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Brain energetic landscapes shape state dysregulation in major depressive disorder: a morphological network controllability perspective.

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1 match between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

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  1. [1] § Methods › Differential analysis of state transition probability and energy ↔ ejc_bs_code/control/plotWeightedControlEnergyvsTransitionProbabilityTrange.R, the whole file · a weak match · score 0.61 · transition probability, transition energy, control energy, TP, brain

Paper

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The authors' code

R · 91 lines · 5 KB · no license · 1 match

  1. # plot weighted control energy vs. transition probabilities for a range of T values
  2. # compare to correlation between system-weighted interstate distance and transition probabilities
  3. # do this for the 7 Yeo cognitive systems
  4. # then also for whole brain control, with comparison to null
  5. args <- commandArgs(TRUE)
  6. name_root <- args[1]
  7. numClusters <- as.numeric(args[2])
  8. basedir <- args[3]
  9. c <- args[4]
  10. library(ggplot2)
  11. library(R.matlab)
  12. library(RColorBrewer)
  13. library(lm.beta)
  14. library(reshape2)
  15. library(viridis)
  16. library(gridExtra)
  17. masterdir <- paste(basedir,'results/',name_root,'/',sep='')
  18. source(paste(basedir,'code/plottingfxns/plottingfxns.R',sep=''))
  19. source(paste(basedir,'code/miscfxns/statfxns.R',sep=''))
  20. clusterNames <- readMat(paste(basedir,'results/',name_root,'/clusterAssignments/k',numClusters,name_root,'.mat',sep=''))
  21. clusterNames <- unlist(clusterNames$clusterAssignments[[1]][[5]])
  22. clusterColors <- getClusterColors(numClusters)
  23. RNcolors <- c('#005C9F','#FF8400')
  24. savedir <- paste(masterdir,'analyses/control_energy/EvsTP_plots/WeightedControl/',sep = '')
  25. dir.create(path = savedir,recursive = TRUE)
  26. ### load transition probabilities ###
  27. restTP <- readMat(paste(masterdir,'analyses/transitionprobabilities/RestCombTransitionProbabilitiesNoPersist_k',
  28. numClusters,name_root,'.mat',sep = ''))$transitionProbability
  29. restTP <- colMeans(restTP) # group average
  30. nbackTP <- readMat(paste(masterdir,'analyses/nbackblocks/TransProbsNoPersist2back_k',numClusters,name_root,'.mat',sep = ''))$BlockTransitionProbability
  31. nbackTP <- colMeans(nbackTP,na.rm=T)
  32. onDiag = (1:numClusters) + (numClusters*(0:(numClusters-1))) # construct indices to select only persistence probabilites
  33. offDiag = 1:(numClusters^2); offDiag <- offDiag[-onDiag] # construct indices to select only transition probabilites
  34. Centroids <- readMat(paste(masterdir,'analyses/centroids/OverallClusterCentroids_k',
  35. numClusters,name_root,'.mat',sep = ''))$kClusterCentroids
  36. xf <- Centroids[,rep(1:numClusters,times=numClusters)]
  37. x0 <- Centroids[,rep(1:numClusters,each=numClusters)]
  38. InterStateDistance <- colSums((xf - x0)^2)
  39. ### load weighted control energies ###
