Quantitative Methods

Authors and titles for q-bio.QM in Mar 2024

[1]  arXiv:2403.00093 [pdf, ps, other]

Title: Synthesizing study-specific controls using generative models on open access datasets for harmonized multi-study analyses

Authors: Shruti P. Gadewar, Alyssa H. Zhu, Iyad Ba Gari, Sunanda Somu, Sophia I. Thomopoulos, Paul M. Thompson, Talia M. Nir, Neda Jahanshad

Subjects: Quantitative Methods (q-bio.QM)

[2]  arXiv:2403.00716 [pdf, ps, other]

Title: Few-shot genes selection: subset of PAM50 genes for breast cancer subtypes classification

Authors: Leandro Y. S. Okimoto, Rayol Mendonca-Neto, Fabíola G. Nakamura, Eduardo F. Nakamura, David Fenyö, Claudio T. Silva

Journal-ref: BMC Bioinformatics 25, 92 (2024)

Subjects: Quantitative Methods (q-bio.QM)

[3]  arXiv:2403.00842 [pdf, ps, other]

Title: Implementation of an AI-based MRD evaluation and prediction model for multiple myeloma

Authors: Jianfeng Chen, Jize Xiong, Yixu Wang, Qi Xin, Hong Zhou

Comments: 7 pages, 6 figures

Subjects: Quantitative Methods (q-bio.QM)

[4]  arXiv:2403.00875 [pdf, other]

Title: Enhancing Protein Predictive Models via Proteins Data Augmentation: A Benchmark and New Directions

Authors: Rui Sun, Lirong Wu, Haitao Lin, Yufei Huang, Stan Z. Li

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Biomolecules (q-bio.BM)

[5]  arXiv:2403.01332 [pdf, other]

Title: Chaining thoughts and LLMs to learn DNA structural biophysics

Authors: Tyler D. Ross, Ashwin Gopinath

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[6]  arXiv:2403.01678 [pdf, other]

Title: Structured methods for parameter inference and uncertainty quantification for mechanistic models in the life sciences

Authors: Michael J. Plank, Matthew J. Simpson

Subjects: Quantitative Methods (q-bio.QM)

[7]  arXiv:2403.02050 [pdf, other]

Title: Piezoelectricity and flexoelectricity in biological cells: The role of cell structure and organelles

Authors: Akepogu Venkateshwarlu, Akshayveer, Sundeep Singh, Roderick Melnik

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

[8]  arXiv:2403.02102 [pdf, ps, other]

Title: Tractography derived quantitative estimates of tissue microstructure depend on streamline length: A characterization and method of adjustment

Authors: Richard G. Carson, Alexander Leemans

Comments: 8 figures in main text; 7 figures in Supplementary Material

Subjects: Quantitative Methods (q-bio.QM)

[9]  arXiv:2403.02359 [pdf, other]

Title: Fluid ejections in nature

Authors: Elio J. Challita, Pankaj Rohilla, M. Saad Bhamla

Comments: 30 pages, 9 figures. Paper accepted and scheduled for publication in Annual Reviews. This is not the final version

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

[10]  arXiv:2403.02361 [pdf, ps, other]

Title: Renal function changes in chronic hepatitis B patients

Authors: Jinhua Zhao, Lili Wu, Xiaoan Yang, Zhilaing Gao, Hong Deng

Comments: Over the 48-week duration of combined treatment in patients with chronic hepatitis B (CHB), it was found that both Tenofovir Disoproxil Fumarate (TDF) and Entecavir (ETV) did not lead to an increase in renal injury

Subjects: Quantitative Methods (q-bio.QM)

[11]  arXiv:2403.02603 [pdf, other]

Title: Drug resistance revealed by in silico deep mutational scanning and mutation tracker

Authors: Dong Chen, Gengzhuo Liu, Hongyan Du, Junjie Wee, Rui Wang, Jiahui Chen, Jana Shen, Guo-Wei Wei

Subjects: Quantitative Methods (q-bio.QM)

[12]  arXiv:2403.02733 [pdf, ps, other]

Title: Early quantum computing applications on the path towards precision medicine

Authors: Frederik F. Flöther

Subjects: Quantitative Methods (q-bio.QM); Quantum Physics (quant-ph)

[13]  arXiv:2403.02984 [pdf, other]

