Point clouds are commonly used in many scientific fields. Each point of a cloud is typically associated with additional values or features. Thus, having the ability to identify if and how a given feature is structured along the cloud can provide insights for many applications. Here, we present the Structure Index, a graph-based method to quantify the distribution of features over data in arbitrary dimensional spaces. Spaces can be defined by neurons, time stamps, pixels, genes, etc... The image illustrates how the Structure Index eases the interpretation of neural representations from the brain head-direction system. Sebastian, Esparza and de la Prida 2024.
Image Credit: Julio Esparza
Education Articles
Ten simple rules for establishing an experimental lab
PLOS Computational Biology: published January 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011778
Ten simple rules for using large language models in science, version 1.0
PLOS Computational Biology: published January 31, 2024 | https://doi.org/10.1371/journal.pcbi.1011767
Research Articles
The spinal cord facilitates cerebellar upper limb motor learning and control; inputs from neuromusculoskeletal simulation
PLOS Computational Biology: published January 2, 2024 | https://doi.org/10.1371/journal.pcbi.1011008
Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces
PLOS Computational Biology: published January 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011768
Wildlife vaccination strategies for eliminating bovine tuberculosis in white-tailed deer populations
PLOS Computational Biology: published January 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011287
Harnessing the flexibility of neural networks to predict dynamic theoretical parameters underlying human choice behavior
PLOS Computational Biology: published January 4, 2024 | https://doi.org/10.1371/journal.pcbi.1011678
Landscape quantifies the intermediate state and transition dynamics in ecological networks
PLOS Computational Biology: published January 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011766
Detecting shifts in nonlinear dynamics using Empirical Dynamic Modeling with Nested-Library Analysis
PLOS Computational Biology: published January 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011759
sc2MeNetDrug: A computational tool to uncover inter-cell signaling targets and identify relevant drugs based on single cell RNA-seq data
PLOS Computational Biology: published January 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011785
Differences in boundary behavior in the 3D vertex and Voronoi models
PLOS Computational Biology: published January 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011724
Explaining the flaws in human random generation as local sampling with momentum
PLOS Computational Biology: published January 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011739
The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea
PLOS Computational Biology: published January 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011721
Genome replication in asynchronously growing microbial populations
PLOS Computational Biology: published January 5, 2024 | https://doi.org/10.1371/journal.pcbi.1011753
Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells
PLOS Computational Biology: published January 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011151
Are we really Bayesian? Probabilistic inference shows sub-optimal knowledge transfer
PLOS Computational Biology: published January 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011769
Mapping the dynamics of visual feature coding: Insights into perception and integration
PLOS Computational Biology: published January 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011760
Near-term forecasting of Covid-19 cases and hospitalisations in Aotearoa New Zealand
PLOS Computational Biology: published January 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011752
Plasticity of growth laws tunes resource allocation strategies in bacteria
PLOS Computational Biology: published January 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011735
Adaptive foraging of pollinators fosters gradual tipping under resource competition and rapid environmental change
PLOS Computational Biology: published January 9, 2024 | https://doi.org/10.1371/journal.pcbi.1011762
Joint representation of molecular networks from multiple species improves gene classification
PLOS Computational Biology: published January 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011773
High-performing neural network models of visual cortex benefit from high latent dimensionality
PLOS Computational Biology: published January 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011792
Systems approach for congruence and selection of cancer models towards precision medicine
PLOS Computational Biology: published January 10, 2024 | https://doi.org/10.1371/journal.pcbi.1011754
Tracking conformational transitions of the gonadotropin hormone receptors in a bilayer of (SDPC) poly-unsaturated lipids from all-atom molecular dynamics simulations
PLOS Computational Biology: published January 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011415
Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue
PLOS Computational Biology: published January 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011717
Transformations of sensory information in the brain suggest changing criteria for optimality
PLOS Computational Biology: published January 11, 2024 | https://doi.org/10.1371/journal.pcbi.1011783
Controlling target brain regions by optimal selection of input nodes
PLOS Computational Biology: published January 12, 2024 | https://doi.org/10.1371/journal.pcbi.1011274
Transcription factor interactions explain the context-dependent activity of CRX binding sites
PLOS Computational Biology: published January 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011802
Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression
PLOS Computational Biology: published January 16, 2024 | https://doi.org/10.1371/journal.pcbi.1011803
Virtual neural network-guided optimization of non-invasive brain stimulation in Alzheimer’s disease
PLOS Computational Biology: published January 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011164
Diffusive mediator feedbacks control the health-to-disease transition of skin inflammation
PLOS Computational Biology: published January 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011693
