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This paper presents DINO-RotateMatch, a deep-learning framework designed to address the chal lenges of image matching in large-scale 3D reconstruction from unstructured Internet images. The method integrates a dataset-adaptive image pairing…
A major hindrance to studies of microbial diversity has been that the vast majority of microbes cannot be cultured in the laboratory and thus are not amenable to traditional methods of characterization. Environmental shotgun sequencing…
Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We…
In medical imaging, chromosome straightening plays a significant role in the pathological study of chromosomes and in the development of cytogenetic maps. Whereas different approaches exist for the straightening task, typically geometric…
The Segmented Planar Imaging Detector for Electro-Optical Reconnaissance (SPIDER) is an optical interferometric imaging device that aims to offer an alternative to the large space telescope designs of today with reduced size, weight and…
Tracking the formation and evolution of dark matter haloes is a critical aspect of any analysis of cosmological $N$-body simulations. In particular, the mass assembly of a halo and its progenitors, encapsulated in the form of its merger…
Acute Myeloid Leukemia (AML) remains a clinical challenge due to its extreme molecular heterogeneity and high relapse rates. While precision medicine has introduced mutation-specific therapies, many patients still lack effective,…
This paper proposes a novel algorithm to reassemble an arbitrarily shredded image to its original status. Existing reassembly pipelines commonly consist of a local matching stage and a global compositions stage. In the local stage, a key…
We investigate a densely packed, non-random arrangement of forty-six chromosomes (46,XY) in human nuclei. Here, we model systems-level chromosomal crosstalk by unifying intrinsic parameters (chromosomal length and number of genes) across…
Molecular structure generation from mass spectrometry is fundamental for understanding cellular metabolism and discovering novel compounds. Although tandem mass spectrometry (MS/MS) enables the high-throughput acquisition of fragment…
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a…
We present a method combining affinity prediction with region agglomeration, which improves significantly upon the state of the art of neuron segmentation from electron microscopy (EM) in accuracy and scalability. Our method consists of a…
We develop an accelerated Genetic Algorithm (GA) system constructed by the cooperation of field-programmable gate array (FPGA) and optimized parameters of the GA. We found the enhanced decay of mutation rate makes convergence of the GA much…
DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past…
Recent advances in machine learning (ML) and computer vision tools have enabled applications in a wide variety of arenas such as financial analytics, medical diagnostics, and even within the Department of Defense. However, their widespread…
The formal version of our work has been published in BMC Bioinformatics and can be found here: http://www.biomedcentral.com/1471-2105/13/S6/S1 Motivation: To tackle the problem of huge memory usage associated with de Bruijn graph-based…
Colloidal lithography [1] is how patterns are reproduced in a variety of natural systems and is used more and more as an efficient fabrication tool in bio-, opto-, and nano-technology. Nanoparticles in the colloid are made to form a mask on…
Recent analysis identified distinct genomic subtypes of lower-grade glioma tumors which are associated with shape features. In this study, we propose a fully automatic way to quantify tumor imaging characteristics using deep learning-based…
Chromosome analysis and identification from metaphase images is a critical part of cytogenetics based medical diagnosis. It is mainly used for identifying constitutional, prenatal and acquired abnormalities in the diagnosis of genetic…
Ultrasound (US) is widely accepted in clinic for anatomical structure inspection. However, lacking in resources to practice US scan, novices often struggle to learn the operation skills. Also, in the deep learning era, automated US image…