On the relevance of quality score metadata in genomic sequence data for omics applications

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Optimised set of oligonucleotides for bulk rna barcoding and sequencing

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The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

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Systematic benchmarking of single-cell ATAC-sequencing protocols

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Benchmarking of scATAC-seq protocols demonstrates the effects of data quality on downstream analyses. ...

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Communication-efficient distributed training of machine learning models

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In this thesis, we explore techniques for addressing the communication bottleneck in data-parallel distributed training of deep learning models. We investigate algorithms that either reduce the size of the messages that are exchanged between workers, or th ...

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Multiomic analysis of HER2-enriched and AR-positive breast carcinoma with apocrine differentiation and an oligometastatic course: a case report

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Breast carcinoma is the most prevalent cancer among women globally. It has variable clinical courses depending on the stage and clinical-biological features. This case report describes a 56-year-old female with invasive breast cancer without estrogen or pr ...

FRONTIERS MEDIA SA2023

Generative power of a protein language model trained on multiple sequence alignments

Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023

On the assessment of high-quality images: advances on the JPEG AIC-3 activity

Touradj Ebrahimi, Michela Testolina, Evgeniy Upenik

Recent advances in image compression have made it both possible and desirable for image quality to approach the visually lossless range. However, the most commonly used subjective visual quality assessment protocols, e.g. those reported in ITU-T Rec. BT.50 ...

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JPEG AIC-3 Dataset: Towards Defining the High Quality to Nearly Visually Lossless Quality Range

Touradj Ebrahimi, Michela Testolina, Davi Nachtigall Lazzarotto

Visual data play a crucial role in modern society, and the rate at which images and videos are acquired, stored, and exchanged every day is rapidly increasing. Image compression is the key technology that enables storing and sharing of visual content in an ...

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On the Performance of Subjective Visual Quality Assessment Protocols for Nearly Visually Lossless Image Compression

Touradj Ebrahimi, Michela Testolina, Davi Nachtigall Lazzarotto

The past decades have witnessed rapid growth in imaging as a major form of communication between individuals. Due to recent advances in capture, storage, delivery and display technologies, consumers demand improved perceptual quality while requiring reduce ...

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Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics

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Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...

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Evaluating the effect of sparse convolutions on point cloud compression

Touradj Ebrahimi, Davi Nachtigall Lazzarotto

The use of point clouds as an imaging modality has been rapidly growing, motivating research on compression methods to enable efficient transmission and storage for many applications. While compression standards relying on conven- tional techniques such as ...

2023