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We introduce and test a method to predict the sequence of DNA molecules from in silico unzipping experiments. The method is based on Bayesian inference and on the Viterbi decoding algorithm. The probability of misprediction decreases…
Various studies that address the compressed sensing problem with Multiple Measurement Vectors (MMVs) have been recently carried. These studies assume the vectors of the different channels to be jointly sparse. In this paper, we relax this…
In this paper we present a collection of results pertaining to haplotyping. The first set of results concerns the combinatorial problem of reconstructing haplotypes from incomplete and/or imperfectly sequenced haplotype data. More…
We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…
Large Language Models (LLMs) have shown impressive abilities in many applications. When a concrete and precise answer is desired, it is important to have a quantitative estimation of the potential error rate. However, this can be…
Inferring the sequence of states from observations is one of the most fundamental problems in Hidden Markov Models. In statistical physics language, this problem is equivalent to computing the marginals of a one-dimensional model with a…
Recent advances in genomics have underscored the surprising ubiquity of DNA copy number variation (CNV). Fortunately, modern genotyping platforms also detect CNVs with fairly high reliability. Hidden Markov models and algorithms have played…
The ability to take into account the characteristics - also called features - of observations is essential in Natural Language Processing (NLP) problems. Hidden Markov Chain (HMC) model associated with classic Forward-Backward probabilities…
Motivation: Assigning RNA-seq reads to their transcript of origin is a fundamental task in transcript expression estimation. Where ambiguities in assignments exist due to transcripts sharing sequence, e.g. alternative isoforms or alleles,…
Most successful applications of deep learning involve similar training and test conditions. However, tasks such as biological sequence design involve searching for sequences that improve desirable properties beyond previously known values,…
We propose a general method for optimally approximating an arbitrary matrix $\mathbf{M}$ by a structured matrix $\mathbf{T}$ (circulant, Toeplitz/Hankel, etc.) and examine its use for estimating the spectra of genomic linkage disequilibrium…
Measurement error in count data is common but underexplored in the literature, particularly in contexts where observed scores are bounded and arise from discrete scoring processes. Motivated by applications in oral reading fluency…
We consider models for which it is important, early in processing, to estimate some variables with high precision, but perhaps at relatively low rates of recall. If some variables can be identified with near certainty, then they can be…
Handling incomplete and heterogeneous data remains a central challenge in real-world machine learning, where missing values may follow complex mechanisms (MCAR, MAR, MNAR) and features can be of mixed types (numerical and categorical).…
Latent Markov (LM) models represent an important tool of analysis of longitudinal data when response variables are affected by time-varying unobserved heterogeneity, which is accounted for by a hidden Markov chain. In order to avoid bias…
Universally achievable error exponents pertaining to certain families of channels (most notably, discrete memoryless channels (DMC's)), and various ensembles of random codes, are studied by combining the competitive minimax approach,…
Standard practice in Hidden Markov Model (HMM) selection favors the candidate with the highest full-sequence likelihood, although this is equivalent to making a decision based on a single realization. We introduce a \emph{fragment-based}…
Mixtures of Hidden Markov Models (MHMMs) are frequently used for clustering of sequential data. An important aspect of MHMMs, as of any clustering approach, is that they can be interpretable, allowing for novel insights to be gained from…
The paper studies optimal coding of hidden Markov sources (HMS), which represent a broad class of practical sources obtained through noisy acquisition processes, beside their explicit modeling use in speech processing and recognition, image…
Let G be a finite strongly connected aperiodic directed graph in which each edge carries a label from a finite alphabet A. Then G induces a trellis coded quantizer for encoding an alphabet A memoryless source. A source sequence of long…