The regulatory process of Drosophila has been thoroughly studied for understanding a great variety of systems biology principles. While pattern-forming gene networks are further analysed in the transcription step, post-transcriptional events (e.g. translation, protein processing) play an important role in establishing protein expression patterns and levels. Since post-transcriptional regulation of gap genes in Drosophila depends on spatiotemporal interactions between mRNAs and gap proteins, proper physically-inspired stochastic models are required to study the existing link between both quantities. Previous research attempts have shown that the use of Gaussian processes (GPs) and differential equations leads to promising predictions when analysing regulatory networks. Here we aim at further investigating two types of physically-inspired GP models based on a reaction-diffusion equation where the main difference lies on whether the GP prior is placed. While one of them has been studied previously using gap protein data only, the other is novel and yields a simplistic approach requiring only the differentiation of kernel functions. In contrast to other stochastic frameworks, discretising the spatial space is not required here. Both GP models are tested under different conditions depending on the availability of gap gene mRNA expression data. Finally, their performances are assessed on a high-resolution dataset describing the blastoderm stage of the early embryo of Drosophila melanogaster.

This paper develops methodology for 3D radial visualization of high-dimensional datasets. Our display engine is called RadViz3D and extends the classic RadViz that visualizes multivariate data in the 2D plane by mapping every record to a point inside the unit circle. The classic RadViz display has equally-spaced anchor points on the unit circle, with each of them associated with an attribute or feature of the dataset. RadViz3D obtains equi-spaced anchor points exactly for the five Platonic solids and approximately for the other cases via a Fibonacci grid. We show that distributing anchor points at least approximately uniformly on the 3D unit sphere provides a better visualization than in 2D. We also propose a Max-Ratio Projection (MRP) method that utilizes the group information in high dimensions to provide distinctive lower-dimensional projections that are then displayed using Radviz3D. Our methodology is extended to datasets with discrete and mixed features where a generalized distributional transform is used in conjuction with copula models before applying MRP and RadViz3D visualization.

Data-dependent hashing has recently attracted attention due to being able to support efficient retrieval and storage of high-dimensional data such as documents, images, and videos. In this paper, we propose a novel learning-based hashing method called "Supervised Discrete Hashing with Relaxation" (SDHR) based on "Supervised Discrete Hashing" (SDH). SDH uses ordinary least squares regression and traditional zero-one matrix encoding of class label information as the regression target (code words), thus fixing the regression target. In SDHR, the regression target is instead optimized. The optimized regression target matrix satisfies a large margin constraint for correct classification of each example. Compared with SDH, which uses the traditional zero-one matrix, SDHR utilizes the learned regression target matrix and, therefore, more accurately measures the classification error of the regression model and is more flexible. As expected, SDHR generally outperforms SDH. Experimental results on two large-scale image datasets (CIFAR-10 and MNIST) and a large-scale and challenging face dataset (FRGC) demonstrate the effectiveness and efficiency of SDHR.

This paper revisits the special type of a neural network known under two names. In the statistics and machine learning community it is known as a multi-class logistic regression neural network. In the neural network community, it is simply the soft-max layer. The importance is underscored by its role in deep learning: as the last layer, whose autput is actually the classification of the input patterns, such as images. Our exposition focuses on mathematically rigorous derivation of the key equation expressing the gradient. The fringe benefit of our approach is a fully vectorized expression, which is a basis of an efficient implementation. The second result of this paper is the positivity of the second derivative of the cross-entropy loss function as function of the weights. This result proves that optimization methods based on convexity may be used to train this network. As a corollary, we demonstrate that no $L^2$-regularizer is needed to guarantee convergence of gradient descent.

This paper presents a recognition system for handwritten Pashto letters. However, handwritten character recognition is a challenging task. These letters not only differ in shape and style but also vary among individuals. The recognition becomes further daunting due to the lack of standard datasets for inscribed Pashto letters. In this work, we have designed a database of moderate size, which encompasses a total of 4488 images, stemming from 102 distinguishing samples for each of the 44 letters in Pashto. The recognition framework uses zoning feature extractor followed by K-Nearest Neighbour (KNN) and Neural Network (NN) classifiers for classifying individual letter. Based on the evaluation of the proposed system, an overall classification accuracy of approximately 70.05% is achieved by using KNN while 72% is achieved by using NN.

