Jakub M. Tomczak

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  • DIVA: Domain Invariant Variational Autoencoders

    We consider the problem of domain generalization, namely, how to learn representations given data from a set of domains that generalize to data from a previously unseen domain. We propose the Domain Invariant Variational Autoencoder (DIVA), a generative model that tackles this problem by learning three independent latent subspaces, one for the domain, one for the class, and one for any residual variations. We highlight that due to the generative nature of our model we can also incorporate unlabeled data from known or previously unseen domains. To the best of our knowledge this has not been done before in a domain generalization setting. This property is highly desirable in fields like medical imaging where labeled data is scarce. We experimentally evaluate our model on the rotated MNIST benchmark and a malaria cell images dataset where we show that (i) the learned subspaces are indeed complementary to each other, (ii) we improve upon recent works on this task and (iii) incorporating unlabelled data can boost the performance even further.

    05/24/2019 ∙ by Maximilian Ilse, et al. ∙ 11 share

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  • Video Compression With Rate-Distortion Autoencoders

    In this paper we present a a deep generative model for lossy video compression. We employ a model that consists of a 3D autoencoder with a discrete latent space and an autoregressive prior used for entropy coding. Both autoencoder and prior are trained jointly to minimize a rate-distortion loss, which is closely related to the ELBO used in variational autoencoders. Despite its simplicity, we find that our method outperforms the state-of-the-art learned video compression networks based on motion compensation or interpolation. We systematically evaluate various design choices, such as the use of frame-based or spatio-temporal autoencoders, and the type of autoregressive prior. In addition, we present three extensions of the basic method that demonstrate the benefits over classical approaches to compression. First, we introduce semantic compression, where the model is trained to allocate more bits to objects of interest. Second, we study adaptive compression, where the model is adapted to a domain with limited variability, e.g., videos taken from an autonomous car, to achieve superior compression on that domain. Finally, we introduce multimodal compression, where we demonstrate the effectiveness of our model in joint compression of multiple modalities captured by non-standard imaging sensors, such as quad cameras. We believe that this opens up novel video compression applications, which have not been feasible with classical codecs.

    08/14/2019 ∙ by Amirhossein Habibian, et al. ∙ 7 share

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  • Combinatorial Bayesian Optimization using Graph Representations

    This paper focuses on Bayesian Optimization - typically considered with continuous inputs - for discrete search input spaces, including integer, categorical or graph structured input variables. In Gaussian process-based Bayesian Optimization a problem arises, as it is not straightforward to define a proper kernel on discrete input structures, where no natural notion of smoothness or similarity could be provided. We propose COMBO, a method that represents values of discrete variables as vertices of a graph and then use the diffusion kernel on that graph. As the graph size explodes with the number of categorical variables and categories, we propose the graph Cartesian product to decompose the graph into smaller sub-graphs, enabling kernel computation in linear time with respect to the number of input variables. Moreover, in our formulation we learn a scale parameter per subgraph. In empirical studies on four discrete optimization problems we demonstrate that our method is on par or outperforms the state-of-the-art in discrete Bayesian optimization.

    02/01/2019 ∙ by ChangYong Oh, et al. ∙ 2 share

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  • Improving Variational Auto-Encoders using convex combination linear Inverse Autoregressive Flow

    In this paper, we propose a new volume-preserving flow and show that it performs similarly to the linear general normalizing flow. The idea is to enrich a linear Inverse Autoregressive Flow by introducing multiple lower-triangular matrices with ones on the diagonal and combining them using a convex combination. In the experimental studies on MNIST and Histopathology data we show that the proposed approach outperforms other volume-preserving flows and is competitive with current state-of-the-art linear normalizing flow.

    06/07/2017 ∙ by Jakub M. Tomczak, et al. ∙ 0 share

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  • VAE with a VampPrior

    Many different methods to train deep generative models have been introduced in the past. In this paper, we propose to extend the variational auto-encoder (VAE) framework with a new type of prior which we call "Variational Mixture of Posteriors" prior, or VampPrior for short. The VampPrior consists of a mixture distribution (e.g., a mixture of Gaussians) with components given by variational posteriors conditioned on learnable pseudo-inputs. We further extend this prior to a two layer hierarchical model and show that this architecture with a coupled prior and posterior, learns significantly better models. The model also avoids the usual local optima issues related to useless latent dimensions that plague VAEs. We provide empirical studies on six datasets, namely, static and binary MNIST, OMNIGLOT, Caltech 101 Silhouettes, Frey Faces and Histopathology patches, and show that applying the hierarchical VampPrior delivers state-of-the-art results on all datasets in the unsupervised permutation invariant setting and the best results or comparable to SOTA methods for the approach with convolutional networks.

    05/19/2017 ∙ by Jakub M. Tomczak, et al. ∙ 0 share

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  • Learning Deep Architectures for Interaction Prediction in Structure-based Virtual Screening

    We introduce a deep learning architecture for structure-based virtual screening that generates fixed-sized fingerprints of proteins and small molecules by applying learnable atom convolution and softmax operations to each compound separately. These fingerprints are further transformed non-linearly, their inner-product is calculated and used to predict the binding potential. Moreover, we show that widely used benchmark datasets may be insufficient for testing structure-based virtual screening methods that utilize machine learning. Therefore, we introduce a new benchmark dataset, which we constructed based on DUD-E and PDBBind databases.

    10/23/2016 ∙ by Adam Gonczarek, et al. ∙ 0 share

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  • Deep Learning with Permutation-invariant Operator for Multi-instance Histopathology Classification

    The computer-aided analysis of medical scans is a longstanding goal in the medical imaging field. Currently, deep learning has became a dominant methodology for supporting pathologists and radiologist. Deep learning algorithms have been successfully applied to digital pathology and radiology, nevertheless, there are still practical issues that prevent these tools to be widely used in practice. The main obstacles are low number of available cases and large size of images (a.k.a. the small n, large p problem in machine learning), and a very limited access to annotation at a pixel level that can lead to severe overfitting and large computational requirements. We propose to handle these issues by introducing a framework that processes a medical image as a collection of small patches using a single, shared neural network. The final diagnosis is provided by combining scores of individual patches using a permutation-invariant operator (combination). In machine learning community such approach is called a multi-instance learning (MIL).

    12/01/2017 ∙ by Jakub M. Tomczak, et al. ∙ 0 share

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  • Attention-based Deep Multiple Instance Learning

    Multiple instance learning (MIL) is a variation of supervised learning where a single class label is assigned to a bag of instances. In this paper, we state the MIL problem as learning the Bernoulli distribution of the bag label where the bag label probability is fully parameterized by neural networks. Furthermore, we propose a neural network-based permutation-invariant aggregation operator that corresponds to the attention mechanism. Notably, an application of the proposed attention-based operator provides insight into the contribution of each instance to the bag label. We show empirically that our approach achieves comparable performance to the best MIL methods on benchmark MIL datasets and it outperforms other methods on a MNIST-based MIL dataset and two real-life histopathology datasets without sacrificing interpretability.

    02/13/2018 ∙ by Maximilian Ilse, et al. ∙ 0 share

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  • Hyperspherical Variational Auto-Encoders

    The Variational Auto-Encoder (VAE) is one of the most used unsupervised machine learning models. But although the default choice of a Gaussian distribution for both the prior and posterior represents a mathematically convenient distribution often leading to competitive results, we show that this parameterization fails to model data with a latent hyperspherical structure. To address this issue we propose using a von Mises-Fisher (vMF) distribution instead, leading to a hyperspherical latent space. Through a series of experiments we show how such a hyperspherical VAE, or S-VAE, is more suitable for capturing data with a hyperspherical latent structure, while outperforming a normal, N-VAE, in low dimensions on other data types.

    04/03/2018 ∙ by Tim R. Davidson, et al. ∙ 0 share

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  • Sylvester Normalizing Flows for Variational Inference

    Variational inference relies on flexible approximate posterior distributions. Normalizing flows provide a general recipe to construct flexible variational posteriors. We introduce Sylvester normalizing flows, which can be seen as a generalization of planar flows. Sylvester normalizing flows remove the well-known single-unit bottleneck from planar flows, making a single transformation much more flexible. We compare the performance of Sylvester normalizing flows against planar flows and inverse autoregressive flows and demonstrate that they compare favorably on several datasets.

    03/15/2018 ∙ by Rianne van den Berg, et al. ∙ 0 share

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  • Hierarchical VampPrior Variational Fair Auto-Encoder

    Decision making is a process that is extremely prone to different biases. In this paper we consider learning fair representation that aim at removing nuisance (sensitive) information from the decision process. For this purpose, we propose to use deep generative modeling and adapt a hierarchical Variational Auto-Encoder to learn fair representations. Moreover, we utilize the mutual information as a useful regularizer for enforcing fairness of a representation. In experiments on two benchmark datasets and two scenarios where the sensitive variables are fully and partially observable, we show that the proposed approach either outperforms or performs on par with the current best model.

    06/26/2018 ∙ by Philip Botros, et al. ∙ 0 share

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