tags	readme documentation obsidian zotero vault

AI Gesture Recognition — Knowledge Vault

Comparative study of 3D hand gesture recognition methods — DTW, Edit-Distance, Three-Cents ($3), and BiLSTM — evaluated on the Huang et al. (2019) dataset with rigorous nested cross-validation, ablation study, and statistical hypothesis testing.

This repository doubles as an Obsidian knowledge vault tightly integrated with Zotero for academic reference management.

Note: The actual project code (implementations, experiments, datasets, results) lives in the main project repository: 👉 Matteo-glz/MLSMM2154_Artificial-Intelligence_gesture_recognition

This repo is the research workspace for that project — literature notes, concept maps, paper annotations, and course material organised in Obsidian.

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Table of Contents

1. Vault Structure
2. Prerequisites
3. Zotero Setup
4. Obsidian Setup
5. Plugin Configuration
   • Zotero Integration
   • Templater
   • Dataview
   • Commander (cmdr)
6. Workflow: Importing a Paper from Zotero
7. Templates Reference
8. Git & Collaboration Notes

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Vault Structure

ai-gesture-recognition/
├── 00_AI_Knowledge_Graph_MOC.md          # Master map of content (both projects)
├── Concepts/                             # ML/AI concept notes (CNNs, Transformers, etc.)
├── Foundations/                          # Math foundations (probability, optimisation, …)
├── Papers/                               # Literature notes (one per paper, keyed by citekey)
│   ├── 00_Papers_MOC.md                  # Full index of paper notes by topic
│   └── images/                           # PDF annotation images exported by Zotero
├── Project - Gesture Recognition/        # Gesture recognition project (MLSMM2154)
├── Project - Movie Recommender System/   # RecSys project (MLSMM2156 Hackathon)
│   ├── 00_HOME.md                        # Main index + best results at a glance
│   ├── Workflow/                         # Pipeline notes (data, split, eval, models, webapp…)
│   ├── Codes/                            # Code explanation notes (all Python files)
│   └── Webapp/                           # Flask server and cascade recommendation pipeline
├── Course - Sequence Modeling/           # Lecture notes + 10 exam Q&A with full derivations
├── Workflows/                            # Reusable ML pipeline notes
├── Templates/                            # Obsidian note templates
│   ├── zotero-import-paper.md            # Primary Zotero import template (Nunjucks)
│   ├── zotero-template.md                # Lightweight Zotero template
│   ├── literature-note.md                # Manual literature note
│   ├── topic-note.md                     # Concept / topic note
│   └── thinking-note.md                  # Fleeting / thinking note
├── Zotero_Import/                        # BibTeX exports from Zotero (gitignored)
├── Daily Notes/                          # Daily log notes
└── .obsidian/                            # Obsidian config (plugins, settings)

Note: The Claude/ folder (AI assistant memory) and Course - Sequence Modeling/ are gitignored and will not be pushed to GitHub.

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Prerequisites

Tool	Version	Purpose
Obsidian	≥ 1.1.1	Note-taking application (desktop)
Zotero	≥ 6	Reference manager
Better BibTeX for Zotero	latest	Citekey generation & BibTeX export
Git	any	Version control

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Zotero Setup

1. Install Zotero

Download and install Zotero for your platform. Create a free account for cloud sync if desired.

2. Install Better BibTeX (BBT)

Better BibTeX generates stable, human-readable citekeys (e.g., Vaswani2017_Transformer) and enables auto-export of .bib files.

1. Download the latest .xpi from the BBT releases page.
2. In Zotero: Tools → Add-ons → Install Add-on From File… and select the .xpi.
3. Restart Zotero.

3. Configure the Citekey Format

The vault uses the pattern [auth:capitalize][year]_[title:select=1:capitalize] to produce keys like Vaswani2017_Transformer. To set this:

1. Open Zotero → Edit → Preferences → Better BibTeX.
2. Under Citation keys, set the format to:

   [auth:capitalize][year]_[shorttitle:capitalize]
   

3. Click Refresh to regenerate all keys.

4. Enable the Zotero Connector (for browser import)

Install the Zotero Connector browser extension. This lets you save papers directly from Google Scholar, arXiv, ACM DL, and most publisher sites into Zotero with one click.

5. (Optional) Export BibTeX to the vault

To keep a local .bib backup:

1. Right-click a Zotero collection → Export Collection…
2. Choose Better BibTeX format.
3. Enable Keep Updated for live auto-export.
4. Save to Zotero_Import/ inside this vault.

These .bib files are gitignored — they contain local file paths that differ between machines.

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Obsidian Setup

1. Open the vault

Clone or download this repository, then in Obsidian: Open folder as vault and select the repository root.

2. Trust plugins

On first open, Obsidian will warn about community plugins. Click Trust author and enable plugins to activate all four plugins listed below.

3. Allow network access (Zotero Integration)

The Zotero Integration plugin communicates with the running Zotero desktop app over a local HTTP connection. Make sure Zotero is open whenever you want to import notes.

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Plugin Configuration

Four community plugins are used. All are pre-installed in .obsidian/plugins/.

Zotero Integration (obsidian-zotero-desktop-connector)

Version: 3.2.1 | Author: mgmeyers

This plugin connects to the running Zotero app and imports paper metadata, abstracts, highlights, and PDF annotations directly into Obsidian notes using a Nunjucks template.

Saved configuration (.obsidian/plugins/obsidian-zotero-desktop-connector/data.json):

Setting	Value	Meaning
database	Zotero	Uses your local Zotero library
noteImportFolder	Papers	New notes land in Papers/
outputPathTemplate	Papers/{{citekey}}.md	One file per paper, named by citekey
imageOutputPathTemplate	Papers/images/{{citekey}}/{{fileName}}	PDF annotation images
templatePath	Templates/zotero-import-paper.md	Template applied to every import
openNoteAfterImport	true	Opens the note immediately after creation

How to import a paper: see Workflow below.

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Templater

Version: 2.20.5 | Author: SilentVoid / Zachatoo

Provides advanced Handlebars-style templating (<% tp.* %> syntax) for new notes. Used alongside the Zotero template's Nunjucks syntax.

Recommended settings (set manually in Obsidian → Settings → Templater):

Setting	Recommended value
Template folder location	Templates
Trigger Templater on new file creation	Enabled
Automatic jump to cursor	Enabled

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Dataview

Version: installed | Author: blacksmithgu

Treats your vault as a queryable database. Use it to generate dynamic lists of unread papers, papers by topic, etc.

Example query — all unread papers:

TABLE authors, year, tags
FROM "Papers"
WHERE status = "unread"
SORT year DESC

Example query — papers tagged transformer:

TABLE title, year
FROM "Papers"
WHERE contains(tags, "transformer")
SORT year ASC

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Commander (cmdr)

Version: installed | Author: phibr0

Adds custom commands to Obsidian's toolbar, ribbon, and context menus. Used here to create a one-click "Import from Zotero" ribbon button so you don't need to open the command palette every time.

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Workflow: Importing a Paper from Zotero

This is the standard workflow to go from a PDF in Zotero to a structured literature note in Obsidian.

Step 1 — Add the paper to Zotero

• From browser: Click the Zotero Connector extension button on any article page (arXiv, ACM, Springer, etc.). Zotero auto-fills all metadata.
• From PDF: Drag the PDF into Zotero. Right-click → Retrieve Metadata for PDF.
• Manual: File → New Item → Journal Article, then fill in fields.

Step 2 — Annotate the PDF (optional but recommended)

Open the PDF inside Zotero (double-click). Use the built-in PDF reader to:

• Highlight text (yellow = key claim, green = method, red = limitation — customise as you like).
• Add comments to highlights.

All highlights are stored in Zotero and will be pulled into Obsidian during import.

Step 3 — Import into Obsidian

1. Make sure Zotero is running.
2. In Obsidian, open the Command Palette (Cmd/Ctrl + P).
3. Run Zotero Integration: Import notes.
4. Search for the paper by title, author, or citekey.
5. Press Enter — Obsidian creates Papers/<citekey>.md using Templates/zotero-import-paper.md.

The generated note contains:

• YAML frontmatter (title, authors, year, journal, citekey, DOI, tags, status)
• Abstract
• All highlights and annotations with page numbers
• Synthesis scaffold (Core Claim, Method, Key Findings, Limitations, Relevance)
• Backlink to open the item in Zotero

Step 4 — Complete the synthesis

Open the new note and fill in the Synthesis section. Then link to concept notes:

## Connections
- Core architecture → [[Concepts/Attention_Transformer]]
- Compared with → [[Papers/Hochreiter1997]]

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Templates Reference

Templates/zotero-import-paper.md (primary)

Used automatically by the Zotero Integration plugin. Variables use Nunjucks syntax ({{variable}}). Key variables:

Variable	Description
{{title}}	Paper title
{{authors}}	Author list
{{date | format("YYYY")}}	Publication year
{{publicationTitle}}	Journal or conference name
{{citekey}}	Better BibTeX citekey
{{DOI}}	DOI string
{{abstractNote}}	Abstract text
{{desktopURI}}	Deep-link to open item in Zotero
{{annotations}}	Array of PDF annotations
annotation.annotatedText	Highlighted text
annotation.page	Page number
annotation.comment	Your annotation comment

Templates/zotero-template.md (lightweight)

A simpler alternative with the same Nunjucks variables, without the synthesis callout blocks. Useful for quick imports.

Templates/literature-note.md

For manually created literature notes (no Zotero import). Uses Templater <% tp.* %> syntax.

Templates/topic-note.md

For concept or topic notes in Concepts/ and Foundations/.

Templates/thinking-note.md

Fleeting / atomic thinking notes for the daily workflow.

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Git & Collaboration Notes

What is tracked

• All .md note files (Concepts/, Foundations/, Papers/, Course - Sequence Modeling/, etc.)
• Obsidian plugin binaries and manifests (.obsidian/plugins/)
• Obsidian core settings (.obsidian/app.json, community-plugins.json, core-plugins.json)
• The Zotero Integration data.json (so template and output path config is shared)
• All templates in Templates/

What is gitignored

Path	Reason
Claude/	AI assistant memory — personal and session-specific
.obsidian/workspace.json	Local UI state (open tabs, panels) — differs per machine
.obsidian/plugins/*/data.json	Most plugin settings contain local paths; exception: Zotero Integration
Zotero_Import/*.bib	BibTeX exports contain absolute local file paths
.DS_Store, ._*	macOS metadata
__pycache__/, .venv/	Python build artefacts

Cloning on a new machine

git clone https://github.com/<your-username>/ai-gesture-recognition.git

Then:

1. Open the folder as an Obsidian vault.
2. Install and start Zotero with Better BibTeX.
3. The Zotero Integration plugin will use the committed data.json — no manual reconfiguration needed.