Deep learning reveals a neurocomputational mechanism predicting depression risk in adolescents.
The 3 matches
- [1] § MATERIALS AND METHODS › The analysis of visual anger code › Clustering analysis ↔ subgroup.R, lines 41 to 82 · score 0.67 · consensus matrix, silhouette score, distance, subgroups, clustering · Report a mismatch
- [2] § MATERIALS AND METHODS › Prediction models in early adulthood ↔ ANN_perturbation.R, lines 175 to 262 · score 0.65 · linear regression, baseline models, emotional symptoms, AIC, R2, predict · Report a mismatch
- [3] § RESULTS › Computational marker detected specifically in MDD patients ↔ stratify_val.R, lines 1 to 40 · score 0.52 · MDD control, STRATIFY, AUD, BN, activation, brain scores · Report a mismatch
Paper
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The authors' code
R · 233 lines · 8.5 KB · CC-BY-4.0 · 1 match
- require('R.matlab')
- require(tidyverse)
- require(dplyr)
- require(ggplot2)
- require(rstatix)
- library(philentropy)
- library(cluster)
- library(jsonlite)
- ########################################################################
- ######################## K means clustering ###########################
- ########################################################################
- angry_neutral_occipital = readMat('data/ANN_mapping/angry_mu_seed100_occipital.mat')$angry.mu.seed100.occipital %>%
- as.data.frame # [1332, 256]
- ############# The optimal number of clusters #############
- #### elbow method ####
- set.seed(123)
- wcss <- numeric()
- for (k in 1:7) {
- kmeans_result <- kmeans(angry_neutral_occipital, centers=k, nstart=25, iter.max=20)
- wcss[k] <- kmeans_result$tot.withinss
- }
- ggplot() +
- geom_line(aes(x=1:7, y=wcss), color='blue', linewidth=1) +
- geom_point(aes(x=1:7, y=wcss), color='red', size=3) +
- labs(x='Number of clusters', y='WCSS') +
- scale_x_continuous(breaks=1:7) +
- theme_bw() + theme(panel.border = element_blank(), panel.grid.minor = element_blank(),
- panel.grid.major = element_blank(), axis.line = element_line(colour = "black"),
- text=element_text(size=13, family='Arial'))
- # ggsave(filename='elbow.tiff',
- # width=1300,
- # height=1000,
- # units='px',
- # bg = "white",
- # dpi=300)
- #### silhouette method ####
- silhouette_scores <- numeric()
- for (k in 2:7) {
- kmeans_result <- kmeans(angry_neutral_occipital, centers=k, nstart=25, iter.max=20)
- silhouette_obj <- silhouette(kmeans_result$cluster, dist(angry_neutral_occipital))
- silhouette_scores[k-1] <- mean(silhouette_obj[, "sil_width"])
- }
- ggplot() +
- geom_line(aes(x=2:7, y=silhouette_scores), color='blue', linewidth=1) +
- geom_point(aes(x=2:7, y=silhouette_scores), color='red', size=3) +
- labs(x='Number of clusters', y='Average silhouette width') +
- scale_x_continuous(breaks=2:7) +
- theme_bw() + theme(panel.border = element_blank(), panel.grid.minor = element_blank(),
- panel.grid.major = element_blank(), axis.line = element_line(colour = "black"),
- text=element_text(size=13, family='Arial'))
- # ggsave(filename='silhouette.tiff',
- # width=1300,
- # height=1000,
- # units='px',
- # bg = "white",
- # dpi=300)
- ###################### stability testing ##################
- num_clusters <- 2
- num_repeats <- 50
- consensus_matrix <- matrix(0, nrow = nrow(angry_neutral_occipital), ncol = nrow(angry_neutral_occipital))
- for (i in 1:num_repeats) {
- set.seed(i)
- cluster_result <- kmeans(angry_neutral_occipital, centers = num_clusters, nstart = 25)
- # Update consensus matrix
- for (j in 1:num_clusters) {
- cluster_members <- which(cluster_result$cluster == j)
- consensus_matrix[cluster_members, cluster_members] <- consensus_matrix[cluster_members, cluster_members] + 1
- }
- }
- consensus_matrix <- consensus_matrix / num_repeats
- ############ T-SNE for visualization ###########
- df_pca <- read_csv('data/tsne_cluster2.csv') %>%
- convert_as_factor(cluster)
- ggplot(df_pca, aes(x = PC1, y = PC2, color = as.factor(cluster))) +
- geom_point(alpha = 0.5) + xlab('') + ylab('') +
