Predicting individual differences of fear and cognitive learning and extinction.
The 11 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
- [1] § Results › Acquisition ↔ scripts/11. pipeline_modelling.r, lines 105–148 · score 0.95 · lACC, lCEB, lPFC, rAMY, rPFC, lAMY
- [2] § Results › Acquisition ↔ scripts/12. pipeline_generalisability.r, lines 106–149 · score 0.95 · lACC, lCEB, lPFC, rAMY, rPFC, lAMY
- [3] § Methods › Functional connectivity (FC) ↔ scripts/06. pipeline_FC.py, lines 286–391 · score 0.94 · wavelet coherence, Euclidean distance, Manhattan distance, Wasserstein distance, mutual information, cross correlation
- [4] § Results › Extinction ↔ scripts/11. pipeline_modelling.r, lines 105–148 · score 0.88 · lCEB, lPFC, rAMY, lAMY, lHIP, rACC
- [5] § Results › Extinction ↔ scripts/12. pipeline_generalisability.r, lines 106–149 · score 0.88 · lCEB, lPFC, rAMY, lAMY, lHIP, rACC
- [6] § Methods › Structural connectivity (SC) › Learning measures › SCR measures ↔ scripts/09b. pipeline_EDA_DCM.m, lines 17–82 · score 0.68 · CS interval, CS onset, latency, flexible, events, linear
- [7] § Methods › Preprocessing of neuroimaging data ↔ scripts/03. pipeline_denoising.py, lines 91–151 · score 0.60 · global signals, Satterthwaite, WM, CSF, denoising, regressors
- [8] § Results › Learning measures ↔ scripts/10. pipeline_learning.r, lines 93–168 · score 0.58 · linear mixed, learning scores, behavioural, CS, renewal, extinction
- [9] § Methods › Behavioural responses › Predicting individual differences ↔ scripts/12. pipeline_generalisability.r, lines 191–230 · score 0.54 · nested cross validation, fold, trained, split, LASSO, predict
- [10] § Methods › ROI extraction ↔ scripts/05. pipeline_SUIT.m, the whole file · a weak match · score 0.54 · cerebellar nuclei, ACPC, FreeSurfer, atlas, T1w, space
- [11] § Methods › Behavioural responses › Predicting individual differences ↔ scripts/11. pipeline_modelling.r, lines 191–230 · score 0.54 · nested cross validation, fold, trained, split, LASSO, predict
Paper
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The authors' code
R · 310 lines · 10 KB · no license · 3 matches
- library(dplyr)
- library(tidyr)
- library(tibble)
- library(glmnet)
- library(caret)
- library(emmeans)
- library(car)
- require(doMC)
- # Set-Up and Configuration
- cl <- parallel::makeCluster(24)
- doParallel::registerDoParallel(cl)
- norm = 1
- tasK = "AC"
- cutoff = 50
- root_dir = "E:"
- base_dir = file.path(root_dir, "data")
- group_dir = file.path(base_dir, "group")
- fig_dir = file.path(root_dir,"figures")
- # load helper functions: normData, scale2, composite_score, etc.
- source(file.path(base_dir,"scripts","misc_funs.R"))
- # Data Loading and Preprocessing
- dat_learn_EDA = read.csv(file.path(base_dir, "datasets", "stat-bf_desc-EDA_df.csv"), sep='\t')
- dat_learn_beh = read.csv(file.path(base_dir, "datasets", "stat-logit_desc-beh_df.tsv"), sep='\t')
- dat_learn = bind_rows(dat_learn_EDA, dat_learn_beh) %>% filter(!is.na(learning))
- covariates = c("age","sex")
- demographics = read.csv2(file.path(base_dir, "datasets", "demographics.csv"), sep='\t')
- comb_AG = gen_combs(unique(dat_learn$AG))
- comb_AG = list(
- # c("A08"), # PL
- # c("A03"), # FLr
- # c("A03","A05"), # FLc
- # c("A03","A05","A09"),# FLs
- # c("A02","A03","A05","A09"), # FLel
- # c("A03","A05","A09","A12"), # FLst
- # c("A02","A03","A05","A09","A12"), # FL
- c("A02","A03","A05","A08","A09","A12")) # All
- # dupls = read.csv(file.path(base_dir, "desc-duplicates_df.tsv"), sep='\t')
- # excl_subs = dupls[dupls$keep==0,c("participant","AG","study")]
- # dat_learn = anti_join(dat_learn, excl_subs, by=c("participant","AG","study"))
- dat_learn_corrs = dat_learn %>% group_by(AG,study,task) %>% group_modify(~ normData(.x))
- df_learndemo = demographics %>%
- right_join(dat_learn, by=c("participant","AG","study","task"), multiple='all')
- # dat_excl_conn = read.csv(file.path(base_dir, "desc-ExcludeSubsConn_table.tsv"), sep='\t')
- # Connectivity Data Handling
- dat_FC = read.csv(file.path(base_dir, "datasets", "desc-FC_df.tsv"), sep='\t')
- # dat_FC = subset(dat_FC, !(participant %in% dat_excl_conn[dat_excl_conn$pipeline=="FC",]$participant_id))
- dat_DTI = read.csv(file.path(group_dir, "SC", "desc-SC_df.tsv"), sep='\t')
- dat_DTI = subset(dat_DTI, !(participant %in% dat_excl_conn[dat_excl_conn$pipeline=="DTI",]$participant_id))
- dat_spDCM = read.csv(file.path(group_dir,"EC","desc-EC_df.tsv"), sep='\t')
- dat_spDCM = subset(dat_spDCM, !(participant %in% dat_excl_conn[dat_excl_conn$pipeline=="spDCM",]$participant_id))
- df_comb = data.frame(); df_coefs = data.frame(); df_pred = data.frame(); df_counts = data.frame()
- # Group-wise and Modality-wise Processing
- l = list(FC=dat_FC, SC=dat_DTI, EC=dat_spDCM)
- l = list(FC=dat_FC)
- for (nAG in 1:length(comb_AG)) {
- AGs = comb_AG[[nAG]]
- for (n in 1:length(l)) {
- if (names(l[n]) == 'FC') {
- metric = c('corrLW','xcorr','EuclideanDist','ManhattanDist','WassersteinDist','dtw','MI','mscohe','wavcohe')
- inv = c('EuclideanDist','ManhattanDist','WassersteinDist','dtw')
- absl = c('corrLW')
- dat_conn = dat_FC
- pair='pair_und'
- } else if (names(l[n]) == 'SC') {
- metric = 'streamlines'
- dat_conn = dat_DTI
- pair='pair_und'
- } else {
- metric = 'spDCM'
- dat_conn = dat_spDCM
- pair='pair_dir'
- }
- dat_conn = subset(dat_conn, hemisphere!="bilateral")
- df_join = right_join(df_learndemo, dat_conn, by=c("participant","AG","study"), multiple='all')
- ####### CHOOSE WHICH AGs TO INCLUDE IN THE ANALYSIS HERE #######
- df_join = df_join %>% subset(AG %in% AGs)
- if (dim(df_join)[1]==0) {next}
- ################################################################
- df_sel = df_join %>% group_by(participant, AG, study) %>%
- filter(if_all(!!metric, ~ all(!is.na(.x))))
- # df_sel will contain the final sample - that is, excluding subs with any NAs
- # Calculate the composite score
- if (names(l[n]) == 'FC') {
- df_sel = composite_score(df_sel, cols=metric, inv=inv, absl=absl, keep_ori="corrLW")
- metric = "composite"
- }
- selvars = unique(c("participant","AG","study","task",pair,metric,"learning",covariates))
- # Standardisation of Learning/connectivity Estimates
