Related papers: Trellis BMA: Coded Trace Reconstruction on IDS Cha…
In models to generate program source code from natural language, representing this code in a tree structure has been a common approach. However, existing methods often fail to generate complex code correctly due to a lack of ability to…
In the trace reconstruction problem, the goal is to reconstruct an unknown string $x$ of length $n$ from multiple traces obtained by passing $x$ through the deletion channel. In the relaxed problem of $approximate$ trace reconstruction, the…
The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata…
Gene regulatory network reconstruction is a fundamental problem in computational biology. We recently developed an algorithm, called PANDA (Passing Attributes Between Networks for Data Assimilation), that integrates multiple sources of…
DNA Data storage has recently attracted much attention due to its durable preservation and extremely high information density (bits per gram) properties. In this work, we propose a hybrid coding strategy comprising of generalized…
Effective anomaly detection in time series is pivotal for modern industrial applications and financial systems. Due to the scarcity of anomaly labels and the high cost of manual labeling, reconstruction-based unsupervised approaches have…
The problem of storing large amounts of information safely for a long period of time has become essential. One of the most promising new data storage mediums are the polymer-based data storage systems, like the DNA-storage system. These…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Digital information can be encoded in the building-block sequence of macro-molecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive.…
In this paper, we propose a novel iterative encoding algorithm for DNA storage to satisfy both the GC balance and run-length constraints using a greedy algorithm. DNA strands with run-length more than three and the GC balance ratio far from…
Motivated by the sequence reconstruction problem initiated by Levenshtein, reconstruction codes were introduced by Cai \emph{et al}. to combat errors when a fixed number of noisy channels are available. The central problem on this topic is…
We present many new results related to reliable (interactive) communication over insertion-deletion channels. Synchronization errors, such as insertions and deletions, strictly generalize the usual symbol corruption errors and are much…
A novel processing-in-storage (PRinS) architecture based on Resistive CAM (ReCAM) is described and proposed for Smith-Waterman (S-W) sequence alignment. The ReCAM massively-parallel compare operation finds matching base-pairs in a fixed…
In this letter, we propose a trellis-coded nonorthogonal multiple access (NOMA) scheme. The signals for different users are produced by trellis coded modulation (TCM) and then superimposed on different power levels. By interpreting the…
DNA exhibits remarkable potential as a data storage solution due to its impressive storage density and long-term stability, stemming from its inherent biomolecular structure. However, developing this novel medium comes with its own set of…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
Trace-wise noise is a type of noise often seen in seismic data, which is characterized by vertical coherency and horizontal incoherency. Using self-supervised deep learning to attenuate this type of noise, the conventional blind-trace deep…
Search is a key service within constraint programming systems, and it demands the restoration of previously accessed states during the exploration of a search tree. Restoration proceeds either bottom-up within the tree to roll back…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
We address the problem of reconstructing sparse signals from noisy and compressive measurements using a feed-forward deep neural network (DNN) with an architecture motivated by the iterative shrinkage-thresholding algorithm (ISTA). We…