We gratefully acknowledge support from
the Simons Foundation and member institutions.

Quantitative Biology

Authors and titles for recent submissions

[ total of 94 entries: 1-78 | 79-94 ]
[ showing 78 entries per page: fewer | more | all ]

Fri, 17 May 2024

[1]  arXiv:2405.10112 [pdf, ps, other]
Title: Spatial Cognition: a Wave Hypothesis
Authors: Robert Worden
Comments: 15 pages
Subjects: Neurons and Cognition (q-bio.NC); Populations and Evolution (q-bio.PE)
[2]  arXiv:2405.10110 [pdf, other]
Title: Source identification using different moment hierarchies
Authors: Jan Friedrich, Sarah Schraven, Fabian Kiessling, Michael Herty
Subjects: Quantitative Methods (q-bio.QM); Optimization and Control (math.OC)
[3]  arXiv:2405.10078 [pdf, other]
Title: Spurious reconstruction from brain activity
Authors: Ken Shirakawa, Yoshihiro Nagano, Misato Tanaka, Shuntaro C. Aoki, Kei Majima, Yusuke Muraki, Yukiyasu Kamitani
Subjects: Neurons and Cognition (q-bio.NC)
[4]  arXiv:2405.10070 [pdf, other]
Title: HeMiTo-dynamics: a characterisation of mammalian prion toxicity using non-dimensionalisation, linear stability and perturbation analyses
Authors: Johannes G. Borgqvist, Christoffer Gretarsson Alexandersen
Comments: 25 pages and 4 figures
Subjects: Quantitative Methods (q-bio.QM)
[5]  arXiv:2405.10035 [pdf, ps, other]
Title: A quality control analysis of the resting state hypothesis via permutation entropy on EEG recordings
Authors: Alessio Perinelli, Leonardo Ricci
Comments: 17 pages, 6 figures. Submitted to: Chaos
Subjects: Neurons and Cognition (q-bio.NC)
[6]  arXiv:2405.09953 [pdf, ps, other]
Title: Zero-shot counting with a dual-stream neural network model
Authors: Jessica A.F. Thompson, Hannah Sheahan, Tsvetomira Dumbalska, Julian Sandbrink, Manuela Piazza, Christopher Summerfield
Subjects: Neurons and Cognition (q-bio.NC)
[7]  arXiv:2405.09813 [pdf, other]
Title: Revisiting the exclusion principle in epidemiology at its ultimate limit
Authors: Nir Gavish
Comments: 17 pages, 5 figures
Subjects: Populations and Evolution (q-bio.PE)
[8]  arXiv:2405.09809 [pdf, other]
Title: Biomarker Selection for Adaptive Systems
Authors: Joshua Pickard, Cooper Stansbury, Amit Surana, Anthony Bloch, Indika Rajapakse
Subjects: Molecular Networks (q-bio.MN); Optimization and Control (math.OC)
[9]  arXiv:2405.09748 [pdf, other]
Title: A Mathematical Reconstruction of Endothelial Cell Networks
Authors: Okezue Bell, Anthony Bell
Comments: 14 pages, 9 figures
Subjects: Cell Behavior (q-bio.CB); Combinatorics (math.CO); Group Theory (math.GR); Quantitative Methods (q-bio.QM)
[10]  arXiv:2405.09699 [pdf, ps, other]
Title: Mapping Differential Protein-Protein Interaction Networks using Affinity Purification Mass Spectrometry
Authors: Prashant Kaushal, Manisha R. Ummadi, Gwendolyn M. Jang, Yennifer Delgado, Sara K. Makanani, Sophie F. Blanc, Decan M. Winters, Jiewei Xu, Benjamin Polacco, Yuan Zhou, Erica Stevenson, Manon Eckhardt, Lorena Zuliani-Alvarez, Robyn Kaake, Danielle L. Swaney, Nevan Krogan, Mehdi Bouhaddou