  40. yeo <- readMat(paste(basedir,'data/yeo7netlabelsLaus250.mat',sep=''))$network7labels
  41. yeo <- yeo[-length(yeo)] # remove brainstem
  42. Systems <- c('VIS','SOM','DAT','VAT','LIM','FPN','DMN')
  43. B.matrix <- lapply(1:length(Systems), function(S) sapply(1:numClusters^2, function(K) (1+(yeo==S))^2)) # for weighted control, reconstruct B matrix to use for weighted distance calculation
  44. names(B.matrix) <- Systems
  45. InterStateDistance.weighted <- lapply(Systems, function(S) colSums((xf-x0)^2/B.matrix[[S]])) # interstate distance weighted by input matrix
  46. names(InterStateDistance.weighted) <- Systems
  47. weightedcontrol <- lapply(Systems, function(Sys) readMat(paste(masterdir,'analyses/control_energy/model_task_inputs/TransitionEnergies_c',c,Sys,'WeightedControl_k',
  48. numClusters,'.mat',sep='')))
  49. names(weightedcontrol) <- Systems
  50. E.null <- weightedcontrol[['SOM']]$E.identity[offDiag,] # get whole brain control from a random system, doesn't matter bc E.identity is always the same.
  51. E.null <- array(E.null,dim=c(dim(E.null)[1],1,dim(E.null)[2])) # add a 3rd dimension
  52. E.null = list(WB=E.null)
  53. ### load whole brain control energies ###
  54. E.wholebrain <- readMat(paste(masterdir,'analyses/control_energy/Tsweep/c',c,'_k',numClusters,
  55. '/GroupAverageTransitionEnergies_k',numClusters,'.mat',sep=''))
  56. E.brain <- E.wholebrain$E.full[offDiag,]
  57. E.null.full <- list(BCT=E.wholebrain$E.BCTnull[offDiag,,])
  58. t.rng <- as.numeric(E.wholebrain$T.rng)
  59. for(method in c('pearson','spearman')){
  60. rest.plots.weighted <- lapply(Systems, function(S) p.Tsweep(as.numeric(weightedcontrol[[S]]$T.rng),weightedcontrol[[S]]$E.full[offDiag,],E.null,restTP[offDiag],
  61. InterStateDistance.weighted[[S]][offDiag],RNcolors[1],ttl=paste('Rest: ',S,'-Weighted',sep=''),method=method,leg=FALSE))
  62. # tack on whole brain control plot for rest
  63. rest.plots.uniform <- list(p.Tsweep(t.rng,E.brain,E.null.full,restTP[offDiag],InterStateDistance[offDiag],RNcolors[1],ttl='Rest: Uniform',method=method,leg = FALSE))
  64. rest.plots <- c(rest.plots.uniform,rest.plots.weighted)
  65. ggsave(plot = arrangeGrob(grobs=rest.plots,nrow=2),filename = paste(savedir,'AllTSweepsControlEnergyVsRestTP_c',c,method,'_k',numClusters,'.pdf',sep =''),
  66. units = 'cm',height = 9,width = 18)
  67. nback.plots.weighted <- lapply(Systems, function(S) p.Tsweep(as.numeric(weightedcontrol[[S]]$T.rng),weightedcontrol[[S]]$E.full[offDiag,],E.null,nbackTP[offDiag],
  68. InterStateDistance.weighted[[S]][offDiag],RNcolors[2],ttl=paste('2-back: ',S,'-Weighted',sep=''),method=method,leg=FALSE))
  69. # tack on whole brain control plot for nback
  70. nback.plots.uniform <- list(p.Tsweep(t.rng,E.brain,E.null.full,nbackTP[offDiag],InterStateDistance[offDiag],RNcolors[2],ttl='2-back: Uniform',method=method,leg = FALSE))
  71. nback.plots <- c(nback.plots.uniform,nback.plots.weighted)
  72. ggsave(plot = arrangeGrob(grobs=nback.plots,nrow=2),filename = paste(savedir,'AllTSweepsControlEnergyVs2BackTP_c',c,method,'_k',numClusters,'.pdf',sep =''),
  73. units = 'cm',height = 9,width = 18)
  74. }

