Related papers: DNA Sequence Alignment by Window based Optical Cor…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
In this paper, we address the problem of searching for semantically similar images from a large database. We present a compact coding approach, supervised quantization. Our approach simultaneously learns feature selection that linearly…
Data-efficient image classification is a challenging task that aims to solve image classification using small training data. Neural network-based deep learning methods are effective for image classification, but they typically require…
Coherent photonic computing uses both the phase and amplitude of light to implement linear operations such as dot products and matrix multiplication but requires phase stability between the interfering paths. This poses a challenge for such…
Discovering causal relationships from observational data is a crucial problem and it has applications in many research areas. The PC algorithm is the state-of-the-art constraint based method for causal discovery. However, runtime of the PC…
Aligning the entire genome of an organism is a compute-intensive task. Pre-alignment filters substantially reduce computation complexity by filtering potential alignment locations. The base-count filter successfully removes over 68% of the…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…
Deep learning is able to functionally simulate the human brain and thus, it has attracted considerable interest. Optics-assisted deep learning is a promising approach to improve the forward-propagation speed and reduce the power…
Nearest Neighbor Search (NNS) has recently drawn a rapid increase of interest due to its core role in managing high-dimensional vector data in data science and AI applications. The interest is fueled by the success of neural embedding,…
Despite the recent progress in genome sequencing and assembly, many of the currently available assembled genomes come in a draft form. Such draft genomes consist of a large number of genomic fragments (scaffolds), whose order and/or…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
The Jaccard similarity index is an important measure of the overlap of two sets, widely used in machine learning, computational genomics, information retrieval, and many other areas. We design and implement SimilarityAtScale, the first…
As electronic computing approaches its performance limits, photonic accelerators have emerged as promising alternatives. Photonic accelerators exploiting semiconductor-laser synchronization have been studied for decision-making. While…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
The main objective of this paper is to solve the optimization problem that is associated with the classification of DNA samples in PCR plates for Sanger sequencing. To achieve this goal, we design an integer linear programming model. Given…
Algorithmic sequence alignment identifies similar segments shared between pairs of documents, and is fundamental to many NLP tasks. But it is difficult to recognize similarities between distant versions of narratives such as translations…
Motivation: High-coverage sequencing data have significant, yet hard to exploit, redundancy. Most FASTQ compressors cannot efficiently compress the DNA stream of large datasets, since the redundancy between overlapping reads cannot be…
Cell Painting is a microscopy-based, high-content imaging assay that produces rich morphological profiles of cells and can support drug discovery by quantifying cellular responses to chemical perturbations. At scale, however, Cell Painting…