Comments: 29 pages, 3 figures
Subjects: Quantitative Methods (q-bio.QM); Molecular Networks (q-bio.MN)
[11]  arXiv:2405.09664 [pdf, other]
Title: Seasonality and susceptibility from measles time series
Authors: Niket Thakkar, Sonia Jindal, Katherine Rosenfeld
Subjects: Populations and Evolution (q-bio.PE)
[12]  arXiv:2405.09647 [pdf, ps, other]
Title: Dynamics of antibody binding and neutralization during viral infection
Authors: Zhenying Chen, Hasan Ahmed, Cora Hirst, Rustom Antia
Subjects: Populations and Evolution (q-bio.PE); Biomolecules (q-bio.BM)
[13]  arXiv:2405.09595 [pdf, other]
Title: Simplicity within biological complexity
Authors: Natasa Przulj, Noel Malod-Dognin
Comments: 29 pages, 4 figures
Subjects: Other Quantitative Biology (q-bio.OT); Artificial Intelligence (cs.AI)
[14]  arXiv:2405.10183 (cross-list from cs.NE) [pdf, other]
Title: A Guide to Tracking Phylogenies in Parallel and Distributed Agent-based Evolution Models
Authors: Matthew Andres Moreno, Anika Ranjan, Emily Dolson, Luis Zaman
Subjects: Neural and Evolutionary Computing (cs.NE); Populations and Evolution (q-bio.PE)
[15]  arXiv:2405.09886 (cross-list from cs.LG) [pdf, ps, other]
Title: MTLComb: multi-task learning combining regression and classification tasks for joint feature selection
Authors: Han Cao, Sivanesan Rajan, Bianka Hahn, Ersoy Kocak, Daniel Durstewitz, Emanuel Schwarz, Verena Schneider-Lindner
Comments: 33 pages, 3 figures, 5 tables
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Biomolecules (q-bio.BM)
[16]  arXiv:2405.09851 (cross-list from eess.IV) [pdf, other]
Title: Region of Interest Detection in Melanocytic Skin Tumor Whole Slide Images -- Nevus & Melanoma
Authors: Yi Cui, Yao Li, Jayson R. Miedema, Sharon N. Edmiston, Sherif Farag, J.S. Marron, Nancy E. Thomas
Comments: 5 figures, NeurIPS 2022 Workshop
Subjects: Image and Video Processing (eess.IV); Computer Vision and Pattern Recognition (cs.CV); Quantitative Methods (q-bio.QM)
[17]  arXiv:2405.09756 (cross-list from cs.LG) [pdf, other]
Title: An Autoencoder and Generative Adversarial Networks Approach for Multi-Omics Data Imbalanced Class Handling and Classification
Authors: Ibrahim Al-Hurani, Abedalrhman Alkhateeb, Salama Ikki
Subjects: Machine Learning (cs.LG); Neural and Evolutionary Computing (cs.NE); Genomics (q-bio.GN)
[18]  arXiv:2405.09649 (cross-list from physics.bio-ph) [pdf, other]
Title: Challenges and opportunities for digital twins in precision medicine: a complex systems perspective
Authors: Manlio De Domenico, Luca Allegri, Guido Caldarelli, Valeria d'Andrea, Barbara Di Camillo, Luis M. Rocha, Jordan Rozum, Riccardo Sbarbati, Francesco Zambelli
Subjects: Biological Physics (physics.bio-ph); Adaptation and Self-Organizing Systems (nlin.AO); Quantitative Methods (q-bio.QM)

