updated readme

README.md

@@ -1,6 +1,45 @@
+# 🔥 FLARE
+Fine-grained Learning for Aligment of spectra-molecule REpresentation
+
+###  Yan Zhou Chen, Soha Hassoun
+#### Department of Computer Science, Tufts University
+This repository provides the implementation of FALRE. Given a mass spectrum, FLARE can be used to rank a set of molecular candidates. Further, FLARE enables visualization of peak-to-node attribution.
+
+## 🛠 Set up
+### Clone repository
+```
+git clone https://github.com/hassounlab/flare
+cd flare
+```
+### Set up environment and install dependencies
+```
+conda create -n flare python=3.11
+conda activate flare
+pip install -r requirements.txt
+```
+
+## Usage
+Modify params.yaml as necessary
+
+```
+# preprocess data
+python subformula_assign/assign_subformulae.py --spec-files ../data/sample/data.tsv --output-dir ../data/sample/subformulae --labels-file ../data/sample/data.tsv --max-formulae 60
+
+# train 
+python train.py
+
+# test
+python test.py
+```
+## 🙏 Acknowledgments
+- **Loss Objective**: [FILIP](https://arxiv.org/abs/2111.07783)
+- **Training Data**: [MassSpecGym](https://github.com/pluskal-lab/MassSpecGym)
+- **Subformula Assigner Code**: [MIST](https://github.com/samgoldman97/mist/tree/main_v2)
+
+## APP Configuration
 ---
 title: Flare
-emoji: 🌍
+emoji: 🔥 
 colorFrom: green
 colorTo: blue
 sdk: streamlit
@@ -8,13 +47,4 @@ pinned: false
 python_version: 3.11.7
 ---
 
-Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
-# FILIP-MS
-FILIP contrastive learning for metabolite annotation
-
-## Magma preprocessing
-`python run_magma.py --data_pth '/r/hassounlab/spectra_data/msgym/MassSpecGym.tsv' --output_dir '/data/yzhouc01/FILIP-MS/data/magma/' --workers 50`
-
-### test candidates
-
-`python run_fragmentation_only.py --d '/r/hassounlab/spectra_data/msgym/MassSpecGym.tsv' -c '/r/hassounlab/spectra_data/msgym/molecules/MassSpecGym_retrieval_candidates_mass.json' -o '/data/yzhouc01/FILIP-MS/data/msgym_mass_cands.pkl' -w 50`
+Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference