Sébastien Gradit, PhD

Sébastien Gradit, PhD

Bioinformatician leveraging AI to advance diagnostics and therapeutics using genomic and multi-omics data.

Graph Report - sebgra.github.io (2026-10-16)

Graph Report - sebgra.github.io (2026-10-16)

Corpus Check

  • 157 files · ~89,692 words
  • Verdict: corpus is large enough that graph structure adds value.
  • Unclassified: 54 file(s) not represented in the graph (top: .scss 19, (none) 10, .css 8)

Summary

  • 451 nodes · 772 edges · 33 communities (17 shown, 16 thin omitted)
  • Extraction: 80% EXTRACTED · 19% INFERRED · 1% AMBIGUOUS · INFERRED: 148 edges (avg confidence: 0.86)
  • Token cost: 445,541 input · 0 output

Community Hubs (Navigation)

  • Minified Theme JS Bundle
  • Archive & Profile Includes
  • Jekyll Site Configuration
  • CV & Talkmap Python Scripts
  • CV Career & Projects
  • NPM Package Manifest
  • CGR DNA Classifier Models
  • Hicberg Research Output
  • Markdown Page Generators
  • CV Pages & Data
  • About & Community Pages
  • Blog Posts & Archives
  • JeBiF Outreach Activities
  • Optimizers & Overfitting
  • Analytics Providers
  • 1D CNN on DNA
  • Comment Provider Embeds
  • Terms & Privacy
  • Web App Manifest
  • Portfolio Templates
  • Placeholder Paper 1
  • Placeholder Paper 2
  • Placeholder Paper 3
  • Site Logo Theme
  • CV JSON Update Script
  • Google+ Comments
  • 404 Page
  • Placeholder Avatar

God Nodes (most connected - your core abstractions)

  1. base_path include - 34 edges
  2. e() - 16 edges
  3. Archive Item (generic/publication/teaching) - 15 edges
  4. Default Layout - 15 edges
  5. ICTE 2024 Poster - Hicberg - 15 edges
  6. N() - 14 edges
  7. o() - 14 edges
  8. l() - 14 edges
  9. s() - 14 edges
  10. create_cv_json() - 14 edges

Surprising Connections (you probably didn’t know these)

  • Authors Data (placeholder authors) –semantically_similar_to–> Author Profile (Sebastien Gradit, PhD) [INFERRED] [semantically similar] _data/authors.yml → _config.yml
  • UI Text Localization (en, es, fr, tr, pt, it, zh, ...) –references–> Jekyll Site Configuration [INFERRED] _data/ui-text.yml → _config.yml
  • Draft Post (placeholder) –references–> Jekyll Site Configuration [INFERRED] _drafts/post-draft.md → _config.yml
  • Main Navigation Menu –references–> Jekyll Collections (teaching, publications, portfolio, talks, softwares) [INFERRED] _data/navigation.yml → _config.yml
  • Tutorial 1 on Relevant Topic (template) –references–> Jekyll Collections (teaching, publications, portfolio, talks, softwares) [INFERRED] _templates/_talks/2013-03-01-tutorial-1.md → _config.yml

Import Cycles

  • None detected.

Hyperedges (group relationships)

  • Jekyll content collection templates — _templates__publications_2009_10_01_paper_title_number_1_template, _templates__publications_2010_10_01_paper_title_number_2_template, _templates__talks_2012_03_01_talk_1_template, _templates__talks_2013_03_01_tutorial_1_template, _templates__teaching_2014_spring_teaching_1_template, _config_collections [INFERRED 0.85]
  • Staticman comment data store — _data_comments_layout_comments_comment_1470944006665_comment, _data_comments_layout_comments_comment_1470944162041_comment, _data_comments_markup_syntax_highlighting_comment_1470969665387_comment, _data_comments_welcome_to_jekyll_comment_1470942205700_comment, _data_comments_welcome_to_jekyll_comment_1470942247755_comment, _data_comments_welcome_to_jekyll_comment_1470942265819_comment, _data_comments_welcome_to_jekyll_comment_1470942493518_comment, _config_staticman [INFERRED 0.95]
  • Local/Docker site build pipeline — readme_local_development, readme_docker_workflow, docker_compose_jekyll_site_service, _config_docker_docker_config_override, _config_site_config [INFERRED 0.85]
  • Analytics provider strategy selected by site.analytics.provider — _includes_analytics, _includes_analytics_providers_google, _includes_analytics_providers_google_universal, _includes_analytics_providers_google_analytics_4, _includes_analytics_providers_custom [EXTRACTED 1.00]
  • Pluggable comment provider embeds driven by site.comments — _includes_comments_providers_custom, _includes_comments_providers_discourse, _includes_comments_providers_disqus, _includes_comments_providers_facebook, _includes_comments_providers_google_plus [INFERRED 0.85]
  • Archive list item template variants (publication, talk, CV) — _includes_archive_single, _includes_archive_single_cv, _includes_archive_single_talk, _includes_archive_single_talk_cv [INFERRED 0.95]
  • Comments rendering flow — _includes_comments, _includes_comments_providers_scripts, _includes_comments_providers_staticman, _includes_comment_provider_switch, _includes_comment [EXTRACTED 1.00]
  • Includes localized via ui-text data — _includes_paginator, _includes_post_pagination, _includes_read_time, _includes_social_share, _includes_tag_list, _includes_footer, _data_ui_text_localization [EXTRACTED 1.00]
  • Jekyll layout inheritance chain (compress -> default -> page layouts) — _layouts_compress, _layouts_default, _layouts_single, _layouts_archive, _layouts_talk, _layouts_splash, _layouts_archive_taxonomy, _layouts_cv_layout [EXTRACTED 1.00]
  • Archive-layout listing pages rendering items via archive-single include — _pages_category_archive, _pages_collection_archive, _pages_page_archive, _pages_portfolio, _pages_publications, _includes_archive_single [EXTRACTED 1.00]
  • Pages sharing /nmp/ redirect_from (conflicting redirects) — _pages_hackathons, _pages_non_menu_page, _pages_community_involvement [EXTRACTED 1.00]
  • Hicberg research dissemination (paper, thesis, talks) — _publications_2025_xx_xx_hicberg_paper, _publications_2024_12_17_thesis_manuscript, _talks_talk_ismb_2023, _talks_talk_icte_2024, _talks_talk_jobim_2024, _talks_talk_inception_2024 [INFERRED 0.95]
  • Yeast retrotransposon findings via Hicberg — retrotransposons, cohesin, two_micron_plasmid, saccharomyces_cerevisiae [EXTRACTED 1.00]
  • Jekyll archive listing pages — _pages_sitemap, _pages_tag_archive, _pages_teaching, _pages_year_archive, archive_single_include [EXTRACTED 1.00]
  • Hicberg ambiguous-read reassignment pipeline — files_icte_2024_poster_hi_c, files_icte_2024_poster_ambiguous_reads, files_icte_2024_poster_statistical_inference_reassignment, files_icte_2024_poster_polymer_contact_law, files_icte_2024_poster_hicberg [EXTRACTED 1.00]
  • Hicberg yeast retrotransposon findings — files_icte_2024_poster_retrotransposons, files_icte_2024_poster_cohesin, files_icte_2024_poster_two_micron_plasmid, files_icte_2024_poster_saccharomyces_cerevisiae, files_jobim_2024_poster_pdf_157_ty1_benchtop_validation [INFERRED 0.85]
  • Academic template placeholder assets (sample papers, slides, avatar) — files_paper1_sample_pdf, files_paper2_sample_pdf, files_paper3_sample_pdf, files_slides1_sample_slides, files_slides2_sample_slides, files_slides3_sample_slides, images_profile_placeholder_avatar [INFERRED 0.85]
  • DNA CNN pipeline: one-hot encoding -> convolution -> max pooling — images_post_images_article_1_one_hot_encoding, images_post_images_article_1_convolution_example, images_post_images_article_1_max_pooling, images_post_images_article_1_receptor_field [INFERRED 0.85]
  • Training curves comparison: SGD vs Adam vs Adam+Dropout — images_post_images_article_1_sgd_results, images_post_images_article_1_adam_results, images_post_images_article_1_dropout_effect [INFERRED 0.85]
  • CGR-to-CNN DNA Classification Pipeline — images_post_images_article_2_chaos_game_representation, images_post_images_article_2_cnn_conv_dropout_backbone, images_post_images_article_2_dna_sequence_classification [INFERRED 0.85]
  • CNN Model Variants (Base, CNN+SVM, DNA-LeNet) — images_post_images_article_2_base_model_1, images_post_images_article_2_cnn_svm, images_post_images_article_2_dna_lenet [INFERRED 0.85]
  • Classifier comparison for DNA sequence classification (SVM vs base NN vs LeNet) — images_post_images_article_2_svm, images_post_images_article_2_base_neural_model, images_post_images_article_2_lenet, images_post_images_article_2_dna_sequence_classification [INFERRED 0.85]

Communities (33 total, 16 thin omitted)

Community 0 - “Minified Theme JS Bundle”

Cohesion: 0.06 Nodes (54): a(), At(), Be(), bt(), c(), e(), ct(), $e() (+46 more)

Community 1 - “Archive & Profile Includes”

Cohesion: 0.09 Nodes (55): UI Text Localization (site.data.ui-text[site.locale]), Archive Item (generic/publication/teaching), Archive Item (CV publication), Post front-matter metadata (title, venue, citation, paperurl, slidesurl, bibtexurl, teaser), Archive Item (talk), Archive Item (CV talk), Author Profile Sidebar, Author data (site.author / site.data.authors) (+47 more)

Community 2 - “Jekyll Site Configuration”

Cohesion: 0.06 Nodes (43): Author Profile (Sebastien Gradit, PhD), Jekyll Collections (teaching, publications, portfolio, talks, softwares), Custom Domain sebastiengradit.com, Docker Config Override (empty url), Institut Pasteur, Jekyll Plugins (feed, gist, paginate, sitemap, redirect-from, jemoji), Kramdown GFM Markdown + Rouge, Publication Categories (books, manuscripts, conferences) (+35 more)

Community 3 - “CV & Talkmap Python Scripts”

Cohesion: 0.09 Nodes (13): create_cv_json(), DateTimeEncoder, extract_author_info(), main(), parse_config(), parse_education(), parse_markdown_cv(), parse_portfolio() (+5 more)

Community 4 - “CV Career & Projects”

Cohesion: 0.11 Nodes (38): Bioequivalence simulations (Danone Nutricia Research), Curriculum Vitae (academic/ML), ESM-2 protein foundation model, Hicberg paper (Genome Research, 2026), Foot orthotics biomechanical models (CABOMA, Universite de Montreal), Deep learning prediction of 2-micron plasmid interactions from nucleosome occupancy, Curriculum Vitae (industry), S. cerevisiae rDNA behavior under stress (heat, oxidative) (+30 more)

Community 5 - “NPM Package Manifest”

Cohesion: 0.06 Nodes (32): bugs, url, contributors, dependencies, fitvids, jquery, jquery-smooth-scroll, magnific-popup (+24 more)

Community 6 - “CGR DNA Classifier Models”

Cohesion: 0.11 Nodes (23): Base Model Training Loss/Accuracy Curves, Base CNN Model Architecture Diagram, Base Model Training Curves (jpg), Base Neural Network Model (~92% train / ~80% val acc, overfitting after ~300 epochs), CGR Quadrant Grid Diagram, CGR Examples per Class (7 classes), CGR Path Construction Diagram, CGR Representation 32x32 per Class (+15 more)

Community 7 - “Hicberg Research Output”

Cohesion: 0.17 Nodes (21): Softwares Page, Talk Map Page, Talks, Presentations and Posters Page, PhD Thesis: Using statistical profiling to decipher hidden chromatin contacts resulting from repeated sequences, Hicberg: Reconstruction of genomic signals from repeated elements (Genome Research), ICTE 2024 Poster: Hicberg, Inception 2024 Talk (Institut Pasteur), ISMB/ECCB 2023: Statistical inference of repeated sequence contacts in Hi-C maps (+13 more)

Community 9 - “CV Pages & Data”

Cohesion: 0.15 Nodes (15): _config.yml, CV JSON data, CV Data (site.data.cv, JSON Resume schema), Site Navigation Data (site.data.navigation), CV Template Include, Archive Layout with Content, CV, CV (JSON) (+7 more)

Community 10 - “About & Community Pages”

Cohesion: 0.18 Nodes (15): About Page (Hi I’m Sébastien Gradit), AI models for omics data, bioinfo-fr.net blog, Hicberg (genomics tool), Pasteur Institute, Sébastien Gradit, Community Involvement, Jeunes Bioinformaticiens de France (JeBiF) (+7 more)

Community 11 - “Blog Posts & Archives”

Cohesion: 0.22 Nodes (10): Sitemap Page, Posts by Tags Page, Teaching Page, Blog Posts Year Archive Page, Bioinformatics and AI: A First Step, Bioinformatics and AI: CNNs for bioinformatics, Teaching Experience 2 (template), archive-single.html include (+2 more)

Community 12 - “JeBiF Outreach Activities”

Cohesion: 0.48 Nodes (7): Les aventures de Nounours (outreach), BioStream live streams, JOBIM 2024 Poster - JeBiF RSG France, ISCB Student Council (RSG France), JeBiF - Association des Jeunes Bioinformaticiens de France, JOBIM conference (JeBiF@JOBIM), Les Bioinformations newsletter

Community 13 - “Optimizers & Overfitting”

Cohesion: 0.33 Nodes (6): Adam Optimizer, Adam Training Results (loss/accuracy curves), Dropout Effect Training Results, Overfitting, SGD Optimizer, SGD Training Results (loss/accuracy curves)

Community 14 - “Analytics Providers”

Cohesion: 0.60 Nodes (6): Analytics Provider Dispatcher, Custom Analytics Snippet, Legacy Google Analytics (ga.js) Include, Google Analytics 4 (gtag) Include, Google Universal Analytics Include, site.analytics config (provider, google.tracking_id)

Community 15 - “1D CNN on DNA”

Cohesion: 0.40 Nodes (6): 1D Convolution on One-Hot DNA Diagram, 1D Convolutional Neural Network for DNA, DNA Double Helix Illustration, Max Pooling Diagram, One-Hot Encoding of DNA Sequence, Receptive Field Diagram

Community 16 - “Comment Provider Embeds”

Cohesion: 0.67 Nodes (4): Discourse Comments Embed, Disqus Comments Embed, Facebook Comments SDK, site.comments config (discourse.server, disqus.shortname, facebook.appid)

Community 17 - “Terms & Privacy”

Cohesion: 0.67 Nodes (3): Terms and Privacy Policy Page, Disqus comments, Google Analytics

Ambiguous Edges - Review These

  • Community Involvement → Page not in menu [AMBIGUOUS] _pages/community_involvement.md · relation: conceptually_related_to
  • Hackathons → Page not in menu [AMBIGUOUS] _pages/hackathons.md · relation: conceptually_related_to
  • Paper 1 (placeholder sample PDF) → Slides 1 (placeholder slides) [AMBIGUOUS] files/slides1.pdf · relation: conceptually_related_to
  • Paper 2 (placeholder sample PDF) → Slides 2 (placeholder slides) [AMBIGUOUS] files/slides2.pdf · relation: conceptually_related_to
  • Paper 3 (placeholder sample PDF) → Slides 3 (placeholder slides) [AMBIGUOUS] files/slides3.pdf · relation: conceptually_related_to

Knowledge Gaps

  • 86 isolated node(s): fitvids, jquery, jquery-smooth-scroll, magnific-popup, onchange (+81 more) These have ≤1 connection - possible missing edges or undocumented components. (Counts symbols only; 172 node(s) total have ≤1 connection when file, concept and rationale nodes are included.)
  • 16 thin communities (<3 nodes) omitted from report — run graphify query to explore isolated nodes.

Suggested Questions

Questions this graph is uniquely positioned to answer:

  • Why does Scripts Include connect Archive & Profile Includes to Minified Theme JS Bundle, Analytics Providers? High betweenness centrality (0.078) - this node is a cross-community bridge.
  • Are the 10 inferred relationships involving e() (e.g. with main.min.js and et()) actually correct? e() has 10 INFERRED edges - model-reasoned connections that need verification.
  • What connects fitvids, jquery, jquery-smooth-scroll to the rest of the system? 86 weakly-connected nodes found - possible documentation gaps or missing edges.
  • Should Minified Theme JS Bundle be split into smaller, more focused modules? Cohesion score 0.06393606393606394 - nodes in this community are weakly interconnected.
  • Why does base_path include connect Archive & Profile Includes to Comment Provider Embeds, CV Pages & Data, About & Community Pages? High betweenness centrality (0.057) - this node is a cross-community bridge.

Low-confidence Hints

AMBIGUOUS edges — the extractor was unsure. Verify before acting on these.

  • What is the exact relationship between Community Involvement and Page not in menu? Edge tagged AMBIGUOUS (relation: conceptually_related_to) - confidence is low.
  • What is the exact relationship between Hackathons and Page not in menu? Edge tagged AMBIGUOUS (relation: conceptually_related_to) - confidence is low.