Thu, 16 May 2024

[19]  arXiv:2405.09413 [pdf, ps, other]
Title: Three Dimensional Spatial Cognition: Bees and Bats
Authors: Robert Worden
Comments: 22 pages; program can be downloaded from www.bayeslanguage.org/bb/BB.zip
Subjects: Neurons and Cognition (q-bio.NC)
[20]  arXiv:2405.09395 [pdf, other]
Title: Matching domain experts by training from scratch on domain knowledge
Authors: Xiaoliang Luo, Guangzhi Sun, Bradley C. Love
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Computation and Language (cs.CL)
[21]  arXiv:2405.09389 [pdf, ps, other]
Title: Phylotrack: C++ and Python libraries for in silico phylogenetic tracking
Authors: Emily Dolson, Santiago Rodriguez-Papa, Matthew Andres Moreno
Subjects: Populations and Evolution (q-bio.PE); Neural and Evolutionary Computing (cs.NE)
[22]  arXiv:2405.09327 [pdf, other]
Title: Leveraging graphical model techniques to study evolution on phylogenetic networks
Authors: Benjamin Teo, Paul Bastide, Cécile Ané
Subjects: Populations and Evolution (q-bio.PE); Computation (stat.CO)
[23]  arXiv:2405.09216 [pdf, ps, other]
Title: The Genomic Landscape of Oceania
Authors: Consuelo D. Quinto-Cortés, Carmina Barberena Jonas, Sofía Vieyra-Sánchez, Stephen Oppenheimer, Ram González-Buenfil, Kathryn Auckland, Kathryn Robson, Tom Parks, J. Víctor Moreno-Mayar, Javier Blanco-Portillo, Julian R. Homburger, Genevieve L. Wojcik, Alissa L. Severson, Jonathan S. Friedlaender, Francoise Friedlaender, Angela Allen, Stephen Allen, Mark Stoneking, Adrian V. S. Hill, George Aho, George Koki, William Pomat, Carlos D. Bustamante, Maude Phipps, Alexander J. Mentzer, Andrés Moreno-Estrada, Alexander G. Ioannidis
Subjects: Populations and Evolution (q-bio.PE)
[24]  arXiv:2405.08970 [pdf, ps, other]
Title: Impact of Hypoglycemia on Glucose Variability Over Time for Individuals with Open Source Automated Insulin Delivery Systems
Authors: Arsalan Shahid, Dana M. Lewis
Subjects: Quantitative Methods (q-bio.QM)
[25]  arXiv:2405.08849 [pdf, ps, other]
Title: Rooting of thornless blackberry cuttings as induced by the extract of white willow (Salix alba L.) shoots collected in different times
Authors: Kocher Omer Salih, Aram Akram Mohammed, Ibrahim Maaroof Noori
Subjects: Other Quantitative Biology (q-bio.OT)
[26]  arXiv:2405.08827 [pdf, ps, other]
Title: A Dynamical Systems Approach to Predicting Patient Outcome after Cardiac Arrest
Authors: Richard J Povinelli, Mathew Dupont
Comments: Computing in Cardiology, 2023
Subjects: Quantitative Methods (q-bio.QM); Dynamical Systems (math.DS)
[27]  arXiv:2405.08979 (cross-list from cs.LG) [pdf, other]
Title: drGAT: Attention-Guided Gene Assessment of Drug Response Utilizing a Drug-Cell-Gene Heterogeneous Network
Authors: Yoshitaka Inoue, Hunmin Lee, Tianfan Fu, Augustin Luna
Subjects: Machine Learning (cs.LG); Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)

