliga bilder, reproducerar vissa egenskaper (receptiva fält) hos nervceller i lager IV i den primära synbarken och att de koder som det producerar är lämpliga för lagring i associativa minnesmodeller. Vidare visar jag hur ett enkelt autoassociativt minne kan modifieras till att fungera som ett generellt sekvenslärande system genom att utrustas med synapsdynamik. Jag undersöker hur ett abstrakt attraktorminnessystem kan implementeras i en detaljerad modell baserad på data om hjärnbarken. Denna modell kan sedan analyseras med verktyg som simulerar experiment som kan utföras på en riktig hjärnbark. Hypotesen att hjärnbarken till avsevärd del fungerar som ett attraktorminne undersöks och visar sig leda till prediktioner för dess kopplingsstruktur. Jag diskuterar också metodologiska aspekter på beräkningsneurobiologin idag. / In this thesis I take a modular approach to cortical function. I investigate how the cerebral cortex may realise a number of basic computational tasks, within the framework of its generic architecture. I present novel mechanisms for certain assumed computational capabilities of the cerebral cortex, building on the established notions of attractor memory and sparse coding. A sparse binary coding network for generating efficient representations of sensory input is presented. It is demonstrated that this network model well reproduces the simple cell receptive field shapes seen in the primary visual cortex and that its representations are efficient with respect to storage in associative memory. I show how an autoassociative memory, augmented with dynamical synapses, can function as a general sequence learning network. I demonstrate how an abstract attractor memory system may be realised on the microcircuit level -- and how it may be analysed using tools similar to those used experimentally. I outline some predictions from the hypothesis that the macroscopic connectivity of the cortex is optimised for attractor memory function. I also discuss methodological aspects of modelling in computational neuroscience. / QC 20100916