Results 41 to 50 of about 127,298 (253)

Topological Data Analysis for Speech Processing

INTERSPEECH 2023, 2023
We apply topological data analysis (TDA) to speech classification problems and to the introspection of a pretrained speech model, HuBERT. To this end, we introduce a number of topological and algebraic features derived from Transformer attention maps and embeddings.
Eduard Tulchinskii, Kristian Kuznetsov, Laida Kushnareva, Daniil Cherniavskii, Serguei Barannikov, Irina Piontkovskaya, Sergey I. Nikolenko, Evgeny Burnaev   +7 more
openaire   +3 more sources

Subtype‐specific enhancer RNAs define transcriptional regulators and prognosis in breast cancers

Molecular Oncology, EarlyView.
This study employed machine learning methodologies to perform the subtype‐specific classification of RNA‐seq data sets, which are mapped on enhancers from TCGA‐derived breast cancer patients. Their integration with gene expression (referred to as ProxCReAM eRNAs) and chromatin accessibility profiles has the potential to identify lineage‐specific and ...
Aamena Y. Patel, Peyman Zarrineh, Nathnael T. Tuffa, Jigar H. Sheth, Sumitra Mohan, Mudassar Iqbal, Sankari Nagarajan   +6 more
wiley   +1 more source

Probing omics data via harmonic persistent homology

Scientific Reports
Identifying molecular signatures from complex disease patients with underlying symptomatic similarities is a significant challenge in the analysis of high-dimensional multi-omics data.
Davide Gurnari, Aldo Guzmán-Sáenz, Filippo Utro, Aritra Bose, Saugata Basu, Laxmi Parida   +5 more
doaj   +1 more source

Chromatic Topological Data Analysis

CoRR
Exploring the shape of point configurations has been a key driver in the evolution of TDA (short for topological data analysis) since its infancy. This survey illustrates the recent efforts to broaden these ideas to model spatial interactions among multiple configurations, each distinguished by a color.
Sebastiano Cultrera di Montesano, Ondrej Draganov, Herbert Edelsbrunner, Morteza Saghafian   +3 more
openaire   +2 more sources

Classification based on Topological Data Analysis

CoRR, 2021
تحليل البيانات الطوبولوجية (TDA) هو مجال ناشئ يهدف إلى اكتشاف المعلومات الطوبولوجية المخفية في مجموعة البيانات. تم استخدام أدوات TDA بشكل شائع لإنشاء مرشحات وواصفات طوبولوجية لتحسين طرق التعلم الآلي (ML). تقترح هذه الورقة خوارزمية تطبق TDA مباشرة على مشاكل التصنيف متعددة الفئات، حتى مجموعات البيانات غير المتوازنة، دون أي مرحلة أخرى من تعلم الآلة. أنشأت
Rolando Kindelan, José Ángel Garfias Frías, Mauricio Cerda, Nancy Hitschfeld   +3 more
openaire   +2 more sources

Developmental programmes drive cellular plasticity, disease progression and therapy resistance in lung adenocarcinoma

Molecular Oncology, EarlyView.
This study shows that lung adenocarcinomas exploit developmental branching morphogenesis to acquire a therapy resistant basal‐like tumour cell state. This process was found to be regulated by combined TP53 loss‐of‐function and type‐I interferon signalling, identifying a novel axis for biomarker and therapeutic target discovery.
Kamila J Bienkowska, Stephany Gallardo, Nur S. Zainal, Leena Arora, Matthew Ellis, Maria‐Antoinette Lopez, Judith Austine, Sai Pittla, Serena J Chee, Aiman Alzetani, Emily C Shaw, Christian H Ottensmeier, Gareth J Thomas, Christopher J Hanley   +13 more
wiley   +1 more source

Feasibility of topological data analysis for event-related fMRI [PDF]

Network Neuroscience, 2019
Recent fMRI research shows that perceptual and cognitive representations are instantiated in high-dimensional multivoxel patterns in the brain. However, the methods for detecting these representations are limited. Topological data analysis (TDA) is a new
Cameron T. Ellis, Michael Lesnick, Gregory Henselman-Petrusek, Bryn Keller, Jonathan D. Cohen   +4 more
doaj   +1 more source

A novel quinazolinone insulin receptor inhibitor and its synergy with an EGFR inhibitor in glucose‐driven glioblastoma

Molecular Oncology, EarlyView.
The novel styrylquinazolinone‐based molecule W1B effectively suppresses glioblastoma by inhibiting IGF1R and EGFR. In high‐glucose microenvironments driving tumor resistance, W1B acts synergistically with the EGFR inhibitor dacomitinib. This combination safely blocks compensatory survival signaling in zebrafish xenograft models. Showcasing promising in
Patryk Rurka, Wioleta Cieślik, Wojciech Płaziński, Katarzyna Stępnik, Anna Boguszewska‐Czubara, Elżbieta Kot, Robert Musioł, Mateusz Jasica, Anna Mrozek‐Wilczkiewicz, Katarzyna Malarz   +9 more
wiley   +1 more source

Molecular dynamics simulations of positively selected codons in FcγRI reveal novel biochemical binding properties

FEBS Open Bio, EarlyView.
Evolutionary analysis across 32 placental mammals identified positive selection at residues H148 and W149 in the immune receptor FcγR1. Ancestral reconstruction combined with molecular dynamics simulations reveals how these mutations may influence receptor structure and dynamics, providing insight into the evolution of antibody recognition and immune ...
David A. Young, Omar Arias‐Gaguancela, Fiona Gibson, Morgan Grainger, Jodie Score, Amit Nathubhai, Mauricio Cafiero, Lee Richard Machado   +7 more
wiley   +1 more source

Topological Data Analysis of Spatial Systems

, 2022
In this chapter, we discuss applications of topological data analysis (TDA) to spatial systems. We briefly review the recently proposed level-set construction of filtered simplicial complexes, and we then examine persistent homology in two cases studies: street networks in Shanghai and hotspots of COVID-19 infections.
Michelle Feng, Abigail Hickok, Mason A. Porter   +2 more
openaire   +2 more sources