Wed, 15 May 2024

[28]  arXiv:2405.08735 [pdf, other]
Title: Competition in the nutrient-driven self-cycling fermentation process
Authors: Stacey R. Smith?, Tyler Meadows, Gail S.K. Wolkowicz
Comments: 17 pages, 2 figures
Subjects: Populations and Evolution (q-bio.PE); Dynamical Systems (math.DS)
[29]  arXiv:2405.08601 [pdf, ps, other]
Title: The Requirement for Cognition, in an Equation
Authors: Robert Worden
Comments: 12 pages
Subjects: Neurons and Cognition (q-bio.NC); Populations and Evolution (q-bio.PE)
[30]  arXiv:2405.08523 [pdf, other]
Title: How forest insect outbreaks depend on forest size and tree distribution: an individual-based model results
Authors: Janusz Uchmański
Subjects: Populations and Evolution (q-bio.PE); Probability (math.PR)
[31]  arXiv:2405.08397 [pdf, other]
Title: Self-supervised contrastive learning unveils cortical folding pattern linked to prematurity
Authors: Julien Laval (BAOBAB), Aymeric Gaudin (BAOBAB), Vincent Frouin (BAOBAB), Jessica Dubois (UNIACT), Andrea Gondova (UNIACT), Jean-François Mangin (BAOBAB), Joël Chavas (BAOBAB), Denis Rivière (BAOBAB)
Journal-ref: MIDL 2024, Jul 2024, Paris, France
Subjects: Neurons and Cognition (q-bio.NC)
[32]  arXiv:2405.08391 [pdf, ps, other]
Title: Cerebralization of mathematical quantities and physical features in neural science: a critical evaluation
Authors: Laurent Goffart (CGGG)
Subjects: Neurons and Cognition (q-bio.NC)
[33]  arXiv:2405.08409 (cross-list from nlin.AO) [pdf, ps, other]
Title: Bifurcation analysis of a two-neuron central pattern generator model for both oscillatory and convergent neuronal activities
Authors: Kotaro Muramatsu, Hiroshi Kori
Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Neurons and Cognition (q-bio.NC)
[34]  arXiv:2405.08404 (cross-list from math.PR) [pdf, other]
Title: Genetic contribution of an advantaged mutant in the biparental Moran model -- finite selection
Authors: Camille Coron (INRAE), Yves Le Jan
Subjects: Probability (math.PR); Populations and Evolution (q-bio.PE)
[35]  arXiv:2405.08384 (cross-list from math.AP) [pdf, other]
Title: Group Dispersal Modelling revisited
Authors: Mario Ayala (BioSP, TUM), Jérôme Coville (BioSP), Samuel Soubeyrand (BioSP)
Subjects: Analysis of PDEs (math.AP); Probability (math.PR); Quantitative Methods (q-bio.QM)
[36]  arXiv:2405.08304 (cross-list from cs.CL) [pdf, other]
Title: Computational Thought Experiments for a More Rigorous Philosophy and Science of the Mind
Authors: Iris Oved, Nikhil Krishnaswamy, James Pustejovsky, Joshua Hartshorne
Comments: 6 pages, 4 figures, to appear at CogSci 2024
Subjects: Computation and Language (cs.CL); Artificial Intelligence (cs.AI); Neurons and Cognition (q-bio.NC)
[37]  arXiv:2405.08217 (cross-list from cs.LG) [pdf, other]
Title: Data Valuation with Gradient Similarity
Authors: Nathaniel J. Evans, Gordon B. Mills, Guanming Wu, Xubo Song, Shannon McWeeney
Subjects: Machine Learning (cs.LG); Genomics (q-bio.GN); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)
[38]  arXiv:2405.08040 (cross-list from physics.soc-ph) [pdf, other]
Title: No evidence of systematic proximity ascertainment bias in early COVID-19 cases in Wuhan Reply to Weissman (2024)
Authors: Florence Débarre, Michael Worobey
Comments: Reply to Weissman (2024) arXiv:2401.08680
Subjects: Physics and Society (physics.soc-ph); Populations and Evolution (q-bio.PE)
[39]  arXiv:2405.08031 (cross-list from cs.LG) [pdf, ps, other]
Title: HGTDR: Advancing Drug Repurposing with Heterogeneous Graph Transformers
Authors: Ali Gharizadeh, Karim Abbasi, Amin Ghareyazi, Mohammad R.K. Mofrad, Hamid R. Rabiee
Comments: Accepted for Publication in Bioinformatics (11-Feb-2024)
Subjects: Machine Learning (cs.LG); Artificial Intelligence (cs.AI); Quantitative Methods (q-bio.QM)

Tue, 14 May 2024 (showing first 39 of 43 entries)

