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Increasing Expressivity of a Hyperspherical VAE
Davidson, Tim R., Tomczak, Jakub M., Gavves, Efstratios
Learning suitable latent representations for observed, high-dimensional data is an important research topic underlying many recent advances in machine learning. While traditionally the Gaussian normal distribution has been the go-to latent parameterization, recently a variety of works have successfully proposed the use of manifold-valued latents. In one such work (Davidson et al., 2018), the authors empirically show the potential benefits of using a hyperspherical von Mises-Fisher (vMF) distribution in low dimensionality. However, due to the unique distributional form of the vMF, expressivity in higher dimensional space is limited as a result of its scalar concentration parameter leading to a 'hyperspherical bottleneck'. In this work we propose to extend the usability of hyperspherical parameterizations to higher dimensions using a product-space instead, showing improved results on a selection of image datasets.
Combining docking pose rank and structure with deep learning improves protein-ligand binding mode prediction
Morrone, Joseph A., Weber, Jeffrey K., Huynh, Tien, Luo, Heng, Cornell, Wendy D.
We present a simple, modular graph-based convolutional neural network that takes structural information from protein-ligand complexes as input to generate models for activity and binding mode prediction. Complex structures are generated by a standard docking procedure and fed into a dual-graph architecture that includes separate sub-networks for the ligand bonded topology and the ligand-protein contact map. This network division allows contributions from ligand identity to be distinguished from effects of protein-ligand interactions on classification. We show, in agreement with recent literature, that dataset bias drives many of the promising results on virtual screening that have previously been reported. However, we also show that our neural network is capable of learning from protein structural information when, as in the case of binding mode prediction, an unbiased dataset is constructed. We develop a deep learning model for binding mode prediction that uses docking ranking as input in combination with docking structures. This strategy mirrors past consensus models and outperforms the baseline docking program in a variety of tests, including on cross-docking datasets that mimic real-world docking use cases. Furthermore, the magnitudes of network predictions serve as reliable measures of model confidence
Self-Paced Contextual Reinforcement Learning
Klink, Pascal, Abdulsamad, Hany, Belousov, Boris, Peters, Jan
Generalization and adaptation of learned skills to novel situations is a core requirement for intelligent autonomous robots. Although contextual reinforcement learning provides a principled framework for learning and generalization of behaviors across related tasks, it generally relies on uninformed sampling of environments from an unknown, uncontrolled context distribution, thus missing the benefits of structured, sequential learning. We introduce a novel relative entropy reinforcement learning algorithm that gives the agent the freedom to control the intermediate task distribution, allowing for its gradual progression towards the target context distribution. Empirical evaluation shows that the proposed curriculum learning scheme drastically improves sample efficiency and enables learning in scenarios with both broad and sharp target context distributions in which classical approaches perform sub-optimally.
A mathematical theory of cooperative communication
Wang, Pei, Wang, Junqi, Paranamana, Pushpi, Shafto, Patrick
Cooperative communication plays a central role in theories of human cognition, language, development, and culture, and is increasingly relevant in human-algorithm and robot interaction. Existing models are algorithmic in nature and do not shed light on the statistical problem solved in cooperation or on constraints imposed by violations of common ground. We present a mathematical theory of cooperative communication that unifies three broad classes of algorithmic models as approximations of Optimal Transport (OT). We derive a statistical interpretation for the problem approximated by existing models in terms of entropy minimization, or likelihood maximizing, plans. We show that some models are provably robust to violations of common ground, even supporting online, approximate recovery from discovered violations, and derive conditions under which other models are provably not robust. We do so using gradient-based methods which introduce novel algorithmic-level perspectives on cooperative communication. Our mathematical approach complements and extends empirical research, providing strong theoretical tools derivation of a priori constraints on models and implications for cooperative communication in theory and practice.
Semantic Preserving Generative Adversarial Models
Harel, Shahar, Maor, Meir, Ronen, Amir
Shahar Harel, Meir Maor †, Amir Ronen ‡ SparkBeyond L TD Israel Abstract We introduce generative adversarial models in which the discriminator is replaced by a calibrated (non-differentiable) classifier repeatedly enhanced by domain relevant features. The role of the classifier is to prove that the actual and generated data differ over a controlled semantic space. We demonstrate that such models have the ability to generate objects with strong guarantees on their properties in a wide range of domains. They require less data than ordinary GANs, provide natural stopping conditions, uncover important properties of the data, and enhance transfer learning. Our techniques can be combined with standard generative models. We demonstrate the usefulness of our approach by applying it to several unrelated domains: generating good locations for cellular antennae, molecule generation preserving key chemical properties, and generating and extrapolating lines from very few data points. Intriguing open problems are presented as well. 1 Introduction Generative adversarial networks (GANs) (Goodfellow et al. 2014) achieved many impressive results. Recent literature surveys as well as a large code repository can be found at (Creswell et al. 2017; Kurach et al. 2018; Hindupur). Arguably however, most of these results were obtained for generation of images, text, and videos. First, humans have very good judgment of the quality of the generated objects and hence can fine-tune the generative model until it is satisfactory. Second, there exists a huge amount of available data that can be used for model training. This is unlikely to be the case in a wide range of important domains (e.g.
