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Motivation: The study of diverse enzyme superfamilies can provide important insight into the relationships between protein sequence, structure and function. It is often challenging, however, to discover these relationships across a large…
Decoding sequences that stem from multiple transmissions of a codeword over an insertion, deletion, and substitution channel is a critical component of efficient deoxyribonucleic acid (DNA) data storage systems. In this paper, we consider a…
We propose an algorithm for detecting communities of links in networks which uses local information, is based on a new evaluation function, and allows for pervasive overlaps of communities. The complexity of the clustering task requires the…
We consider the problem of recovering a set of correlated signals (e.g., images from different viewpoints) from a few linear measurements per signal. We assume that each sensor in a network acquires a compressed signal in the form of linear…
Graph clustering is a fundamental problem that has been extensively studied both in theory and practice. The problem has been defined in several ways in literature and most of them have been proven to be NP-Hard. Due to their high practical…
Robotic and animal mapping systems share many of the same objectives and challenges, but differ in one key aspect: where much of the research in robotic mapping has focused on solving the data association problem, the grid cell neurons…
Non-overlapping codes are block codes that have arisen in diverse contexts of computer science and biology. Applications typically require finding non-overlapping codes with large cardinalities, but the maximum size of non-overlapping codes…
With their ability to handle an increased amount of information, multivariate and multichannel signals can be used to solve problems normally not solvable with signals obtained from a single source. One such problem is the decomposition…
Backpropagation of error (backprop) is a powerful algorithm for training machine learning architectures through end-to-end differentiation. However, backprop is often criticised for lacking biological plausibility. Recently, it has been…
We discuss the parallelization of algorithms for solving polynomial systems symbolically by way of triangular decomposition. Algorithms for solving polynomial systems combine low-level routines for performing arithmetic operations on…
A class of two-bit bit flipping algorithms for decoding low-density parity-check codes over the binary symmetric channel was proposed in [1]. Initial results showed that decoders which employ a group of these algorithms operating in…
Circular permutation connects the N and C termini of a protein and concurrently cleaves elsewhere in the chain, providing an important mechanism for generating novel protein fold and functions. However, their in genomes is unknown because…
We consider a wireless sensors network scenario where two nodes detect correlated sources and deliver them to a central collector via a wireless link. Differently from the Slepian-Wolf approach to distributed source coding, in the proposed…
Template matching is widely used for many applications in image and signal processing and usually is time-critical. Traditional methods usually focus on how to reduce the search locations by coarse-to-fine strategy or full search combined…
The variation in DNA copy number carries information on the modalities of genome evolution and misregulation of DNA replication in cancer cells; its study can be helpful to localize tumor suppressor genes, distinguish different populations…
Neural image compression, based on auto-encoders and overfitted representations, relies on a latent representation of the coded signal. This representation needs to be compact and uses low resolution feature maps. In the decoding process,…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
A quantum error correcting protocol can be substantially improved by taking into account features of the physical noise process. We present an efficient decoder for the surface code which can account for general noise features, including…
Topological quantum error-correcting codes are defined by geometrically local checks on a two-dimensional lattice of quantum bits (qubits), making them particularly well suited for fault-tolerant quantum information processing. Here, we…
We address the challenge of applying existing convolutional neural network (CNN) architectures to compressed images. Existing CNN architectures represent images as a matrix of pixel intensities with a specified dimension; this desired…