- df = df_sel[selvars] %>% group_by(AG,study,task,across(all_of(pair))) %>% group_modify(~ normData(.x)) %>%
- pivot_wider(names_from=all_of(pair), values_from=all_of(metric), values_fn=mean) %>% ungroup()
- if (names(l[n]) == 'EC') {
- mVp = df_sel %>% group_by(participant, AG, study) %>% mutate(mVp=mean(spDCM_Var)) %>%
- select(participant, AG, study, mVp) %>% distinct()
- mVp$mVp = 1-range01(mVp$mVp)
- df = left_join(df, select(mVp, mVp))
- }
- df$const <- factor(rep(1, each=length(df$participant)))
- df_acq = subset(df, task == "acquisition")
- df_ext = subset(df, task == "extinction")
- df_ren = subset(df, task == "renewal")
- if (tasK=="AC") {
- mdf = df_acq
- } else if (tasK=="EX") {
- mdf = df_ext
- } else {
- mdf = df_ren
- }
- pairs = colnames(mdf %>% dplyr::select(starts_with(
- c('AMY','CEB','HIP','ACC','PFC','lAMY','lCEB','lHIP','lACC','lPFC','rAMY','rCEB','rHIP','rACC','rPFC'))))
- # LASSO Regression Model Setup
- y <- mdf$learning
- xx <- mdf %>% ungroup() %>% dplyr::select(all_of(c(pairs,covariates)))
- x = data.matrix(makeX(xx, na.impute = TRUE))
- myalpha = 1
- if (!is.null(covariates)) {
- force.vars = as.integer(!Reduce('|', lapply(covariates, function(y) startsWith(as.character(colnames(x)), y))))
- } else {
- force.vars = rep(1, ncol(xx))
- }
- # Cross-Validation and Lambda Optimization
- tymea = "mse"
- lambda_max <- max(abs(colSums(x*y,na.rm=T)))/nrow(x)
- epsilon <- .0001
- K <- 1000
- lambdapath <- round(exp(seq(log(lambda_max), log(lambda_max*epsilon), length.out = K)), digits = 10)
- lbpath = lambdapath
- ls = foreach(i = 1:100, .combine='rbind', .packages="glmnet") %dopar% {
- fit <- cv.glmnet(x, y, alpha=myalpha, nfolds=10, standardize=T, penalty.factor=force.vars,
- type.measure=tymea, parallel=T, lambda=lbpath)
- errors = data.frame(fit$lambda,fit$cvm)
- }
- ls <- aggregate(ls[, 2], list(ls$fit.lambda), mean)
- bestindex = which(ls[2]==min(ls[2]))[1]
- lbd = ls[bestindex,1]
- if (names(l[n]) == 'EC') {
- ws = 1-mdf$mVp
- } else {ws = NULL}
- # df_res = dataf(x,y,lbd,force.vars,tymea,ws,names(l[n]),df_pred)
- # final_fit = rbind(df_comb,df_res)
- # Custom Nested Cross-Validation
- fit_lasso_cus = function (x, y, lambda, penalty.factor, type.measure, weights) {
- results = data.frame()
- final_df = data.frame()
- pred_df = data.frame()
- for (i in 1:10) {
- cv_folds <- vfold_cv(data.frame(x), v = 10)
- for (j in seq_along(cv_folds$splits)) {
- split <- cv_folds$splits[[j]]
- train_data <- analysis(split)
- test_data <- assessment(split)
- x_train <- data.matrix(train_data)
- y_train <- y[as.integer(rownames(train_data))]
- x_test <- data.matrix(test_data)
- test_idx <- as.integer(rownames(test_data))
- y_test <- y[test_idx]
- # Fit model
- fit <- glmnet(x_train, y_train, alpha = 1, lambda = lambda, penalty.factor = penalty.factor,
- type.measure=type.measure, weights=weights)
- # Predict on test set
- y_pred <- predict(fit, newx = x_test)
- # Save predictions
- pred_df = bind_rows(pred_df,
- data.frame(
- iteration = i,
- fold = j,
- subject = test_idx,
- y_true = y_test,
- y_pred = as.vector(y_pred)
- )
- )
- # Save coefficients
- coefs = coef(fit)
- coef_df = as.data.frame(as.matrix(coefs)) %>%
- rownames_to_column("connection") %>%
- rename(coefficient = 2) %>%
- filter(coefficient != 0) %>%
- mutate(iteration = i, fold = j)
- final_df <- bind_rows(final_df, coef_df)
- }
- }
- group_df = final_df %>%
- group_by(connection) %>%
- summarise(
- times_selected = n(),
- avg_coefficient = mean(coefficient)
- ) %>%
- arrange(desc(times_selected))
- return(group_df)
- }