Neural network integral representations with the ReLU activation function
Dereventsov, Anton, Petrosyan, Armenak, Webster, Clayton
We derive a formula for neural network integral representations on the sphere with the ReLU activation function under the finite $L_1$ norm (with respect to Lebesgue measure on the sphere) assumption on the outer weights. In one dimensional case, we further solve via a closed-form formula all possible such representations. Additionally, in this case our formula allows one to explicitly solve the least $L_1$ norm neural network representation for a given function.
Meta-Learning Deep Energy-Based Memory Models
Bartunov, Sergey, Rae, Jack W, Osindero, Simon, Lillicrap, Timothy P
We study the problem of learning associative memory -- a system which is able to retrieve a remembered pattern based on its distorted or incomplete version. Attractor networks provide a sound model of associative memory: patterns are stored as attractors of the network dynamics and associative retrieval is performed by running the dynamics starting from a query pattern until it converges to an attractor. In such models the dynamics are often implemented as an optimization procedure that minimizes an energy function, such as in the classical Hopfield network. In general it is difficult to derive a writing rule for a given dynamics and energy that is both compressive and fast. Thus, most research in energy-based memory has been limited either to tractable energy models not expressive enough to handle complex high-dimensional objects such as natural images, or to models that do not offer fast writing. We present a novel meta-learning approach to energy-based memory models (EBMM) that allows one to use an arbitrary neural architecture as an energy model and quickly store patterns in its weights. We demonstrate experimentally that our EBMM approach can build compressed memories for synthetic and natural data, and is capable of associative retrieval that outperforms existing memory systems in terms of the reconstruction error and compression rate.
Transfer Brain MRI Tumor Segmentation Models Across Modalities with Adversarial Networks
Giacomello, Edoardo, Loiacono, Daniele, Mainardi, Luca
In this work, we present an approach to brain cancer segmentation in Magnetic Resonance Images (MRI) using Adversarial Networks, that have been successfully applied to several complex image processing problems in recent years. Most of the segmentation approaches presented in the literature exploit the data from all the contrast modalities typically acquired in the clinical practice: T1-weighted, T1-weighted contrast-enhanced, T2-weighted, and T2-FLAIR. Unfortunately, often not all these modalities are available for each patient. Accordingly, in this paper, we extended a previous segmentation approach based on Adversarial Networks to deal with this issue. In particular, we trained a segmentation model for each modality at once and evaluated the performances of these models. Thus, we investigated the possibility of transferring the best among these single-modality models to the other modalities. Our results suggest that such a transfer learning approach allows achieving better performances for almost all the target modalities.
Irregular Convolutional Auto-Encoder on Point Clouds
Yuhui, Zhang, Gutmann, Greg, Akihiko, Konagaya
We proposed a novel graph convolutional neural network that could construct a coarse, sparse latent point cloud from a dense, raw point cloud. With a novel non-isotropic convolution operation defined on irregular geometries, the model then can reconstruct the original point cloud from this latent cloud with fine details. Furthermore, we proposed that it is even possible to perform particle simulation using the latent cloud encoded from some simulated particle cloud (e.g. fluids), to accelerate the particle simulation process. Our model has been tested on ShapeNetCore dataset for Auto-Encoding with a limited latent dimension and tested on a synthesis dataset for fluids simulation. We also compare the model with other state-of-the-art models, and several visualizations were done to intuitively understand the model.
Dynamic Self-training Framework for Graph Convolutional Networks
Zhou, Ziang, Zhang, Shenzhong, Huang, Zengfeng
Graph neural networks (GNN) such as GCN, GAT, MoNet have achieved state-of-the-art results on semi-supervised learning on graphs. However, when the number of labeled nodes is very small, the performances of GNNs downgrade dramatically. Self-training has proved to be effective for resolving this issue, however, the performance of self-trained GCN is still inferior to that of G2G and DGI for many settings. Moreover, additional model complexity make it more difficult to tune the hyper-parameters and do model selection. We argue that the power of self-training is still not fully explored for the node classification task. In this paper, we propose a unified end-to-end self-training framework called \emph{Dynamic Self-traning}, which generalizes and simplifies prior work. A simple instantiation of the framework based on GCN is provided and empirical results show that our framework outperforms all previous methods including GNNs, embedding based method and self-trained GCNs by a noticeable margin. Moreover, compared with standard self-training, hyper-parameter tuning for our framework is easier.