plotWeightedControlEnergyvsTransitionProbabilityTrange.R at commit 47cd3d2, no license · at the source

Overview

Authors: Jinpeng Niu1,2, Jie Xia1,2, Qingjin Liu1,2, Yaohui He1,2, Wei Li1,2, Kangjia Chen1,2, Xi Zhang1,2,3, Jiang Qiu4, Huafu Chen1,2, Jiao Li1,2, Wei Liao1,2
  1. The Clinical Hospital of Chengdu Brain Science Institute, School of Life Science and Technology, University of Electronic Science and Technology of China,Chengdu, 611731 P.R. China
  2. Brain-Computer Interface & Brain-Inspired Intelligence Key Laboratory of Sichuan Province, Chengdu, 611731 P. R. China
  3. Department of Radiology, Xinqiao Hospital, Army Medical University,Chongqing, 400037 P.R. China
  4. Key Laboratory of Cognition and Personality, Faculty of Psychology, Southwest University,Chongqing, 400715 P.R. China
Journal: Translational psychiatry, volume 16, issue 1, article 270
Dates: received 4 December 2025; accepted 24 March 2026; published online 6 April 2026
Type: Research article · Language: English
License: CC BY-NC-ND
Identifiers: DOI 10.1038/s41398-026-04025-2 · PMID 41942448 · PMCID PMC13183912 · OpenAlex W7150982754
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: human (organism), depression (population)
Methods: Statistics, Preprocessing, fMRI & imaging, Smoothing, state filtering, decompositions
Keywords: Psychiatric disorders, Neuroscience
MeSH: Brain*, Energy Metabolism*, Major Depressive Disorder*, Nerve Net*, Adult, Female, Gyrus Cinguli, Humans, Magnetic Resonance Imaging, Male, Middle Aged (* major topic)
Topic: Functional Brain Connectivity Studies (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: Fundamental Research Funds for the Central Universities; National Natural Science Foundation of China (National Science Foundation of China)
Citations: not cited yet (Europe PMC); 79 references in the paper

Abstract

The abstract is not reproduced here: the paper's license (CC BY-NC-ND) does not allow it. Read it in the paper, at the publisher or on Europe PMC.

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netneurolab/neuromaps

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Size: 90 files, 48 scripts
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isebenius/MIND

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NeuroenergeticsLab/control_costs

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smweinst.github.io/nest-method

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singlesp/energy_landscape

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rmarkello/pyls

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Read it in the paper: doi.org/10.1038/s41398-026-04025-2.

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Data

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Code and data availability statement

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Read it in the paper: doi.org/10.1038/s41398-026-04025-2.

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Version 1, 29 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 2 keywords, 11 MeSH terms, 2 funders, 79 references.

Cite

This paper

Niu, J., Xia, J., Liu, Q., He, Y., Li, W., Chen, K., Zhang, X., Qiu, J., Chen, H., Li, J., & Liao, W. (2026). Brain energetic landscapes shape state dysregulation in major depressive disorder: a morphological network controllability perspective. Translational psychiatry, 16(1), 270. https://doi.org/10.1038/s41398-026-04025-2

BibTeX

@article{niu2026brain,
author = {Niu, Jinpeng and Xia, Jie and Liu, Qingjin and He, Yaohui and Li, Wei and Chen, Kangjia and Zhang, Xi and Qiu, Jiang and Chen, Huafu and Li, Jiao and Liao, Wei},
title = {{Brain energetic landscapes shape state dysregulation in major depressive disorder: a morphological network controllability perspective}},
journal = {Translational psychiatry},
year = {2026},
month = apr,
volume = {16},
number = {1},
pages = {270},
publisher = {Nature Publishing Group},
issn = {2158-3188},
doi = {10.1038/s41398-026-04025-2},
url = {https://doi.org/10.1038/s41398-026-04025-2},
pmid = {41942448},
pmcid = {PMC13183912}
}

RIS

TY - JOUR
AU - Niu, Jinpeng
AU - Xia, Jie
AU - Liu, Qingjin
AU - He, Yaohui
AU - Li, Wei
AU - Chen, Kangjia
AU - Zhang, Xi
AU - Qiu, Jiang
AU - Chen, Huafu
AU - Li, Jiao
AU - Liao, Wei
TI - Brain energetic landscapes shape state dysregulation in major depressive disorder: a morphological network controllability perspective
T2 - Translational psychiatry
J2 - Transl Psychiatry
PY - 2026
DA - 2026/04/06
VL - 16
IS - 1
SP - 270
SN - 2158-3188
PB - Nature Publishing Group
DO - 10.1038/s41398-026-04025-2
UR - https://doi.org/10.1038/s41398-026-04025-2
LA - en
ER -

CSL-JSON

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