- ffit = fit_lasso_cus(x,y,lbpath,force.vars,tymea,ws) %>% filter(times_selected > cutoff)
- ffit$mod=names(l[n])
- ffit$group=paste(AGs,collapse='_')
- # Poisson regression
- # Set-Up and Parallelized Simulation
- tp = foreach(niter = 1:10, .combine='rbind', .packages=c("dplyr","doMC","tibble","glmnet")) %dopar% {
- mdf2 = mdf[sample(nrow(mdf), 80),]
- lambda_max <- max(abs(colSums(x*y,na.rm=T)))/nrow(x)
- lbpath <- round(exp(seq(log(lambda_max), log(lambda_max*epsilon), length.out = K)), digits = 10)
- # LASSO Regression and Feature Selection
- ls = foreach(i = 1:100, .combine='rbind', .packages="glmnet") %dopar% {
- fit <- cv.glmnet(x, y, alpha=myalpha, nfolds=10, standardize=T, penalty.factor=force.vars,
- type.measure=tymea, parallel=T, lambda=lbpath)
- errors = data.frame(fit$lambda,fit$cvm)
- }
- ls <- aggregate(ls[, 2], list(ls$fit.lambda), mean)
- bestindex = which(ls[2]==min(ls[2]))[1]
- lbd = ls[bestindex,1]
- if (names(l[n]) == 'EC') {
- ws = 1-mdf2$mVp
- } else {ws = NULL}
- fit.lasso = glmnet(x=x,y=y,lambda=lbd, alpha=myalpha, penalty.factor=force.vars, type.measure=tymea,
- weights=ws)
- results = coef(fit.lasso)
- df_res = as.data.frame(as.matrix(results)) %>% rownames_to_column(var="connection")
- preds = df_res$connection
- # Feature Region Analysis
- df_tempc = data.frame(G = niter, AMY=length(grep("AMY", preds)), ACC=length(grep("ACC", preds)), HIP=length(grep("HIP", preds)), PFC=length(grep("PFC", preds)),
- CEB=length(grep("CEB", preds)), mod=names(l[n]))
- }
- df_counts = rbind(df_counts,tp)
- }
- }
- # Statistical Comparison
- m = df_counts %>% pivot_longer(cols = -c(G,mod)) %>% group_by(G,name)
- model <- glmer(value ~ name + (1|G), family=poisson, data=subset(m, mod==mg))
- summary(model)
- em = emmeans(model, pairwise ~ name, adjust="fdr")
11. pipeline_modelling.r at commit fee4711, no license · at the source
Overview
and 7 other authors
O. T. Wolf14, O. Güntürkün4,18,19, H. H. Quick4,20, R. Kumsta17, D. Timmann2,3,4, T. Spisak3, N. Axmacher1,420 affiliations
- Department of Neuropsychology, Ruhr University Bochum,Bochum, Germany
- Department of Neurology, University Hospital Essen,Essen, Germany
- Center for Translational Neuro- and Behavioral Sciences, University Hospital Essen, University of Duisburg-Essen,Essen, Germany
- Erwin L. Hahn Institute for Magnetic Resonance Imaging, University of Duisburg-Essen,Essen, Germany
- Department of Imaging Neuroscience, UCL Queen Square Institute of Neurology, University College London,London, UK
- University of Bonn, Transdisciplinary Research Area “Life & Health”, Centre for Artificial Intelligence and Neuroscience,Bonn, Germany
- Turner Institute for Brain and Mental Health, School of Psychological Sciences, Monash University,Clayton, Australia
- Monash Biomedical Imaging, Monash University,Clayton, Australia
- CIFAR Azrieli Global Scholars Program, CIFAR,Toronto, Canada
- Department of Medical Psychology & Medical Sociology, Ruhr University Bochum,Bochum, Germany
- Institute of Medical Psychology and Behavioral Immunobiology, University Hospital Essen,Essen, Germany
- Department of Psychology and Neurosciences, Leibniz Research Centre for Working Environment and Human Factors at the Technical University of Dortmund (IfADo),Dortmund, Germany
- Department of Neurology, BG University Hospital Bergmannsheil, Ruhr University Bochum,Bochum, Germany
- Department of Cognitive Psychology, Ruhr University Bochum,Bochum, Germany
- Institute of Psychology, Department of Educational Sciences and Psychology, TU Dortmund University,Dortmund, Germany
