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Background: Long reads provide valuable information regarding the sequence composition of genomes. Long reads are usually very noisy which renders their alignments on the reference genome a daunting task. It may take days to process datasets enough to sequence a human genome on a single node. Hence, it is of primary importance to have an aligner which can operate on distributed clusters of computers with high performance in accuracy and speed. Results: In this paper, we presented IMOS, an aligner for mapping noisy long reads to the reference genome. It can be used on a single node as well as on distributed nodes. In its single-node mode, IMOS is an Improved version of Meta-aligner (IM)... 

Fundamental limits of communication is studied in a 4 × 4 interference network, in which the transmitters are equipped with cache memories. Each of the receivers requests one file from a library of N equal-size files. The caches at the transmitters are filled without the knowledge of the user demands, such that all possible demand combinations can be satisfied reliably over the interference channel. The achievable normalized delivery time (NDT) is studied under centralized cache placement. By combining the interference alignment (IA) and zero-forcing (ZF) techniques, a novel caching and transmission scheme is presented, and is shown to be optimal for all possible cache sizes; fully... 

Association mapping of genetic diseases has attracted extensive research interest during the recent years. However, most of the methodologies introduced so far suffer from spurious inference of the associated sites due to population inhomogeneities. In this paper, we introduce a statistical framework to compensate for this shortcoming by equipping the current methodologies with a state-of-the-art clustering algorithm being widely used in population genetics applications. The proposed framework jointly infers the disease-associated factors and the hidden population structures. In this regard, a Markov Chain-Monte Carlo (MCMC) procedure has been employed to assess the posterior probability... 

In this paper, learning of tree-structured Gaussian graphical models from distributed data is addressed. In our model, samples are stored in a set of distributed machines where each machine has access to only a subset of features. A central machine is then responsible for learning the structure based on received messages from the other nodes. We present a set of communication-efficient strategies, which are theoretically proved to convey sufficient information for reliable learning of the structure. In particular, our analyses show that even if each machine sends only the signs of its local data samples to the central node, the tree structure can still be recovered with high accuracy. Our... 

In this paper, the metric theory of Diophantine approximation associated with mixed type small linear forms is investigated. We prove Khintchine–Groshev type theorems for both the real and complex number systems. The motivation for these metrical results comes from their applications in signal processing. One such application is discussed explicitly. © Springer Nature Switzerland AG 2020  

We consider the K-user Multiple Input Multiple Output (MIMO) Gaussian interference channel with M antennas at each transmitter and N antennas at each receiver. It is assumed that channel coefficients are constant real numbers and are available at all transmitters and at all receivers. The main objective of this paper is to characterize the number of Degrees of Freedom (DoF) of this channel. Using the real interference alignment technique introduced in [20], we show that MN/M+NK degrees of freedom can be achieved for almost all channel realizations. Also, a new upper-bound on the DoF of this channel is provided. This upper-bound coincides with our achievable DoF for K ≥ Ku≜M+N/gcd(M;N), where... 

We consider the K-user Multiple Input Multiple Output (MIMO) Gaussian interference channel with M antennas at each transmitter and N antennas at each receiver. It is assumed that channel coefficients are constant real numbers and are available at all transmitters and at all receivers. The main objective of this paper is to characterize the number of Degrees of Freedom (DoF) of this channel. Using the real interference alignment technique introduced in Motahari et al., 2014, we show that MN M+N K degrees of freedom can be achieved for almost all channel realizations. Also, a new upper-bound on the DoF of this channel is provided. This upper-bound coincides with our achievable DoF for K K u... 

Remote observation of the state trajectory of nonlinear dynamic systems over limited capacity communication channels is studied. It is shown that two extreme cases are possible: Either the system is fully observable or the error in estimation blows up. The key observation is that such behavior is determined by the relationship between the Shannon capacity and the Lyapunov exponents; the well-known characterizing parameters of a communication channel on one side, and a dynamic system from the other side. In particular, it is proved that for nonlinear systems with initial state x0, the minimum capacity of an additive white Gaussian noise channel required for full observation of the system in... 

In the problems of Genome-Wide Association Study (GWAS), the objective is to associate subsequences of individual's genomes to the observable characteristics called phenotypes. The genome containing the biological information of an individual can be represented by a sequence of length G. Many observable characteristics of the individuals can be related to a subsequence of a given length L, called causal subsequence. The environmental affects make the relation between the causal subsequence and the observable characteristics a stochastic function. Our objective in this paper is to detect the causal subsequence of a specific phenotype using a dataset of N individuals and their observed... 

In this paper, we address the stability problem of a noiseless linear time invariant control system over parallel Gaussian channels with feedback. It is shown that the eigenvalues-rate condition which has been proved as a necessary condition, is also sufficient for stability over parallel Gaussian channels. In fact, it is proved that for stabilizing a control system over the parallel Gaussian channels, it suffices that the Shannon channel capacity obtained by the water filling technique is greater than the sum of the logarithm of the unstable eigenvalues magnitude. In order to prove this sufficient condition, we propose a new nonlinear joint source channel coding for parallel Gaussian... 

This paper is concerned with estimation and stability of control systems over communication links subject to limited capacity, power constraint, fading, noisy feedback, and different transmission rate rather than system sampling rate. A key issue addressed in this paper is that in the presence of noisy feedback associated with channel, which models transmission of finite number of bits over such links as is the case in most practical scenarios, the well-known eigenvalues rate condition is still a tight bound for stability. Based on an information theoretic analysis, necessary conditions are derived for stability of discrete-time linear control systems via the distant controller in the mean... 

This paper is concerned with estimation and stability of control systems over communication links subject to limited capacity, power constraint, fading, noisy feedback, and different transmission rate rather than system sampling rate. A key issue addressed in this paper is that in the presence of noisy feedback associated with channel, which models transmission of finite number of bits over such links as is the case in most practical scenarios, the well-known eigenvalues rate condition is still a tight bound for stability. Based on an information theoretic analysis, necessary conditions are derived for stability of discrete-time linear control systems via the distant controller in the mean... 

Centralized coded caching and delivery is studied for a radio access combination network (RACN), whereby a set of H edge nodes (ENs), connected to a cloud server via orthogonal fronthaul links with limited capacity, serve a total of K user equipments (UEs) over wireless links. The cloud server is assumed to hold a library of N files, each of size F bits; and each user, equipped with a cache of size μ R N F bits, is connected to a distinct set of r ENs each of which equipped with a cache of size μTNF bits, where μT , μ R in [{0,1}] are the fractional cache capacities of the UEs and the ENs, respectively. The objective is to minimize the normalized delivery time (NDT), which refers to the... 

This article addresses the stabilization of noiseless nonlinear dynamic systems over limited capacity communication channels. It is shown that the stability of nonlinear dynamic systems over memory-less communication channels implies an inequality condition between the Shannon channel capacity and the summation of the positive equilibrium Lyapunov exponents of the dynamic system or, equivalently, the logarithms of the magnitude of the unstable eigenvalues of system Jacobian. Furthermore, we propose an encoder, decoder, and a controller to prove that scalar nonlinear dynamic systems are stabilizable under the aforementioned inequality condition over the digital noiseless and the packet...