NeuroScape: Mapping the Neuroscience Research Landscape

Codebase accompanying the article:

Senden, M. (2025). The Evolving Landscape of Neuroscience [Preprint]. bioRxiv. https://doi.org/10.1101/2025.02.13.638094

This repository contains scripts and notebooks for analyzing and visualizing neuroscience research through large-scale data collection, filtering, clustering, and semantic analysis of scientific articles.

Abstract

Neuroscience emerged as a distinct academic discipline during the 20th century and has undergone rapid expansion and diversification. A comprehensive analysis of its evolving landscape becomes increasingly important to retain an overview of cross-domain insights and research questions. This study leverages text-embedding and clustering techniques together with large language models to analyze 461,316 articles published between 1999 and 2023 and reveals the field's structural organization and dominant research domains. Inter-cluster citation analysis uncovers a surprisingly integrated picture and key intellectual hubs that shape the broader research landscape. An analysis of how research clusters align with pre-defined dimensions demonstrates a strong experimental focus, widespread reliance on specific mechanistic explanations rather than unifying theoretical frameworks, and a growing emphasis on applied research. Fundamental research is at the risk of decline and cross-scale integration remains limited. This study provides a framework for understanding neuroscience's trajectory and identifies potential avenues for strengthening the field.

Repository Structure

.
├── config/                 # TOML config files (scraping, clustering, analysis, etc.)
├── notebooks/              # Jupyter notebooks for exploration and results
├── scripts/                # Main processing scripts organized by function
│   ├── ingestion/          # Data collection and cleaning
│   ├── preprocessing/      # Filtering and classification
│   ├── domain_embedding/   # Training & applying domain-specific embeddings
│   ├── clustering/         # Building semantic graphs & community detection
│   ├── graph_analysis/     # Citation/network density analysis
│   └── semantic_analysis/  # Dimension analysis, cluster characterization, trends, etc.
├── src/
│   ├── classes/            # Python classes for data structures and model architectures
│   └── utils/              # Utility modules (parsing, data loading, plotting, etc.)
└── README.md

Data

This repository has been used to collect, curate, and analyze the following dataset:

Senden, M. (2025). NeuroScape (1.0.1) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.14865161

Workflow Overview

1. Scrape Data

   • scripts/ingestion/scraping.py
   • Query PubMed for relevant articles. Neuroscience, multidisciplinary and other (for training discipline classifier).

2. Merge and Clean

   • scripts/ingestion/merge_and_clean.py
   • Consolidate scraped data, remove duplicates, and clean metadata.

3. Initial Embedding

   • scripts/ingestion/initial_embedding.py
   • Generate general-purpose text embeddings (via Voyage AI) for each abstract.

4. Prepare Classifier Training Data

   • scripts/preprocessing/prepare_classifier_training_data.py
   • Create labeled samples for discipline classification (to distinguish neuroscience from other fields).

5. Train Discipline Classifier

   • scripts/preprocessing/train_discipline_classifier.py
   • Train a neural network to identify neuroscientific articles.

6. Filter Data

   • scripts/preprocessing/filter_disciplines.py
   • Retain only articles classified as neuroscience with high confidence.

7. Build Adjacency Matrix

   • scripts/ingestion/build_adjacencies.py
   • Obtains citing and cited articles for each article in the dataset.

8. Train Domain Embedding Model

   • scripts/domain_embedding/train_embedding_model.py
   • Trains a domain-specific embedding model on top of the initial embeddings (through contrastive learning).

9. Domain Embedding

   • scripts/domain_embedding/embed_abstracts.py
   • Re-embeds abstracts in a lower-dimensional, neuroscience-focused space for semantic clustering.

10. Build the Semantic Graph

    • scripts/clustering/graph_construction.py
    • Uses the domain-specific embeddings to construct a similarity graph (e.g., KNN) needed for community detection.

11. Community Detection

    • scripts/clustering/community_detection.py
    • Perform clustering (e.g., Leiden community detection) on the network.

12. Cluster Definition

    • scripts/semantic_analysis/cluster_definition.py
    • Generate descriptive titles, keywords, and descriptions for each cluster.

13. Cluster Distinction

    • scripts/semantic_analysis/cluster_distinction.py
    • Identify key differences between similar clusters.

14. Dimensions Extraction

    • scripts/semantic_analysis/assess_dimensions.py
    • Analyze each cluster across multiple research dimensions (e.g., appliedness, modality).

15. Dimension Categorization

    • scripts/semantic_analysis/assess_dimension_categories.py
    • Categorize clusters along specific sub-dimensions (e.g., fundamental vs clinical research within appliedness).

16. Open Questions

    • scripts/semantic_analysis/extract_open_questions.py
    • Identify important open research questions from recent review articles.

17. Trends Extraction

    • scripts/semantic_analysis/extract_trends.py
    • Compare older vs. recent publications to reveal emerging and declining trends.

18. Density Graph

    • scripts/graph_analysis/cluster_density.py
    • Assess citation density and connections between clusters.

Optional

• scripts/preprocessing/update_embedding.py allows updating the general embeddings with a newer Voyage AI model if desired.

Notebooks

Notebooks handle creation of Figures and Tables for the manuscript, including additional analyses.

Setup Instructions

1. Create a Conda Environment

First, create and activate a Conda environment with Python 3.12:

conda create --name neuroscape_env python==3.12
conda activate neuroscape_env

2. Install PyTorch

Install PyTorch before installing other dependencies. Follow the official instructions based on your system:

• Visit: PyTorch Installation Guide

3. Install Other Dependencies

Once PyTorch is installed, install the remaining dependencies from requirements.txt:

pip install -r requirements.txt

Disclaimer

This repository provides the scripts and workflow used in The Evolving Landscape of Neuroscience study and is intended for research and educational purposes. While I encourage other researchers to use and build upon this work, I am primarily a researcher, not a full-time software developer. As such:

• I welcome issues and pull requests and will try to address them as time permits.
• However, active maintenance is not guaranteed. Users should not expect frequent updates or extensive support.
• The code is provided as is, without warranties regarding performance, correctness, or long-term compatibility.

If you use this repository for your research, I would appreciate a citation to the accompanying manuscript.