[40]  arXiv:2405.07977 [pdf, other]
Title: A Demographic-Conditioned Variational Autoencoder for fMRI Distribution Sampling and Removal of Confounds
Authors: Anton Orlichenko, Gang Qu, Ziyu Zhou, Anqi Liu, Hong-Wen Deng, Zhengming Ding, Julia M. Stephen, Tony W. Wilson, Vince D. Calhoun, Yu-Ping Wang
Comments: 12 pages
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[41]  arXiv:2405.07858 [pdf, ps, other]
Title: Radiogenomic biomarkers for immunotherapy in glioblastoma: A systematic review of magnetic resonance imaging studies
Authors: Prajwal Ghimire, Ben Kinnersley, Golestan Karami, Prabhu Arumugam, Richard Houlston, Keyoumars Ashkan, Marc Modat, Thomas C Booth
Comments: Published in Neuro-Oncology Advances 2024
Subjects: Tissues and Organs (q-bio.TO)
[42]  arXiv:2405.07837 [pdf, ps, other]
Title: Why Decussate? Topological Constraints on 3D Wiring
Authors: Troy Shinbrot, Wise Young
Comments: 15 pages, 8 figures
Journal-ref: The Anatomical Record 291.10 (2008) 1278-1292
Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Geometric Topology (math.GT)
[43]  arXiv:2405.07835 [pdf, other]
Title: Topological Embedding of Human Brain Networks with Applications to Dynamics of Temporal Lobe Epilepsy
Authors: Moo K. Chung, Ji Bi Che, Veena A. Nair, Camille Garcia Ramos, Jedidiah Ray Mathis, Vivek Prabhakaran, Elizabeth Meyerand, Bruce P. Hermann, Jeffrey R. Binder, Aaron F. Struck
Subjects: Neurons and Cognition (q-bio.NC)
[44]  arXiv:2405.07772 [pdf, ps, other]
Title: Characterizing virulence differences in a parasitoid wasp through comparative transcriptomic and proteomic
Authors: Samuel Gornard (EGCE), Pascaline Venon, Florian Lasfont, Thierry Balliau, Laure Marie-Paule Kaiser-Arnauld, Florence Mougel
Subjects: Genomics (q-bio.GN)
[45]  arXiv:2405.07771 [pdf, ps, other]
Title: Cellular dynamics of host-parasitoid interactions: Insights from the encapsulation process in a partially resistant host
Authors: Samuel Gornard (EGCE), Florence Mougel, Isabelle Germon, Véronique Borday-Birraux, Pascaline Venon, Salimata Drabo, Laure Marie-Paule Kaiser-Arnauld
Subjects: Cell Behavior (q-bio.CB)
[46]  arXiv:2405.07622 [pdf, other]
Title: De novo antibody design with SE(3) diffusion
Authors: Daniel Cutting, Frédéric A. Dreyer, David Errington, Constantin Schneider, Charlotte M. Deane
Comments: 20 pages, 11 figures, 4 tables, model weights and samples available at this https URL
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[47]  arXiv:2405.07452 [pdf, ps, other]
Title: PLA-SGCN: Protein-Ligand Binding Affinity Prediction by Integrating Similar Pairs and Semi-supervised Graph Convolutional Network
Authors: Karim Abbasi, Parvin Razzaghi, Amin Ghareyazi, Hamid R. Rabiee
Comments: Accepted for Publication in Briefings of Bioinformatics (13-Dec-2023)
Subjects: Quantitative Methods (q-bio.QM); Machine Learning (cs.LG)
[48]  arXiv:2405.07449 [pdf, ps, other]
Title: Evaluation of In vitro anti-inflammatory activity and Insilico pharmacokinetics and molecular docking study of Horsfieldia iryaghedhi
Authors: Rajapaksha HKK, Fernando MN, Nelumdeniya NRM, Bandara AWMKK, Silva ARN
Subjects: Biomolecules (q-bio.BM)
[49]  arXiv:2405.07394 [pdf, other]
Title: Exact Expressions for the Log-likelihood's Hessian in Multivariate Continuous-Time Continuous-Trait Gaussian Evolution along a Phylogeny
Authors: Woodrow Hao Chi Kiang
Comments: Part of a thesis (DOI:10.3384/9789180755900)
Subjects: Populations and Evolution (q-bio.PE)
[50]  arXiv:2405.07295 [pdf, ps, other]
Title: Environmental enrichment: a biological model of forward transfer in continual learning
Authors: Rajat Saxena, Bruce L. McNaughton
Comments: 23 pages, 5 figures
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI)
[51]  arXiv:2405.07245 [pdf, other]
Title: Ecology, Spatial Structure, and Selection Pressure Induce Strong Signatures in Phylogenetic Structure
Authors: Matthew Andres Moreno, Santiago Rodriguez-Papa, Emily Dolson
Subjects: Populations and Evolution (q-bio.PE); Neural and Evolutionary Computing (cs.NE)
[52]  arXiv:2405.07238 [pdf, ps, other]
Title: Handwriting Anomalies and Learning Disabilities through Recurrent Neural Networks and Geometric Pattern Analysis