- Department of Psychiatry and Psychotherapy, Center for Mind, Brain and Behavior, Philipps-Universität Marburg,Marburg, Germany
- Genetic Psychology Lab, Ruhr University Bochum,Bochum, Germany
- Department of Biopsychology, Ruhr University Bochum,Bochum, Germany
- Research Center One Health Ruhr, Bochum, Germany
- High Field and Hybrid MR Imaging, University Hospital Essen,Essen, Germany
Abstract
The ability to acquire new information and to modify previously learned knowledge are critical in an ever-changing world. However, the efficacy of learning is notably variable among individuals, with extinction learning being the epitome of such variability. Abundant studies have identified a core network of brain regions including the amygdala, hippocampus, dorsal anterior cingulate cortex (ACC), ventromedial prefrontal cortex (PFC) and, more recently, the cerebellum, as key players in learning and extinction. Yet, the precise interactions within this network and their relationship to individual learning abilities and extinction have remained largely unexplored. In the present study, we examined how functional (FC), effective (EC), and structural (SC) connectivity patterns in the core learning network allow the prediction of individual differences in the efficacy of learning, extinction, and renewal. Analysing a large dataset of over 500 participants across a multitude of paradigms, our results revealed that FC predicted better acquisition, with a central role of ACC and hippocampus, whereas SC, involving ACC and amygdala, predicted higher levels of extinction learning. EC results suggested a predominantly inhibitory coupling among core learning network nodes, with paradigm-specific EC connectivity patterns predicting learning. Our predictions not only generalised between fear and cognitive predictive learning paradigms but were also successful in predicting learning from task-related FC and simulated data. Together, these results describe the multimodal neural determinants of learning, extinction, and renewal, and may inform individualised interventions for affective disorders based on neural connectivity patterns.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above, with 11 matches between paragraphs and lines of code.
caadgomes/extinction-learning-study
fee4711f283aecc8a70bc17eb87db3336a2a5874, 28 February 2026Availability: 1 check, the latest on 29 September 2026: the link answers
- 29 September 2026: the link answers
18 files
- scripts/
01. pipeline_BIDS.py , Python, 828 lines - scripts/
02. pipeline_fmriprep.py , Python, 212 lines - scripts/
03. pipeline_denoising.py , Python, 397 lines, 1 match - scripts/
04. pipeline_ROIs.py , Python, 641 lines - scripts/
05. pipeline_SUIT.m , MATLAB, 111 lines, 1 match - scripts/
06. pipeline_FC.py , Python, 816 lines, 1 match - scripts/
07. pipeline_SC.py , Python, 764 lines - scripts/
08. pipeline_EC.m , MATLAB, 436 lines - scripts/
09a. pipeline_EDA.m , MATLAB, 115 lines - scripts/
09b. pipeline_EDA_DCM.m , MATLAB, 402 lines, 1 match - scripts/
09c. pipeline_EDA_SF.m , MATLAB, 246 lines - scripts/
10. pipeline_learning.r , R, 274 lines, 1 match - scripts/
11. pipeline_modelling.r , R, 310 lines, 3 matches - scripts/
12. pipeline_generalisabilit , R, 311 lines, 3 matchesy.r - scripts/
13. pipeline_LOGO.py , Python, 132 lines - scripts/
misc_funs.R , R, 121 lines - scripts/
simulation_regression.R , R, 71 lines - README.md, Text, 62 lines
Code availability
The code for data preprocessing and analysis is available at https://
Reproduced under the paper's license (CC BY), from the paper cited above.