- scale_color_manual(values = c('1' = '#C4777D', '2' = '#809EC4')) +
- theme_minimal() + theme(panel.border = element_blank(), panel.grid.minor = element_blank(),
- panel.grid.major = element_blank(), axis.text = element_blank(),
- text=element_text(size=13, family='Arial'),
- legend.position = 'none')
- # ggsave(filename='vis2.tiff',
- # width=1300,
- # height=1300,
- # units='px',
- # bg = "white",
- # dpi=300)
- ##########################################################################
- ################ The demographic difference between two clusters ##############
- ##########################################################################
- data <- read_csv('data/IMAGEN_covariate/IMAGEN_data/score_symptom_dawba_adrs.csv') %>%
- convert_as_factor(id, cluster, sex, hand, site)
- data$cluster <- ifelse(data$cluster == 0, 1, 0)
- data$cluster <- as.factor(data$cluster)
- # chi square test for handedness, sex, site
- chi_table <- table(data$cluster, data$site)
- chisq.test(chi_table)
- # t test for ses
- t.test(ses ~ cluster, data = data)
- ##########################################################################
- ################ The symptom difference between two clusters ##############
- ##########################################################################
- # Load the symptom data
- data <- read_csv('data/IMAGEN_covariate/IMAGEN_data/score_symptom_dawba_adrs.csv') %>%
- convert_as_factor(id, cluster, sex, hand, site)
- data$cluster <- ifelse(data$cluster == 0, 1, 0)
- data$cluster <- as.factor(data$cluster)
- data <- as.data.frame(lapply(data, function(x) if(is.numeric(x)) scale(x) else x))
- model <- lm(adrs_sum ~ cluster + sex + ses + hand + site, data = data)
- summary(model)
- confint(model)
- ########### The proportion of case and control in two clusters ###########
- data <- read_csv('data/IMAGEN_covariate/IMAGEN_data/score_symptom_dawba_adrs.csv') %>%
- convert_as_factor(id, cluster, sex, hand, site)
- data %>%
- group_by(cluster) %>%
- summarise(mean=mean(dep, na.rm = TRUE), std=sd(dep, na.rm=TRUE), n= sum(!is.na(dep)))
- band <- read_csv('data/IMAGEN_covariate/IMAGEN_data/DAWBA_band.csv') %>%
- convert_as_factor(id)
- band <- band[,c(1, 2, 9, 11)]
- band$sp19_low <- ifelse(band$sspphband < 4, 0, 1)
- band$dep19_low <- ifelse(band$sdepband < 4, 0, 1)
- band$ep19_low <- ifelse(band$seatband < 4, 0, 1)
- band$internal19_low <- ifelse(band$sspphband >= 4 | band$sdepband >= 4 | band$seatband >= 4, 1, 0)
- data <- merge(data, band[,c(1,5,6,8)], by='id', all.x = TRUE)
- # The number of cases in low-efficiency group: control: 654, case: 51
- table(data[data$cluster==0,]$internal19_low)
- # The number of cases in high-efficiency group: control: 388, case: 9
- table(data[data$cluster==1,]$internal19_low)
- #### chi-squared test ####
- counts <- matrix(c(654, 51, 388, 9), nrow = 2, byrow = TRUE)
- colnames(counts) <- c("0", "1")
- rownames(counts) <- c("Cluster 0", "Cluster 1")
- chi_test <- chisq.test(counts)
- chi_test
- ##########################################################################
- ################ Information gain for two clusters ##############
- ##########################################################################
- InfoGain <- function(data, num_bins=40) {
- randomdis = log2(num_bins) # random distribution
- mean_data = 2 * (data - min(data)) / (max(data) - min(data)) - 1 # normalize to [-1, 1]
- bins = cut(mean_data, breaks = num_bins)
- counts = table(bins) # the number of data points in each bin
- probabilities = counts / sum(counts) # convert to probabilities
- entropy <- -sum(probabilities * log2(probabilities + 1e-10))
- gain <- randomdis - entropy
- return(gain)
- }
- # Compute the 95%CI for the difference in information gain between two groups
- InfoGain_twogroup <- function(data_C1, data_C2, n_iter = 1000){
- result <- data.frame(information1=numeric(1), information2=numeric(1), lower=numeric(1),
- upper=numeric(1), more=numeric(1))
- diffs = numeric(n_iter)
- info1_all = InfoGain(colMeans(data_C1))
- info2_all = InfoGain(colMeans(data_C2))
- for (j in 1:n_iter){
- # Sample with replacement
- idx1 = sample(nrow(data_C1), replace = TRUE)
- sample_C1 = data_C1[idx1, ]
- idx2 = sample(nrow(data_C2), replace = TRUE)
- sample_C2 = data_C2[idx2, ]
- info1_sample = InfoGain(colMeans(sample_C1))
- info2_sample = InfoGain(colMeans(sample_C2))
- diffs[j] = info2_sample - info1_sample # information
- }
- # 95%CI
- ci_p = quantile(diffs, c(0.025, 0.975))
- result[1,] <- c(info1_all, info2_all, ci_p[1], ci_p[2],
- ifelse(ci_p[1]>=0 & ci_p[2]>0, 2, ifelse(
- ci_p[1]<0 & ci_p[2]<=0, 1, 0)))
- result_info <- list(diffs, result)
- return(result_info)
- }
- set.seed(123)
- angry_neutral_occipital = readMat('data/ANN_mapping/angry_mu_seed100_occipital.mat')$angry.mu.seed100.occipital %>%
- as.data.frame # [1332, 256]
- kmeans_result <- kmeans(angry_neutral_occipital, centers=2, nstart=25, iter.max=20)
- id <- fromJSON('data/id_json/total_id_occipital.json')
- id_label <- data.frame(id=id, cluster=kmeans_result$cluster)
- id_label$id <- gsub('\\.npy$', '', id_label$id)
- data <- cbind(id_label$cluster, angry_neutral_occipital)
- colnames(data)[1] <- 'cluster'
- data_C1 <- filter(data, cluster == 1)
- data_C2 <- filter(data, cluster == 2)
- data_C1 <- data_C1[, -1]
- data_C2 <- data_C2[, -1]
- result_info <- InfoGain_twogroup(data_C1, data_C2)
subgroup.R, under CC-BY-4.0 · at the source
Overview
and 22 other authors
Penny Gowland23, Antoine Grigis24, Herve Lemaitre24,25, Jean-Luc Martinot26,27, Marie-Laure Paillère Martinot26,28, Eric Artiges26,27, Frauke Nees29, Dimitri Papadopoulos Orfanos21, Luise Poustka30,31, Hedi Kebir12, Ulrike Schmidt32,33, Julia Sinclair34, Michael N Smolka6, Sarah Hohmann16, Nathalie Holz16, Henrik Walter31,35, Robert Whelan36, Sylvane Desrivières9, Gunter Schumann2,12,31, Qiang Luo37,38, STRATIFY/ESTRA Consortium, IMAGEN Consortium38 affiliations
- School of Artificial Intelligence, Shenzhen University, Shenzhen, China
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, Shanghai, China
- MIND & AI Lab, Department of Psychology, The University of Hong Kong, Hong Kong SAR, China
- SRT AI, Society & Social Dynamics, Faculty of Social Sciences, The University of Hong Kong, Hong Kong SAR, China
- Department of Psychiatry and Psychotherapy, University of Tübingen and German Center for Mental Health (DZPG), Site Tübingen, Germany
- Department of Psychiatry and Psychotherapy, Technische Universität Dresden, Dresden, Germany
- Department of Psychiatry, University of Cambridge, Cambridge CB2 0SZ, UK
- Behavioural and Clinical Neuroscience Institute, Department of Psychology, University of Cambridge, Cambridge CB2 3EB, UK
- Social Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, London SE5 8AF, UK
- School of Psychology, Institute for Mental Health, University of Birmingham, Birmingham, UK
- Oxford Institute of Clinical Psychology Training and Research, Oxford University, Oxford, UK
- Centre for Population Neuroscience and Stratified Medicine (PONS), Department of Psychiatry and Psychotherapy, Charité Universitätsmedizin Berlin, Germany
- Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Psychiatry and Psychotherapy, Campus Charité Mitte, Charitéplatz 1, Berlin, Germany
- Department of Education and Psychology, Freie Universität Berlin, Berlin, Germany
- Psychology Department, B44 University Road, University of Southampton, Southampton SO17 1PS, UK
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, 68159 Mannheim, Germany; German Center for Mental Health (DZPG), partner site Mannheim-Heidelberg-Ulm
- Department of Neuroimaging, Institute of Psychiatry, Psychology, and Neuroscience, King’s College London, UK
- Discipline of Psychiatry, School of Medicine and Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
- Physikalisch-Technische Bundesanstalt (PTB), Braunschweig and Berlin, Germany