Authors: Vasileios Alevizos, Clark Xu, Sabrina Edralin, Akebu Simasiku, Dimitra Malliarou, Zongliang Yue, Antonis Messinis
Subjects: Quantitative Methods (q-bio.QM)
[53]  arXiv:2405.07123 [pdf, other]
Title: CANA v1.0.0 and schematodes: efficient quantification of symmetry in Boolean automata
Authors: Austin M. Marcus, Jordan Rozum, Herbert Sizek, Luis M. Rocha
Comments: 5 pages 1 figure (two images in figure)
Subjects: Molecular Networks (q-bio.MN); Quantitative Methods (q-bio.QM)
[54]  arXiv:2405.07110 [pdf, other]
Title: A Vector Representation for Phylogenetic Trees
Authors: Cedric Chauve, Caroline Colijn, Louxin Zhang
Subjects: Populations and Evolution (q-bio.PE); Data Structures and Algorithms (cs.DS); Combinatorics (math.CO)
[55]  arXiv:2405.06851 [pdf, other]
Title: Nonlinear classification of neural manifolds with contextual information
Authors: Francesca Mignacco, Chi-Ning Chou, SueYeon Chung
Comments: 5 pages, 5 figures
Subjects: Neurons and Cognition (q-bio.NC); Disordered Systems and Neural Networks (cond-mat.dis-nn); Statistical Mechanics (cond-mat.stat-mech); Neural and Evolutionary Computing (cs.NE); Machine Learning (stat.ML)
[56]  arXiv:2405.06836 [pdf, other]
Title: Improving Targeted Molecule Generation through Language Model Fine-Tuning Via Reinforcement Learning
Authors: Salma J. Ahmed, Mustafa A. Elattar
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[57]  arXiv:2405.06732 [pdf, other]
Title: A Global Data-Driven Model for The Hippocampus and Nucleus Accumbens of Rat From The Local Field Potential Recordings (LFP)
Authors: Maedeh Sadeghi (1), Mahdi Aliyari Shoorehdeli (1), Shole jamali (2), Abbas Haghparast (2) ((1) Fault Detection and Identification (FDI) Laboratory, Faculty of Electrical Engineering, K. N. Toosi University of Technology, Tehran, Iran, (2) Neuroscience Research Center, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran)
Subjects: Neurons and Cognition (q-bio.NC); Machine Learning (cs.LG)
[58]  arXiv:2405.06729 [pdf, other]
Title: Fine-tuning Protein Language Models with Deep Mutational Scanning improves Variant Effect Prediction
Authors: Aleix Lafita, Ferran Gonzalez, Mahmoud Hossam, Paul Smyth, Jacob Deasy, Ari Allyn-Feuer, Daniel Seaton, Stephen Young
Comments: Machine Learning for Genomics Explorations workshop at ICLR 2024
Subjects: Genomics (q-bio.GN); Machine Learning (cs.LG)
[59]  arXiv:2405.06725 [pdf, other]
Title: On the Shape of Brainscores for Large Language Models (LLMs)
Authors: Jingkai Li
Comments: Published as a workshop paper at ICLR AGI Workshop 2024
Subjects: Neurons and Cognition (q-bio.NC); Artificial Intelligence (cs.AI); Computation and Language (cs.CL); Machine Learning (cs.LG)
[60]  arXiv:2405.06724 [pdf, other]
Title: Boolean matrix logic programming for active learning of gene functions in genome-scale metabolic network models
Authors: Lun Ai, Stephen H. Muggleton, Shi-Shun Liang, Geoff S. Baldwin
Subjects: Molecular Networks (q-bio.MN); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[61]  arXiv:2405.06718 [pdf, ps, other]
Title: Vector-borne threats: Sustainable approaches to their diagnosis and treatment
Authors: Areesha Naveed, Ayesha Haidar, Rameen Atique, Arshi Saeed, Bushra Anwar, Ambreen Talib, Uzma Bilal, Javeria Sharif, Ayesha Nadeem, Sania Tariq, Ayesha Muazzam, Abdul Samad
Comments: 4 Figure, 1 table
Subjects: Other Quantitative Biology (q-bio.OT)
[62]  arXiv:2405.06708 [pdf, other]
Title: LangCell: Language-Cell Pre-training for Cell Identity Understanding
Authors: Suyuan Zhao, Jiahuan Zhang, Yizhen Luo, Yushuai Wu, Zaiqing Nie
Comments: 27 pages, 21 figures, conference
Subjects: Genomics (q-bio.GN); Artificial Intelligence (cs.AI); Computation and Language (cs.CL)
[63]  arXiv:2405.06693 [pdf, other]
Title: SurfPro: Functional Protein Design Based on Continuous Surface
Authors: Zhenqiao Song, Tinglin Huang, Lei Li, Wengong Jin
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[64]  arXiv:2405.06690 [pdf, other]
Title: DrugLLM: Open Large Language Model for Few-shot Molecule Generation
Authors: Xianggen Liu, Yan Guo, Haoran Li, Jin Liu, Shudong Huang, Bowen Ke, Jiancheng Lv
