Related papers: Fundamental Bounds and Approaches to Sequence Reco…

Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…

Depth estimation plays a pivotal role in advancing human-robot interactions, especially in indoor environments where accurate 3D scene reconstruction is essential for tasks like navigation and object handling. Monocular depth estimation,…

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…

The trace reconstruction problem studies the number of noisy samples needed to recover an unknown string $\boldsymbol{x}\in\{0,1\}^n$ with high probability, where the samples are independently obtained by passing $\boldsymbol{x}$ through a…

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…

Positron emission tomography (PET) is a cornerstone of modern radiology. The ability to detect cancer and metastases in whole body scans fundamentally changed cancer diagnosis and treatment. One of the main bottlenecks in the clinical…

We consider the problem of distributed lossy linear function computation in a tree network. We examine two cases: (i) data aggregation (only one sink node computes) and (ii) consensus (all nodes compute the same function). By quantifying…

Synthetic polymer-based storage seems to be a particularly promising candidate that could help to cope with the ever-increasing demand for archival storage requirements. It involves designing molecules of distinct masses to represent the…

In this paper, we consider a concatenated coding based class of DNA storage codes in which the selected molecules are constrained to be taken from an ``inner'' codebook associated with the sequencing channel. This codebook is used in a…

Fault-aware retraining has emerged as a prominent technique for mitigating permanent faults in Deep Neural Network (DNN) hardware accelerators. However, retraining leads to huge overheads, specifically when used for fine-tuning large DNNs…

The inverse design of RNA three-dimensional (3D) structures is crucial for engineering functional RNAs in synthetic biology and therapeutics. While recent deep learning approaches have advanced this field, they are typically optimized and…

Diffusion models have established new state of the art in a multitude of computer vision tasks, including image restoration. Diffusion-based inverse problem solvers generate reconstructions of exceptional visual quality from heavily…

Using multiple nodes and parallel computing algorithms has become a principal tool to improve training and execution times of deep neural networks as well as effective collective intelligence in sensor networks. In this paper, we consider…

This paper presents a novel DNA sequences alignment method based on inverted index. Now most large scale information retrieval system are all use inverted index as the basic data structure. But its application in DNA sequence alignment is…

Recently, Transformer-based encoder-decoder models have demonstrated strong performance in multilingual speech recognition. However, the decoder's autoregressive nature and large size introduce significant bottlenecks during inference.…

Many machine learning tasks can be expressed as the transformation---or \emph{transduction}---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to…

This paper studies the problem of encoding messages into sequences which can be uniquely recovered from some noisy observations about their substrings. The observed reads comprise consecutive substrings with some given minimum overlap. This…

Sequencing a DNA strand, as part of the read process in DNA storage, produces multiple noisy copies which can be combined to produce better estimates of the original strand; this is called trace reconstruction. One can reduce the error rate…

Stereo depth estimation relies on optimal correspondence matching between pixels on epipolar lines in the left and right images to infer depth. In this work, we revisit the problem from a sequence-to-sequence correspondence perspective to…

Burst errors involving simultaneous insertions, deletions, and substitutions occur in practical scenarios, including DNA data storage and document synchronization, motivating developments of channel codes that can correct such errors. In…