Title: Assessing the distribution of cancer stem cells in tumorspheres

Authors: Jerónimo Fotinós, María Paula Marks, Lucas Barberis, Luciano Vellón

Comments: 14 pages, 6 figures, 2 tables

Subjects: Quantitative Methods (q-bio.QM)

[14]  arXiv:2403.03000 [pdf, ps, other]

Title: Possible and Impossible Inferences From Reconstructed Evolutionary Processes using Phylogenies as an Example

Authors: Niklas Hohmann

Subjects: Quantitative Methods (q-bio.QM); Populations and Evolution (q-bio.PE)

[15]  arXiv:2403.03089 [pdf, other]

Title: VQSynery: Robust Drug Synergy Prediction With Vector Quantization Mechanism

Authors: Jiawei Wu, Mingyuan Yan, Dianbo Liu

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)

[16]  arXiv:2403.03274 [pdf, other]

Title: From Noise to Signal: Unveiling Treatment Effects from Digital Health Data through Pharmacology-Informed Neural-SDE

Authors: Samira Pakravan, Nikolaos Evangelou, Maxime Usdin, Logan Brooks, James Lu

Comments: 6 figures

Subjects: Quantitative Methods (q-bio.QM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Dynamical Systems (math.DS)

[17]  arXiv:2403.03318 [pdf, ps, other]

Title: A Novel Method for Clustering Cellular Data to Improve Classification

Authors: Diek W. Wheeler, Giorgio A. Ascoli

Comments: 16 pages, 13 figures

Subjects: Quantitative Methods (q-bio.QM)

[18]  arXiv:2403.03970 [pdf, other]

Title: Inverse resolution of spatially varying diffusion coefficient using Physics-Informed neural networks

Authors: Sukirt Thakur, Ehsan Esmaili, Sarah Libring, Luis Solorio, Arezoo M. Ardekani

Subjects: Quantitative Methods (q-bio.QM)

[19]  arXiv:2403.04027 [pdf, ps, other]

Title: High throughput spectroscopy of pL droplets

Authors: Marc Sulliger, Jaime Ortega Arroyo, Romain Quidant

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

[20]  arXiv:2403.05479 [pdf, ps, other]

Title: The temperature affects the impact levels of synthetic insecticides on a parasitoid wasp used in the biological control of pentatomid pests in soybean crops

Authors: Matheus Rakes, Maíra Chagas Morais, Leandro do Prado Ribeiro, Gabriel Rodrigues Palma, Rafael de Andrade Moral, Daniel Bernardi, Anderson Dionei Grützmacher

Comments: 45 pages

Subjects: Quantitative Methods (q-bio.QM)

[21]  arXiv:2403.06950 [pdf, ps, other]

Title: Applicability of oculomics for individual risk prediction: Repeatability and robustness of retinal Fractal Dimension using DART and AutoMorph

Authors: Justin Engelmann, Diana Moukaddem, Lucas Gago, Niall Strang, Miguel O. Bernabeu

Subjects: Quantitative Methods (q-bio.QM); Computer Vision and Pattern Recognition (cs.CV)

[22]  arXiv:2403.07013 [pdf, other]

Title: AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information

Authors: Jun Xia, Shaorong Chen, Jingbo Zhou, Tianze Ling, Wenjie Du, Sizhe Liu, Stan Z. Li

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Biomolecules (q-bio.BM)

[23]  arXiv:2403.07297 [pdf, ps, other]

Title: Optical detection of bacterial cells on stainless-steel surface with a low-magnification light microscope

Authors: Yuzhen Zhang, Zili Gao, Lili He

Comments: 38 pages, 13 figures, 1 table

Subjects: Quantitative Methods (q-bio.QM)

[24]  arXiv:2403.07475 [pdf, ps, other]

Title: Predicting the Risk of Ischemic Stroke in Patients with Atrial Fibrillation using Heterogeneous Drug-protein-disease Network-based Deep Learning

Authors: Zhiheng Lyu, Jiannan Yang, Zhongzhi Xu, Weilan Wang, Weibin Cheng, Kwok-Leung Tsui, Gary Tse, Qingpeng Zhang

Subjects: Quantitative Methods (q-bio.QM)

[25]  arXiv:2403.07960 [pdf, other]

Title: Unsupervised self-organising map of prostate cell Raman spectra shows disease-state subclustering

Authors: Daniel West, Susan Stepney, Y. Hancock

Comments: 14 pages, 6 figures

Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)