Suppose one is faced with the challenge of tissue segmentation in MR images, without annotators at their center to provide labeled training data. One option is to go to another medical center for a trained classifier. Sadly, tissue classifiers do not generalize well across centers due to voxel intensity shifts caused by center-specific acquisition protocols. However, certain aspects of segmentations, such as spatial smoothness, remain relatively consistent and can be learned separately. Here we present a smoothness prior that is fit to segmentations produced at another medical center. This informative prior is presented to an unsupervised Bayesian model. The model clusters the voxel intensities, such that it produces segmentations that are similarly smooth to those of the other medical center. In addition, the unsupervised Bayesian model is extended to a semi-supervised variant, which needs no visual interpretation of clusters into tissues.

In the space of only a few years, deep generative modeling has revolutionized how we think of artificial creativity, yielding autonomous systems which produce original images, music, and text. Inspired by these successes, researchers are now applying deep generative modeling techniques to the generation and optimization of molecules - in our review we found 45 papers on the subject published in the past two years. These works point to a future where such systems will be used to generate lead molecules, greatly reducing resources spent downstream synthesizing and characterizing bad leads in the lab. In this review we survey the increasingly complex landscape of models and representation schemes that have been proposed. The four classes of techniques we describe are recursive neural networks, autoencoders, generative adversarial networks, and reinforcement learning. After first discussing some of the mathematical fundamentals of each technique, we draw high level connections and comparisons with other techniques and expose the pros and cons of each. Several important high level themes emerge as a result of this work, including the shift away from the SMILES string representation of molecules towards more sophisticated representations such as graph grammars and 3D representations, the importance of reward function design, the need for better standards for benchmarking and testing, and the benefits of adversarial training and reinforcement learning over maximum likelihood based training.

Single Molecule Real-Time (SMRT) sequencing is a recent advancement of Next Gen technology developed by Pacific Bio (PacBio). It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it. To deal with the high error probability of SMRT data, a novel contextual Locality Sensitive Hashing (conLSH) based algorithm is proposed in this article, which can effectively align the noisy SMRT reads to the reference genome. Here, sequences are hashed together based not only on their closeness, but also on similarity of context. The algorithm has $\mathcal{O}(n^{\rho+1})$ space requirement, where $n$ is the number of sequences in the corpus and $\rho$ is a constant. The indexing time and querying time are bounded by $\mathcal{O}( \frac{n^{\rho+1} \cdot \ln n}{\ln \frac{1}{P_2}})$ and $\mathcal{O}(n^\rho)$ respectively, where $P_2 > 0$, is a probability value. This algorithm is particularly useful for retrieving similar sequences, a widely used task in biology. The proposed conLSH based aligner is compared with rHAT, popularly used for aligning SMRT reads, and is found to comprehensively beat it in speed as well as in memory requirements. In particular, it takes approximately $24.2\%$ less processing time, while saving about $70.3\%$ in peak memory requirement for H.sapiens PacBio dataset.

Machine learning, especially deep neural networks, has been rapidly developed in fields including computer vision, speech recognition and reinforcement learning. Although Mini-batch SGD is one of the most popular stochastic optimization methods in training deep networks, it shows a slow convergence rate due to the large noise in gradient approximation. In this paper, we attempt to remedy this problem by building more efficient batch selection method based on typicality sampling, which reduces the error of gradient estimation in conventional Minibatch SGD. We analyze the convergence rate of the resulting typical batch SGD algorithm and compare convergence properties between Minibatch SGD and the algorithm. Experimental results demonstrate that our batch selection scheme works well and more complex Minibatch SGD variants can benefit from the proposed batch selection strategy.

We introduce a dynamic generative model, Bayesian allocation model (BAM), which establishes explicit connections between nonnegative tensor factorization (NTF), graphical models of discrete probability distributions and their Bayesian extensions, and the topic models such as the latent Dirichlet allocation. BAM is based on a Poisson process, whose events are marked by using a Bayesian network, where the conditional probability tables of this network are then integrated out analytically. We show that the resulting marginal process turns out to be a Polya urn, an integer valued self-reinforcing process. This urn processes, which we name a Polya-Bayes process, obey certain conditional independence properties that provide further insight about the nature of NTF. These insights also let us develop space efficient simulation algorithms that respect the potential sparsity of data: we propose a class of sequential importance sampling algorithms for computing NTF and approximating their marginal likelihood, which would be useful for model selection. The resulting methods can also be viewed as a model scoring method for topic models and discrete Bayesian networks with hidden variables. The new algorithms have favourable properties in the sparse data regime when contrasted with variational algorithms that become more accurate when the total sum of the elements of the observed tensor goes to infinity. We illustrate the performance on several examples and numerically study the behaviour of the algorithms for various data regimes.