Comments: 17 pages, 3 figures
Subjects: Biomolecules (q-bio.BM); Computation and Language (cs.CL); Machine Learning (cs.LG)
[65]  arXiv:2405.06663 [pdf, other]
Title: Protein Representation Learning by Capturing Protein Sequence-Structure-Function Relationship
Authors: Eunji Ko, Seul Lee, Minseon Kim, Dongki Kim
Comments: ICLR 2024 MLGenX Workshop (Spotlight)
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[66]  arXiv:2405.06662 [pdf, ps, other]
Title: Language Interaction Network for Clinical Trial Approval Estimation
Authors: Chufan Gao, Tianfan Fu, Jimeng Sun
Subjects: Biomolecules (q-bio.BM); Computation and Language (cs.CL); Machine Learning (cs.LG)
[67]  arXiv:2405.06659 [pdf, other]
Title: ControlMol: Adding Substruture Control To Molecule Diffusion Models
Authors: Qi Zhengyang, Liu Zijing, Zhang Jiying, Cao He, Li Yu
Comments: 9 pages,7 figures
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG); Chemical Physics (physics.chem-ph)
[68]  arXiv:2405.06658 [pdf, other]
Title: ProteinEngine: Empower LLM with Domain Knowledge for Protein Engineering
Authors: Yiqing Shen, Outongyi Lv, Houying Zhu, Yu Guang Wang
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[69]  arXiv:2405.06657 [pdf, other]
Title: Molecular Docking via Weighted Subgraph Isomorphism on Quantum Annealers
Authors: Emanuele Triuzzi, Riccardo Mengoni, Domenico Bonanni, Daniele Ottaviani, Andrea Beccari, Gianluca Palermo
Subjects: Biomolecules (q-bio.BM); Computational Engineering, Finance, and Science (cs.CE); Emerging Technologies (cs.ET)
[70]  arXiv:2405.06655 [pdf, ps, other]
Title: RNA Secondary Structure Prediction Using Transformer-Based Deep Learning Models
Authors: Yanlin Zhou, Tong Zhan, Yichao Wu, Bo Song, Chenxi Shi
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[71]  arXiv:2405.06654 [pdf, other]
Title: PROflow: An iterative refinement model for PROTAC-induced structure prediction
Authors: Bo Qiang, Wenxian Shi, Yuxuan Song, Menghua Wu
Comments: Published at the GEM workshop, ICLR 2024
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[72]  arXiv:2405.06653 [pdf, other]
Title: A unified cross-attention model for predicting antigen binding specificity to both HLA and TCR molecules
Authors: Chenpeng Yu, Xing Fang, Hui Liu
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG)
[73]  arXiv:2405.06651 [pdf, ps, other]
Title: Using GANs for De Novo Protein Design Targeting Microglial IL-3R$α$ to Inhibit Alzheimer's Progression
Authors: Arnav Swaroop
Comments: 9 pages total
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Neurons and Cognition (q-bio.NC)
[74]  arXiv:2405.06649 [pdf, other]
Title: ProLLM: Protein Chain-of-Thoughts Enhanced LLM for Protein-Protein Interaction Prediction
Authors: Mingyu Jin, Haochen Xue, Zhenting Wang, Boming Kang, Ruosong Ye, Kaixiong Zhou, Mengnan Du, Yongfeng Zhang
Subjects: Biomolecules (q-bio.BM); Machine Learning (cs.LG); Molecular Networks (q-bio.MN)
[75]  arXiv:2405.06648 [pdf, other]
Title: Protein atom traps as seeing by neutron scattering
Authors: Georgii Koniukov
Subjects: Biomolecules (q-bio.BM); Mesoscale and Nanoscale Physics (cond-mat.mes-hall); Soft Condensed Matter (cond-mat.soft); Biological Physics (physics.bio-ph)
[76]  arXiv:2405.06645 [pdf, other]
Title: On Recovering Higher-order Interactions from Protein Language Models
Authors: Darin Tsui, Amirali Aghazadeh
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[77]  arXiv:2405.06644 [pdf, ps, other]
Title: The Mathematics of Chlorophyll Photoexcitation
Authors: Archit Chaturvedi
Subjects: Biomolecules (q-bio.BM)
[78]  arXiv:2405.06642 [pdf, other]
Title: PPFlow: Target-aware Peptide Design with Torsional Flow Matching
Authors: Haitao Lin, Odin Zhang, Huifeng Zhao, Dejun Jiang, Lirong Wu, Zicheng Liu, Yufei Huang, Stan Z. Li
Comments: 18 pages
Subjects: Biomolecules (q-bio.BM); Artificial Intelligence (cs.AI); Machine Learning (cs.LG)
[ total of 94 entries: 1-78 | 79-94 ]
[ showing 78 entries per page: fewer | more | all ]

Disable MathJax (What is MathJax?)

Links to: arXiv, form interface, find, q-bio, new, 2405, contact, help  (Access key information)