- Institute of Cognitive and Clinical Neuroscience, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Square J5, Mannheim, Germany
- Department of Psychology, School of Social Sciences, University of Mannheim, 68131 Mannheim, Germany
- Departments of Psychiatry and Psychology, University of Vermont, Burlington, VT 05405, USA
- Sir Peter Mansfield Imaging Centre School of Physics and Astronomy, University of Nottingham, University Park, Nottingham, UK
- NeuroSpin, CEA, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
- Institut des Maladies Neurodégénératives, UMR 5293, CNRS, CEA, Université de Bordeaux, 33076 Bordeaux, France
- Institut National de la Santé et de la Recherche Médicale, INSERM U1299 “Trajectoires développementales en psychiatrie”; Université Paris-Saclay, Ecole Normale supérieure Paris-Saclay, CNRS, Centre Borelli, Gif-sur-Yvette, France
- Research Department, LABD-PSY, Etablissement Public de Santé (EPS) Barthélemy Durand, 91700 Sainte-Geneviève-des-Bois, France
- AP-HP, Sorbonne Université, Department of Child and Adolescent Psychiatry, Pitié-Salpêtrière Hospital, Paris, France
- Institute of Medical Psychology, Ludwig-Maximilians-Universität (LMU) in Munich, Munich, Germany
- Department of Child and Adolescent Psychiatry, Center for Psychosocial Medicine, University Hospital Heidelberg, Heidelberg, Germany
- German Center for Mental Health (DZPG), Site Berlin-Potsdam, Germany
- Department of Psychological Medicine, Section for Eating Disorders, Institute of Psychiatry, Psychology and Neuroscience, King’s College London, London SE5 8AF, UK
- South London and Maudsley NHS Foundation Trust, London, UK
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- Department of Psychiatry and Psychotherapy CCM, Charité—Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
- School of Psychology and Global Brain Health Institute, Trinity College Dublin, Ireland
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Fudan University, Shanghai, China
Abstract
Early detection and prevention of psychiatric disorders, particularly depression, remain as major global health challenges, yet reliable tools for identifying individuals before symptom onset are lacking. Here, we combine functional neuroimaging with computational modeling to identify a mechanistic biomarker of depression risk. In a population-based adolescent cohort (IMAGEN, N = 1332), we found that weakened neural representations of emotional signals were linked to depressive symptoms. Perturbation experiments in a brain-aligned deep learning model showed that this deficit reflects overregularized emotion perception, producing a negative perceptual bias. A neurocomputational signature of this mechanism predicted depression symptom onset up to 4 years later at the IMAGEN follow-up (N = 725), was associated with both a genetic-risk variant and polygenic risk for depression, and improved depression classification in a patient cohort (STRATIFY, N = 411). These findings suggest a possible mechanism linking genetic vulnerability to altered emotion perception and future depression, and propose a predictive computational marker with potential for early detection and prevention.
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 3 matches between paragraphs and lines of code.
Zenodo 18647146
Availability: 1 check, the latest on 27 September 2026: the link answers (HTTP 200)
- 27 September 2026: the link answers (HTTP 200)
5 files
- ANN_perturbation.R, R, 266 lines, 1 match
- mapping_occipital.R, R, 163 lines
- stratify_val.R, R, 45 lines, 1 match
- subgroup.R, R, 233 lines, 1 match
- README.md, Text, 35 lines
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
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;
- 4 scripts, each with its path and the digest of its content;
- 3 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, code, and materials availability
Data from the IMAGEN study are available upon application: https://
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.
Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, issue, pages, dates, 42 authors, 10 MeSH terms, 5 funders, 59 references.
Cite
This paper
Lu, H., Yan, X., Becker, B., Heinz, A., Sahakian, B. J., Langley, C., Zuo, Z., Cao, L., Zhang, Z., Robinson, L., Vaidya, N., Winterer, J., King, S., Walton, C., Banaschewski, T., Barker, G. J., Bokde, A. L., Brühl, R., Flor, H., . . . IMAGEN Consortium. (2026). Deep learning reveals a neurocomputational mechanism predicting depression risk in adolescents. Science advances, 12(32), eaed0772. https://
BibTeX
@article{lu2026deep,
author = {Lu, Han and Yan, Xiaoqian and Becker, Benjamin and Heinz, Andreas and Sahakian, Barbara J and Langley, Christelle and Zuo, Zhaoyu and Cao, Luolong and Zhang, Zuo and Robinson, Lauren and Vaidya, Nilakshi and Winterer, Jeanne and King, Sinead and Walton, Charlotte and Banaschewski, Tobias and Barker, Gareth J and Bokde, Arun LW and Brühl, Rüdiger and Flor, Herta and Garavan, Hugh and Gowland, Penny and Grigis, Antoine and Lemaitre, Herve and Martinot, Jean-Luc and Martinot, Marie-Laure Paillère and Artiges, Eric and Nees, Frauke and Orfanos, Dimitri Papadopoulos and Poustka, Luise and Kebir, Hedi and Schmidt, Ulrike and Sinclair, Julia and Smolka, Michael N and Hohmann, Sarah and Holz, Nathalie and Walter, Henrik and Whelan, Robert and Desrivières, Sylvane and Schumann, Gunter and Luo, Qiang and {STRATIFY/
title = {{Deep learning reveals a neurocomputational mechanism predicting depression risk in adolescents}},
journal = {Science advances},
year = {2026},
month = aug,
volume = {12},
number = {32},
pages = {eaed0772},
publisher = {American Association for the Advancement of Science},
issn = {2375-2548},
doi = {10.1126/
url = {https://
pmid = {42566534},
pmcid = {PMC13450214}
}
RIS
TY - JOUR
AU - Lu, Han
AU - Yan, Xiaoqian
AU - Becker, Benjamin
AU - Heinz, Andreas
AU - Sahakian, Barbara J
AU - Langley, Christelle
AU - Zuo, Zhaoyu
AU - Cao, Luolong
AU - Zhang, Zuo
AU - Robinson, Lauren
AU - Vaidya, Nilakshi
AU - Winterer, Jeanne
AU - King, Sinead
AU - Walton, Charlotte
AU - Banaschewski, Tobias
AU - Barker, Gareth J
AU - Bokde, Arun LW
AU - Brühl, Rüdiger
AU - Flor, Herta
AU - Garavan, Hugh
AU - Gowland, Penny
AU - Grigis, Antoine
AU - Lemaitre, Herve
AU - Martinot, Jean-Luc
AU - Martinot, Marie-Laure Paillère
AU - Artiges, Eric
AU - Nees, Frauke
AU - Orfanos, Dimitri Papadopoulos
AU - Poustka, Luise
AU - Kebir, Hedi
AU - Schmidt, Ulrike
AU - Sinclair, Julia
AU - Smolka, Michael N
AU - Hohmann, Sarah
AU - Holz, Nathalie
AU - Walter, Henrik
AU - Whelan, Robert
AU - Desrivières, Sylvane
AU - Schumann, Gunter
AU - Luo, Qiang
AU - STRATIFY/
AU - IMAGEN Consortium
TI - Deep learning reveals a neurocomputational mechanism predicting depression risk in adolescents
T2 - Science advances
J2 - Sci Adv
PY - 2026
DA - 2026/
VL - 12
IS - 32
SP - eaed0772
SN - 2375-2548
PB - American Association for the Advancement of Science
DO - 10.1126/
UR - https://
LA - en
ER -
CSL-JSON
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The tracing map gets a citation of its own once an author has validated it and it has a DOI.
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