Data similarity is a key concept in many data-driven applications. Many algorithms are sensitive to similarity measures. To tackle this fundamental problem, automatically learning of similarity information from data via self-expression has been developed and successfully applied in various models, such as low-rank representation, sparse subspace learning, semi-supervised learning. However, it just tries to reconstruct the original data and some valuable information, e.g., the manifold structure, is largely ignored. In this paper, we argue that it is beneficial to preserve the overall relations when we extract similarity information. Specifically, we propose a novel similarity learning framework by minimizing the reconstruction error of kernel matrices, rather than the reconstruction error of original data adopted by existing work. Taking the clustering task as an example to evaluate our method, we observe considerable improvements compared to other state-of-the-art methods. More importantly, our proposed framework is very general and provides a novel and fundamental building block for many other similarity-based tasks. Besides, our proposed kernel preserving opens up a large number of possibilities to embed high-dimensional data into low-dimensional space.

Evolution has produced a multi-scale mosaic of interacting adaptive units. Innovations arise when perturbations push parts of the system away from stable equilibria into new regimes where previously well-adapted solutions no longer work. Here we explore the hypothesis that multi-agent systems sometimes display intrinsic dynamics arising from competition and cooperation that provide a naturally emergent curriculum, which we term an autocurriculum. The solution of one social task often begets new social tasks, continually generating novel challenges, and thereby promoting innovation. Under certain conditions these challenges may become increasingly complex over time, demanding that agents accumulate ever more innovations.

Convolution Neural Networks (CNN) have been extremely successful in solving intensive computer vision tasks. The convolutional filters used in CNNs have played a major role in this success, by extracting useful features from the inputs. Recently researchers have tried to boost the performance of CNNs by re-calibrating the feature maps produced by these filters, e.g., Squeeze-and-Excitation Networks (SENets). These approaches have achieved better performance by \textit{Exciting} up the important channels or feature maps while diminishing the rest. However, in the process, architectural complexity has increased. We propose an architectural block that introduces much lower complexity than the existing methods of CNN performance boosting while performing significantly better than them. We carry out experiments on the CIFAR, ImageNet and MS-COCO datasets, and show that the proposed block can challenge the state-of-the-art results. Our method boosts the ResNet-50 architecture to perform comparably to the ResNet-152 architecture, which is a three times deeper network, on classification. We also show experimentally that our method is not limited to classification but also generalizes well to other tasks such as object detection.

Geometric deep learning provides a principled and versatile manner for the integration of imaging and non-imaging modalities in the medical domain. Graph Convolutional Networks (GCNs) in particular have been explored on a wide variety of problems such as disease prediction, segmentation, and matrix completion by leveraging large, multimodal datasets. In this paper, we introduce a new spectral domain architecture for deep learning on graphs for disease prediction. The novelty lies in defining geometric 'inception modules' which are capable of capturing intra- and inter-graph structural heterogeneity during convolutions. We design filters with different kernel sizes to build our architecture. We show our disease prediction results on two publicly available datasets. Further, we provide insights on the behaviour of regular GCNs and our proposed model under varying input scenarios on simulated data.

We present a novel deep learning architecture in which the convolution operation leverages heterogeneous kernels. The proposed HetConv (Heterogeneous Kernel-Based Convolution) reduces the computation (FLOPs) and the number of parameters as compared to standard convolution operation while still maintaining representational efficiency. To show the effectiveness of our proposed convolution, we present extensive experimental results on the standard convolutional neural network (CNN) architectures such as VGG \cite{vgg2014very} and ResNet \cite{resnet}. We find that after replacing the standard convolutional filters in these architectures with our proposed HetConv filters, we achieve 3X to 8X FLOPs based improvement in speed while still maintaining (and sometimes improving) the accuracy. We also compare our proposed convolutions with group/depth wise convolutions and show that it achieves more FLOPs reduction with significantly higher accuracy.