In this paper, we develop a novel Aligned-Spatial Graph Convolutional Network (ASGCN) model to learn effective features for graph classification. Our idea is to transform arbitrary-sized graphs into fixed-sized aligned grid structures, and define a new spatial graph convolution operation associated with the grid structures. We show that the proposed ASGCN model not only reduces the problems of information loss and imprecise information representation arising in existing spatially-based Graph Convolutional Network (GCN) models, but also bridges the theoretical gap between traditional Convolutional Neural Network (CNN) models and spatially-based GCN models. Moreover, the proposed ASGCN model can adaptively discriminate the importance between specified vertices during the process of spatial graph convolution, explaining the effectiveness of the proposed model. Experiments on standard graph datasets demonstrate the effectiveness of the proposed model.

Learning-based hashing algorithms are ``hot topics" because they can greatly increase the scale at which existing methods operate. In this paper, we propose a new learning-based hashing method called ``fast supervised discrete hashing" (FSDH) based on ``supervised discrete hashing" (SDH). Regressing the training examples (or hash code) to the corresponding class labels is widely used in ordinary least squares regression. Rather than adopting this method, FSDH uses a very simple yet effective regression of the class labels of training examples to the corresponding hash code to accelerate the algorithm. To the best of our knowledge, this strategy has not previously been used for hashing. Traditional SDH decomposes the optimization into three sub-problems, with the most critical sub-problem - discrete optimization for binary hash codes - solved using iterative discrete cyclic coordinate descent (DCC), which is time-consuming. However, FSDH has a closed-form solution and only requires a single rather than iterative hash code-solving step, which is highly efficient. Furthermore, FSDH is usually faster than SDH for solving the projection matrix for least squares regression, making FSDH generally faster than SDH. For example, our results show that FSDH is about 12-times faster than SDH when the number of hashing bits is 128 on the CIFAR-10 data base, and FSDH is about 151-times faster than FastHash when the number of hashing bits is 64 on the MNIST data-base. Our experimental results show that FSDH is not only fast, but also outperforms other comparative methods.

Estimating conditional dependence graphs and precision matrices are some of the most common problems in modern statistics and machine learning. When data are fully observed, penalized maximum likelihood-type estimators have become standard tools for estimating graphical models under sparsity conditions. Extensions of these methods to more complex settings where data are contaminated with additive or multiplicative noise have been developed in recent years. In these settings, however, the relative performance of different methods is not well understood and algorithmic gaps still exist. In particular, in high-dimensional settings these methods require using non-positive semidefinite matrices as inputs, presenting novel optimization challenges. We develop an alternating direction method of multipliers (ADMM) algorithm for these problems, providing a feasible algorithm to estimate precision matrices with indefinite input and potentially nonconvex penalties. We compare this method with existing alternative solutions and empirically characterize the tradeoffs between them. Finally, we use this method to explore the networks among US senators estimated from voting records data.

In this paper, we describe our submission to SemEval-2019 Task 4 on Hyperpartisan News Detection. Our system relies on a variety of engineered features originally used to detect propaganda. This is based on the assumption that biased messages are propagandistic in the sense that they promote a particular political cause or viewpoint. We trained a logistic regression model with features ranging from simple bag-of-words to vocabulary richness and text readability features. Our system achieved 72.9% accuracy on the test data that is annotated manually and 60.8% on the test data that is annotated with distant supervision. Additional experiments showed that significant performance improvements can be achieved with better feature pre-processing.

Many vital tasks in network analysis involve prediction over edges and nodes. For instance in node classification, we aim at predicting most likely node's label. In a social network, this might be an interest or preference of the user, or in citation network, the research area the paper belongs to [7]. In link prediction, we intend to model the existence of a link between pair of nodes. Predicted links in social networks may denote real-life friends and in citation networks related but unmentioned references. It is recently recognized, that the majority of real-world networks are naturally dynamic. It means they evolve over time and nodes as well as links can appear or disappear. We know so far, that considering temporal information about the network allows their better understanding and modeling [9,16], especially for supervised machine learning tasks.