cleaned up description

README.md

@@ -12,25 +12,44 @@ python_version: 3.11.7
 
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
 
-# MultiView Projection (MVP) for Spectra Annotation
-
-###  Yan Zhou Chen, Soha Hassoun
-#### Department of Computer Science, Tufts University
-This repository provides the implementation of MultiView Projection (MVP). MVP can be used to rank a set of molecular candidates given a spectrum.
-
-## Table of Contents
-1. [Install & setup]
-2. [Data prep]
-3. [MassSpecGym data download]
-4. [Use our pretrained model]
-5. [Training from scratch]
-6. [References]
-
-## Install & setup
-1. Clone the repository: git clone <REPO_link>
+# 🏆 MultiView Projection (MVP) for Spectra Annotation
+
+
+### Authors  
+**Yan Zhou Chen, Soha Hassoun**  
+Department of Computer Science, Tufts University  
+
+---
+
+MVP is a framework for **ranking molecular candidates given a spectrum**. This repository provides the official implementation, pretrained models, and utilities for data preparation and training.
+
+---
+
+## 📑 Table of Contents
+0. [Quick Test](#quick-test)  
+1. [Install & Setup](#install--setup)  
+2. [Data Preparation](#data-prep)  
+3. [MassSpecGym Data Download](#massspecgym-data-download)  
+4. [Using the Pretrained Model](#use-our-pretrained-model)  
+5. [Training from Scratch](#training-from-scratch)  
+6. [References](#references)  
+
+---
+
+
+## 🚀 Quick Test
+Run MVP instantly with our [interactive app](https://huggingface.co/spaces/HassounLab/MVP) for small-scale experiments.
+
+---
+
+
+## ⚙️ Install & setup
+1. Clone the repository: `git clone https://huggingface.co/spaces/HassounLab/MVP/`
 2. Install evironment or only key packages:
 ```
-conda env create -f environment.yml
+conda create -n mvp python=3.11
+conda activate mvp
+pip install -r requirements.txt
 ``` 
 #### Key packages
 - python
@@ -44,7 +63,9 @@ conda env create -f environment.yml
 - massspecgym
 - lightning
 
-## Data prep
+---
+
+## 📂 Data prep
 We provide sample spectra data and candidates in `data/sample`. 
 For preprocessing:
 1. If using formSpec, compute subformula labels
@@ -75,7 +96,7 @@ python test.py --param_pth params_binnedSpec.yaml
 ```
 
 We provide a notebook showing sample result files in `notebooks/demo.ipynb`
-
+---
 ## MassSpecGym data download
 Our model is trained on [MassSpecGym dataset](https://github.com/pluskal-lab/MassSpecGym). Follow their instruction to download the spectra and candidate dataset.
 
@@ -83,8 +104,7 @@ You can preprocess the MassSpecGym dataset as descirbed in the above section or
 ```
 mkdir data/msgym/
 cd data/msgym
-wget 
-wget 
+wget https://zenodo.org/records/15223987/files/msgym_preprocessed.zip?download=1
 ```
 ## Training from scratch
 To train a model from scratch:
@@ -98,10 +118,14 @@ python train.py --param_pth params_formSpec.yaml
 # If using binnedSpec
 python train.py --param_pth params_binnedSpec.yaml
 ```
+---
 
-## References
+## 📚 References
+Preprint:[Learning from All Views: A Multiview Contrastive Framework for Metabolite Annotation](https://www.biorxiv.org/content/10.1101/2025.11.12.688047v1)
+
+---
 
+## 📧 Contact
+For questions, reach out to: [email protected]
 
-#### Contact
-[email protected]
 =======

app.py

@@ -28,8 +28,8 @@ st.markdown("""
 This web app lets you test our trained model on your own data.
             
 ### 📚 References
-🔗 **Paper:** [Read the publication here](https://github.com/HassounLab/MVP)  
-📦 **Source Code:** [GitHub Repository](https://github.com/HassounLab/MVP)
+🔗 **Preprint:** [Learning from All Views: A Multiview Contrastive Framework for Metabolite Annotation](https://www.biorxiv.org/content/10.1101/2025.11.12.688047v1)  
+📦 **Source Code:** [Hugging Face Repository](https://huggingface.co/spaces/HassounLab/MVP)
 
 ---