Sökning: "Computational proteomics"

Hittade 5 uppsatser innehållade orden Computational proteomics.

1. 1. Messing With The Gap: On The Modality Gap Phenomenon In Multimodal Contrastive Representation Learning

   Uppsats för yrkesexamina på avancerad nivå, Uppsala universitet/Industriell teknik

   Författare :Mohammad Al-Jaff; [2023]
   Nyckelord :Multimodal machine learning; Representation learning; Self-supervised learning; contrastive learning; computer vision; computational biology; bioinformatics;

   Sammanfattning : In machine learning, a sub-field of computer science, a two-tower architecture model is a specialised type of neural network model that encodes paired data from different modalities (like text and images, sound and video, or proteomics and gene expression profiles) into a shared latent representation space. However, when training these models using a specific contrastive loss function, known as the multimodalinfoNCE loss, seems to often lead to a unique geometric phenomenon known as the modality gap. LÄS MER

3. 2. Theoretical Fundamentals of Computational Proteomics and Deep Learning- Based Identification of Chimeric Mass Spectrometry Data

   Master-uppsats, KTH/Skolan för elektroteknik och datavetenskap (EECS)

   Författare :Jens Settelmeier; [2021]
   Nyckelord :Computational proteomics; mass spectrometry; chimera identification; machine learning; deep learning; big data; bioinformatics; Beräkningsproteomik; masspektrometri; kimäridentifiering; maskininlärning; djupinlärning; stora data; bioinformatik;

   Sammanfattning : A complicating factor for peptide identification by MS/MS experiments is the presence of “chimeric” spectra where at least two precursor ions with similar retention time and mass co- elute in the mass spectrometer. This results in a spectrum that is a superposition of the spectra of the individual peptides. LÄS MER

4. 3. Computational study of single protein sensing using nanopores

   Master-uppsats, Uppsala universitet/Materialteori

   Författare :Sebastian Cardoch; [2020]
   Nyckelord :nanopores; protein sensing; mini-proteins; silicon nitride; ionic current; molecular dynamics; density functional theory; amino acids;

   Sammanfattning : Identifying the protein content in a cell in a fast and reliable manner has become a relevant goal in the field of proteomics. This thesis computationally explores the potential for silicon nitride nanopores to sense and distinguish single miniproteins, which are small domains that promise to facilitate the systematic study of larger proteins. LÄS MER

5. 4. Prediction of peptide retention time based on Gaussain Processes

   Master-uppsats, KTH/Skolan för datavetenskap och kommunikation (CSC)

   Författare :Xuanbin Qiu; [2015]
   Nyckelord :Peptide; retention time; gaussian processes;

   Sammanfattning : Shotgun Proteomics is the leading technique for protein identification in complexmixtures. However, it produces a large amount of data which results in aextremely high computational cost for identifying the protein. Retention time(RT) is an important factor to be used to enhance the efficiency of protein identification. LÄS MER

7. 5. Computational methods to estimate error rates forpeptide identifications in mass spectrometry-based proteomics

   Master-uppsats, KTH/Numerisk analys, NA

   Författare :Xiao Liang; [2013]
   Nyckelord :;

   Sammanfattning : In the field of proteomics, tandem mass spectrometry is the core technology which promises to identify peptide components within complex mixtures on a large scale. Currently the bottleneck is to reduce the error rates and assign accurate statistical estimates of peptide identifications. LÄS MER