Quantitative Biology

Authors and titles for Jun 2023

[1]  arXiv:2306.00041 [pdf, other]

Title: Causal Intervention for Measuring Confidence in Drug-Target Interaction Prediction

Authors: Wenting Ye, Chen Li, Yang Xie, Wen Zhang, Hong-Yu Zhang, Bowen Wang, Debo Cheng, Zaiwen Feng

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

[2]  arXiv:2306.00046 [pdf, ps, other]

Title: Quantitative Methods for Optimizing Patient Outcomes in Liver Transplantation

Authors: Raja Al-Bahou, Julia Bruner, Helen Moore, Ali Zarrinpar

Comments: 2 figures, including a graphical abstract

Subjects: Other Quantitative Biology (q-bio.OT)

[3]  arXiv:2306.00089 [pdf, other]

Title: A Data-Driven Computational Model for Engineered Cardiac Microtissues

Authors: Javiera Jilberto, Samuel J. DePalma, Jason Lo, Hiba Kobeissi, Lani Quach, Emma Lejeune, Brendon M. Baker, David Nordsletten

Comments: 19 pages, 7 figures

Subjects: Tissues and Organs (q-bio.TO)

[4]  arXiv:2306.00236 [pdf, other]

Title: Cell motility modes are selected by the interplay of mechanosensitive adhesion and membrane tension

Authors: Yuzhu Chen, David Saintillan, Padmini Rangamani

Comments: 21 pages, 8 figures

Subjects: Cell Behavior (q-bio.CB)

[5]  arXiv:2306.00239 [pdf, ps, other]

Title: An algebraic theory to discriminate qualia in the brain

Authors: Yoshiyuki Ohmura, Wataru Shimaya, Yasuo Kuniyoshi

Subjects: Neurons and Cognition (q-bio.NC); Image and Video Processing (eess.IV)

[6]  arXiv:2306.00471 [pdf, ps, other]

Title: Muller's ratchet in a near-critical regime: tournament versus fitness proportional selection

Authors: Jan Lukas Igelbrink, Adrián González Casanova, Charline Smadi, Anton Wakolbinger

Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR)

[7]  arXiv:2306.00557 [pdf, other]

Title: Improving Protein-peptide Interface Predictions in the Low Data Regime

Authors: Justin Diamond, Markus Lill

Comments: 5 pages, 5 figures, ICLR Machine Learning in Drug Discovery Accepted paper

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

[8]  arXiv:2306.00580 [pdf, other]

Title: Visuomotor feedback tuning in the absence of visual error information

Authors: Sae Franklin, David W. Franklin

Comments: 29 pages, 11 figures. arXiv admin note: substantial text overlap with arXiv:2008.07574

Subjects: Neurons and Cognition (q-bio.NC)

[9]  arXiv:2306.00706 [pdf, ps, other]

Title: Oscillations in p-adic diffusion processes and simulation of the conformational dynamics of protein

Authors: A.Kh. Bikulov, A.P. Zubarev

Comments: 23 pages, 5 figures

Subjects: Biomolecules (q-bio.BM); Statistical Mechanics (cond-mat.stat-mech)

[10]  arXiv:2306.00838 [pdf, ps, other]

Title: The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI

Authors: Ahmed W. Moawad, Anastasia Janas, Ujjwal Baid, Divya Ramakrishnan, Leon Jekel, Kiril Krantchev, Harrison Moy, Rachit Saluja, Klara Osenberg, Klara Wilms, Manpreet Kaur, Arman Avesta, Gabriel Cassinelli Pedersen, Nazanin Maleki, Mahdi Salimi, Sarah Merkaj, Marc von Reppert, Niklas Tillmans, Jan Lost, Khaled Bousabarah, Wolfgang Holler, MingDe Lin, Malte Westerhoff, Ryan Maresca, Katherine E. Link, Nourel hoda Tahon, Daniel Marcus, Aristeidis Sotiras, Pamela LaMontagne, Strajit Chakrabarty, Oleg Teytelboym, Ayda Youssef, Ayaman Nada, Yuri S. Velichko, Nicolo Gennaro, Connectome Students, Group of Annotators, Justin Cramer, Derek R. Johnson, Benjamin Y.M. Kwan, Boyan Petrovic, Satya N. Patro, Lei Wu, Tiffany So, Gerry Thompson, Anthony Kam, Gloria Guzman Perez-Carrillo, Neil Lall, Group of Approvers, et al. (39 additional authors not shown)

Subjects: Other Quantitative Biology (q-bio.OT); Image and Video Processing (eess.IV)

[11]  arXiv:2306.00873 [pdf, ps, other]

Title: Digital contact tracing/notification for SARS-CoV-2: navigating six points of failure

Authors: Joanna Masel, James Petrie, Jason Bay, Wolfgang Ebbers, Aalekh Sharan, Scott Leibrand, Andreas Gebhard, Samuel Zimmerman

Subjects: Populations and Evolution (q-bio.PE)

[12]  arXiv:2306.00900 [pdf, other]

Title: Suppression of chaos in a partially driven recurrent neural network

Authors: Shotaro Takasu, Toshio Aoyagi

Comments: 7 pages, 4 figures

Journal-ref: Physical Review Research, 6, 013172 (2024)

Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Chaotic Dynamics (nlin.CD)

[13]  arXiv:2306.00915 [pdf, ps, other]

Title: The feasibility of artificial consciousness through the lens of neuroscience

Authors: Jaan Aru, Matthew Larkum, James M. Shine

Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Robotics (cs.RO)

[14]  arXiv:2306.00927 [pdf, other]

Title: Second Sight: Using brain-optimized encoding models to align image distributions with human brain activity

Authors: Reese Kneeland, Jordyn Ojeda, Ghislain St-Yves, Thomas Naselaris

Comments: 15 Figures, 19 pages including the appendix

Subjects: Neurons and Cognition (q-bio.NC); Computer Vision and Pattern Recognition (cs.CV); Machine Learning (cs.LG)

[15]  arXiv:2306.00944 [pdf, ps, other]

Title: pgMAP: a pipeline to enable guide RNA read mapping from dual-targeting CRISPR screens

Authors: Phoebe C. R. Parrish, Daniel J. Groso, James D. Thomas, Robert K. Bradley, Alice H. Berger

Comments: 6 pages, 1 figure, code available at this https URL

Subjects: Genomics (q-bio.GN)

[16]  arXiv:2306.01313 [pdf, ps, other]

Title: Cell jamming and unjamming in development: physical aspects

Authors: Ivana Pajic-Lijakovic, Milan Milivojevic

Comments: 18 pages, 4 figures

Subjects: Cell Behavior (q-bio.CB)

[17]  arXiv:2306.01403 [pdf, other]

Title: Dynamical Theory for Adaptive Systems

Authors: Tuan Minh Pham, Kunihiko Kaneko

Comments: 30 pages and 2 figures

Subjects: Populations and Evolution (q-bio.PE); Disordered Systems and Neural Networks (cond-mat.dis-nn); Adaptation and Self-Organizing Systems (nlin.AO); Biological Physics (physics.bio-ph)

[18]  arXiv:2306.01629 [pdf, other]

Title: Number of attractors in the critical Kauffman model is exponential

Authors: T. M. A. Fink, F. C. Sheldon

Comments: 5 pages, 3 figures

Subjects: Molecular Networks (q-bio.MN); Disordered Systems and Neural Networks (cond-mat.dis-nn)

[19]  arXiv:2306.01634 [pdf, ps, other]

Title: A FAIR platform for reproducing mutational signature detection on tumor sequencing data

Authors: Aaron Ge, Tongwu Zhang, Clara Bodelon, Montserrat Garcia-Closas, Jonas Almeida, Jeya Balasubramanian

Comments: Our proposed in-browser platform is publicly available under the MIT license at this https URL No data leaves this privacy-preserving environment, which can be cloned or forked and served from other domains with no restrictions. All the code and relevant data used to create this platform can be found at this https URL

Subjects: Genomics (q-bio.GN)

[20]  arXiv:2306.01745 [pdf, other]

Title: Biomarker Discovery with Quantum Neural Networks: A Case-study in CTLA4-Activation Pathways

Authors: Nam Nguyen

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

[21]  arXiv:2306.01791 [pdf, other]

Title: Understanding Biofilm-Phage Interactions in Cystic Fibrosis Patients Using Mathematical Frameworks

Authors: Blessing O. Emerenini, Doris Hartung, Ricardo N. G Reyes Grimaldo, Claire Canner, Maya Williams, Ephraim Agyingi, Robert Osgood

Subjects: Quantitative Methods (q-bio.QM); Dynamical Systems (math.DS)

[22]  arXiv:2306.01793 [pdf, other]

Title: Hypoxia-resistance heterogeneity in tumours: the impact of geometrical characterization of environmental niches and evolutionary trade-offs. A mathematical approach

Authors: Giulia Chiari, Giada Fiandaca, Marcello Edoardo Delitala

Subjects: Populations and Evolution (q-bio.PE); Analysis of PDEs (math.AP); Numerical Analysis (math.NA); Medical Physics (physics.med-ph)

[23]  arXiv:2306.01794 [pdf, other]

Title: DiffPack: A Torsional Diffusion Model for Autoregressive Protein Side-Chain Packing

Authors: Yangtian Zhang, Zuobai Zhang, Bozitao Zhong, Sanchit Misra, Jian Tang

Comments: 37th Conference on Neural Information Processing Systems (NeurIPS 2023)

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

[24]  arXiv:2306.01802 [pdf, other]

Title: Linear Time GPs for Inferring Latent Trajectories from Neural Spike Trains

Authors: Matthew Dowling, Yuan Zhao, Il Memming Park

Comments: Published at ICML 2023

Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG); Applications (stat.AP); Machine Learning (stat.ML)

[25]  arXiv:2306.01824 [pdf, other]

Title: Enhancing the Protein Tertiary Structure Prediction by Multiple Sequence Alignment Generation

Authors: Le Zhang, Jiayang Chen, Tao Shen, Yu Li, Siqi Sun

Subjects: Quantitative Methods (q-bio.QM); Computational Engineering, Finance, and Science (cs.CE); Machine Learning (cs.LG); Biomolecules (q-bio.BM)