Dataset Information

Computer vision for pattern detection in chromosome contact maps.

ABSTRACT: Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than existing methods on synthetic simulated data, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Our method does not require any prior training dataset and works well with default parameters on data generated with various protocols.

SUBMITTER: Matthey-Doret C

PROVIDER: S-EPMC7670471 | biostudies-literature | 2020 Nov

REPOSITORIES: biostudies-literature

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Publications

Computer vision for pattern detection in chromosome contact maps.

Matthey-Doret Cyril C Baudry Lyam L Breuer Axel A Montagne Rémi R Guiglielmoni Nadège N Scolari Vittore V Jean Etienne E Campeas Arnaud A Chanut Philippe Henri PH Oriol Edgar E Méot Adrien A Politis Laurent L Vigouroux Antoine A Moreau Pierrick P Koszul Romain R Cournac Axel A

Nature communications 20201116 1

Chromosomes of all species studied so far display a variety of higher-order organisational features, such as self-interacting domains or loops. These structures, which are often associated to biological functions, form distinct, visible patterns on genome-wide contact maps generated by chromosome conformation capture approaches such as Hi-C. Here we present Chromosight, an algorithm inspired from computer vision that can detect patterns in contact maps. Chromosight has greater sensitivity than e ...[more]

PMID: 33199682

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Project description:High-frequency oscillations >80 Hz (HFOs) have unique features distinguishing them from spikes and artifactual components that can be well-evidenced in the time-frequency representations. We introduce an unsupervised HFO detector that uses computer-vision algorithms to detect HFO landmarks on two-dimensional (2D) time-frequency maps. To validate the detector, we introduce an analytical model of the HFO based on a sinewave having a Gaussian envelope, for which analytical equations in time-frequency space can be derived, allowing us to establish a direct correspondence between common HFO detection criteria in the time domain with the ones in the frequency domain, used by the computer-vision detection algorithm. The detector identifies potential HFO events on the time-frequency representation, which are classified as true HFOs if criteria regarding the HFO's frequency, amplitude, and duration are met. The detector is validated on simulated HFOs according to the analytical model, in the presence of noise, with different signal-to-noise ratios (SNRs) ranging from -9 to 0 dB. The detector's sensitivity was 0.64 at an SNR of -9 dB, 0.98 at -6 dB, and >0.99 at -3 dB and 0 dB, while its positive prediction value was >0.95, regardless of the SNR. Using the same simulation dataset, our detector is benchmarked against four previously published HFO detectors. The F-measure, a combined metric that takes into account both sensitivity and positive prediction value, was used to compare detection algorithms. Our detector surpassed the other detectors at -6, -3, and 0 dB and had the second best F-score at -9 dB SNR after the MNI detector (0.77 vs. 0.83). The ability to detect HFOs in clinical recordings has been tested on a set of 36 intracranial electroencephalogram (EEG) channels in six patients, with 89% of the detections being validated by two independent reviewers. The results demonstrate that the unsupervised detection of HFOs based on their 2D features in time-frequency maps is feasible and has a performance comparable or better than the most used HFO detectors.

Dataset Information

Computer vision for pattern detection in chromosome contact maps.

Publications

Computer vision for pattern detection in chromosome contact maps.

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