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Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum…
Maximum-likelihood methods are applied to the problem of absorption tomography. The reconstruction is done with the help of an iterative algorithm. We show how the statistics of the illuminating beam can be incorporated into the…
The knowledge of the network topology is imperative to precisely describing the viral dynamics of an SIS epidemic process. In scenarios for which the network topology is unknown, one resorts to reconstructing the network from observing the…
Maximum likelihood iteration is one of the most commonly used reconstruction algorithms in quantum tomography. The main appeal of the method is that it is easy to implement and that it converges reliably to a physically meaningful density…
We investigate the recovery of structures from large-area, low dose exposures that distribute the dose over many identical copies of an object. The reconstruction is done via a maximum likelihood approach that does neither require to…
Recently, ultra high-throughput sequencing of RNA (RNA-Seq) has been developed as an approach for analysis of gene expression. By obtaining tens or even hundreds of millions of reads of transcribed sequences, an RNA-Seq experiment can offer…
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Qualifying gene and isoform expression is one of the primary tasks for RNA-Seq experiments. Given a sequence of counts representing numbers of reads mapped to different positions (exons and junctions) of isoforms, methods based on Poisson…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
The microstructure analyses of porous media have considerable research value for the study of macroscopic properties. As the premise of conducting these analyses, the accurate reconstruction of microstructure digital model is also an…
Maximum-likelihood decoding is one of the central algorithmic problems in coding theory. It has been known for over 25 years that maximum-likelihood decoding of general linear codes is NP-hard. Nevertheless, it was so far unknown whether…
The problem of reconstructing a sequence of independent and identically distributed symbols from a set of equal size, consecutive, fragments, as well as a dependent reference sequence, is considered. First, in the regime in which the…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…
The single nucleotide polymorphism (SNP) is the most widely studied type of genetic variation. A haplotype is defined as the sequence of alleles at SNP sites on each haploid chromosome. Haplotype information is essential in unravelling the…
Motivation: RNA design aims to find RNA sequences that fold into a given target secondary structure, a problem also known as RNA inverse folding. However, not all target structures are designable. Recent advances in RNA designability have…
Event reconstruction is a central step in many particle physics experiments, turning detector observables into parameter estimates; for example estimating the energy of an interaction given the sensor readout of a detector. A corresponding…
Multi-segment reconstruction (MSR) problem consists of recovering a signal from noisy segments with unknown positions of the observation windows. One example arises in DNA sequence assembly, which is typically solved by matching short reads…