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What the map holds:
- 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
- 17 scripts, each with its path and the digest of its content;
- 11 matches between paragraphs of the paper and lines of the code (method lexical-v1);
- neither the text of the paper nor the code itself.
Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability
Public sharing of the raw data is not permitted because participant consent and ethics approvals do not allow unrestricted public data sharing, and the datasets are subject to institutional and legal data-sharing agreements across the contributing institutions. Raw data are available from the corresponding author upon reasonable request and subject to approval by the contributing institutions and a data-sharing agreement where required. Access will be granted to qualified researchers for non-commercial scientific research purposes; decisions are typically made within 4–6 weeks. Source data are provided with this paper.
Reproduced under the paper's license (CC BY), from the paper cited above.
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Version 1, 29 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 27 authors, 2 keywords, 17 MeSH terms, 1 funder, 87 references.
Cite
This paper
Gomes, C. A., Bach, D. R., Razi, A., Batsikadze, G., Elsenbruch, S., Engler, H., Ernst, T. M., Fellner, M. C., Fraenz, C., Genç, E., Klass, A., Labrenz, F., Lissek, S., Merz, C. J., Metzen, D., Nostadt, A., Pawlik, R. J., Schneider, J. E., Tegenthoff, M., . . . Axmacher, N. (2026). Predicting individual differences of fear and cognitive learning and extinction. Nature communications, 17(1), 3780. https://
BibTeX
@article{gomes2026predic
author = {Gomes, C. A. and Bach, D. R. and Razi, A. and Batsikadze, G. and Elsenbruch, S. and Engler, H. and Ernst, T. M. and Fellner, M. C. and Fraenz, C. and Genç, E. and Klass, A. and Labrenz, F. and Lissek, S. and Merz, C. J. and Metzen, D. and Nostadt, A. and Pawlik, R. J. and Schneider, J. E. and Tegenthoff, M. and Thieme, A. and Wolf, O. T. and Güntürkün, O. and Quick, H. H. and Kumsta, R. and Timmann, D. and Spisak, T. and Axmacher, N.},
title = {{Predicting individual differences of fear and cognitive learning and extinction}},
journal = {Nature communications},
year = {2026},
month = apr,
volume = {17},
number = {1},
pages = {3780},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/
url = {https://
pmid = {42026055},
pmcid = {PMC13109375}
}
RIS
TY - JOUR
AU - Gomes, C. A.
AU - Bach, D. R.
AU - Razi, A.
AU - Batsikadze, G.
AU - Elsenbruch, S.
AU - Engler, H.
AU - Ernst, T. M.
AU - Fellner, M. C.
AU - Fraenz, C.
AU - Genç, E.
AU - Klass, A.
AU - Labrenz, F.
AU - Lissek, S.
AU - Merz, C. J.
AU - Metzen, D.
AU - Nostadt, A.
AU - Pawlik, R. J.
AU - Schneider, J. E.
AU - Tegenthoff, M.
AU - Thieme, A.
AU - Wolf, O. T.
AU - Güntürkün, O.
AU - Quick, H. H.
AU - Kumsta, R.
AU - Timmann, D.
AU - Spisak, T.
AU - Axmacher, N.
TI - Predicting individual differences of fear and cognitive learning and extinction
T2 - Nature communications
J2 - Nat Commun
PY - 2026
DA - 2026/
VL - 17
IS - 1
SP - 3780
SN - 2041-1723
PB - Nature Publishing Group
DO - 10.1038/
UR - https://
LA - en
ER -
CSL-JSON
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"family": "Timmann",
"given": "D."
},
{
"family": "Spisak",
"given": "T."
},
{
"family": "Axmacher",
"given": "N."
}
],
"container-title-short":
"volume": "17",
"issue": "1",
"page": "3780",
"DOI": "10.1038/
"PMID": "42026055",
"PMCID": "PMC13109375",
"ISSN": "2041-1723",
"publisher": "Nature Publishing Group",
"URL": "https://
"language": "en",
"issued": {
"date-parts": [
[
2026,
4,
23
]
]
}
}
The tracing map gets a citation of its own once an author has validated it and it has a DOI.
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