A mathematical, classical stratification modeling approach to disentangling the impact of weather on infectious diseases: A case study using spatio-temporally disaggregated Campylobacter surveillance data for England and Wales
PLOS Computational Biology: published January 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011714
Modelling disease mitigation at mass gatherings: A case study of COVID-19 at the 2022 FIFA World Cup
PLOS Computational Biology: published January 18, 2024 | https://doi.org/10.1371/journal.pcbi.1011018
Identifying essential factors for energy-efficient walking control across a wide range of velocities in reflex-based musculoskeletal systems
PLOS Computational Biology: published January 19, 2024 | https://doi.org/10.1371/journal.pcbi.1011771
The structure and robustness of ecological networks with two interaction types
PLOS Computational Biology: published January 19, 2024 | https://doi.org/10.1371/journal.pcbi.1011770
Functional hierarchies in brain dynamics characterized by signal reversibility in ferret cortex
PLOS Computational Biology: published January 19, 2024 | https://doi.org/10.1371/journal.pcbi.1011818
Postinhibitory excitation in motoneurons can be facilitated by hyperpolarization-activated inward currents: A simulation study
PLOS Computational Biology: published January 19, 2024 | https://doi.org/10.1371/journal.pcbi.1011487
PandoGen: Generating complete instances of future SARS-CoV-2 sequences using Deep Learning
PLOS Computational Biology: published January 19, 2024 | https://doi.org/10.1371/journal.pcbi.1011790
Revealing and reshaping attractor dynamics in large networks of cortical neurons
PLOS Computational Biology: published January 19, 2024 | https://doi.org/10.1371/journal.pcbi.1011784
Inferred regulons are consistent with regulator binding sequences in E. coli
PLOS Computational Biology: published January 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011824
Predicting primate tongue morphology based on geometrical skull matching. A first step towards an application on fossil hominins
PLOS Computational Biology: published January 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011808
Regulus infers signed regulatory relations from few samples’ information using discretization and likelihood constraints
PLOS Computational Biology: published January 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011816
Integrated meta-analysis of colorectal cancer public proteomic datasets for biomarker discovery and validation
PLOS Computational Biology: published January 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011828
Examining B-cell dynamics and responsiveness in different inflammatory milieus using an agent-based model
PLOS Computational Biology: published January 23, 2024 | https://doi.org/10.1371/journal.pcbi.1011776
A genome-wide comprehensive analysis of nucleosome positioning in yeast
PLOS Computational Biology: published January 24, 2024 | https://doi.org/10.1371/journal.pcbi.1011799
Inferring country-specific import risk of diseases from the world air transportation network
PLOS Computational Biology: published January 24, 2024 | https://doi.org/10.1371/journal.pcbi.1011775
Chromatin phase separated nanoregions explored by polymer cross-linker models and reconstructed from single particle trajectories
PLOS Computational Biology: published January 24, 2024 | https://doi.org/10.1371/journal.pcbi.1011794
Mutational signature dynamics indicate SARS-CoV-2’s evolutionary capacity is driven by host antiviral molecules
PLOS Computational Biology: published January 25, 2024 | https://doi.org/10.1371/journal.pcbi.1011795
Short-term Hebbian learning can implement transformer-like attention
PLOS Computational Biology: published January 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011843
Spatial constraints and stochastic seeding subvert microbial arms race
PLOS Computational Biology: published January 26, 2024 | https://doi.org/10.1371/journal.pcbi.1011807
Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study
PLOS Computational Biology: published January 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011832
Vision-based collective motion: A locust-inspired reductionist model
PLOS Computational Biology: published January 29, 2024 | https://doi.org/10.1371/journal.pcbi.1011796
Conversion of spikers to bursters in pituitary cell networks: Is it better to disperse for maximum exposure or circle the wagons?
PLOS Computational Biology: published January 30, 2024 | https://doi.org/10.1371/journal.pcbi.1011811
Radiation necrosis after radiation therapy treatment of brain metastases: A computational approach
PLOS Computational Biology: published January 30, 2024 | https://doi.org/10.1371/journal.pcbi.1011400
Spatial and temporal heterogeneity alter the cost of plasticity in Pristionchus pacificus
PLOS Computational Biology: published January 30, 2024 | https://doi.org/10.1371/journal.pcbi.1011823
A neural network model for the evolution of learning in changing environments
PLOS Computational Biology: published January 30, 2024 | https://doi.org/10.1371/journal.pcbi.1011840
AutoEdge-CCP: A novel approach for predicting cancer-associated circRNAs and drugs based on automated edge embedding
PLOS Computational Biology: published January 30, 2024 | https://doi.org/10.1371/journal.pcbi.1011851
Modeling geographic vaccination strategies for COVID-19 in Norway
PLOS Computational Biology: published January 31, 2024 | https://doi.org/10.1371/journal.pcbi.1011426
Methods
Somnotate: A probabilistic sleep stage classifier for studying vigilance state transitions
PLOS Computational Biology: published January 17, 2024 | https://doi.org/10.1371/journal.pcbi.1011793
Implicit model to capture electrostatic features of membrane environment
PLOS Computational Biology: published January 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011296
Statistical integration of multi-omics and drug screening data from cell lines
PLOS Computational Biology: published January 31, 2024 | https://doi.org/10.1371/journal.pcbi.1011809
Software
MEDUSA: A cloud-based tool for the analysis of X-ray diffuse scattering to obtain the bending modulus from oriented membrane stacks
PLOS Computational Biology: published January 8, 2024 | https://doi.org/10.1371/journal.pcbi.1011749
FindAdapt: A python package for fast and accurate adapter detection in small RNA sequencing
PLOS Computational Biology: published January 22, 2024 | https://doi.org/10.1371/journal.pcbi.1011786