pr/1

README.md

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+---
+license: apache-2.0
+---
+
+# Food Allergy Microbiome Dataset (Experimental)
+
+## Dataset Summary
+
+This is an **experimental microbiome dataset** designed for exploratory research in **food allergy classification**. The dataset contains multiple data modalities (DNA embeddings, microbiome embeddings, raw DNA sequences) collected longitudinally at several timepoints.
+
+> **Warning:** This dataset is experimental. Its structure is frozen for ongoing research, and it is **not ready for benchmarking**.
+
+---
+
+## Dataset Structure
+
+The dataset is organized by **data type** and **timepoint**:
+
+```
+.
+├── dna_embeddings
+│   └── month_{1,2,3,6,12,24,36}/dna_embeddings.h5
+├── dna_sequences
+│   └── month_{1,2,3,6,12,24,36}/*.csv
+└── microbiome_embeddings
+    └── month_{1,2,3,6,12,24,36}/microbiome_embeddings.h5
+```
+
+* **DNA embeddings**: `.h5` files with embedding vectors derived from DNA sequences.
+* **Microbiome embeddings**: `.h5` files containing microbiome feature vectors.
+* **DNA sequences**: raw `.csv` files representing sequences or processed features.
+
+**Each timepoint contains multiple samples per subject.**
+File names (e.g., `DRS061544.csv`) serve as sample IDs. Subject IDs and mappings are implicit; users must manage them carefully.
+
+---
+
+## Intended Use
+
+* Task: Exploratory **classification of food allergies**.
+* Users are expected to **define their own train/test splits**.
+* **Critical:** Do **not** split samples randomly; multiple samples per subject exist. Splits should be done at the **subject level** to avoid data leakage.
+
+---
+
+## Data Notes
+
+* Longitudinal: Samples are collected at multiple months (1, 2, 3, 6, 12, 24, 36).
+* Multi-modal: Embeddings and sequences are provided separately; users may combine them as needed.
+* No labels are embedded per file. Labels must be handled separately or mapped from your internal records.
+* This dataset is **research-focused**, not benchmark-ready.
+
+---
+
+## License
+
+This experimental dataset is currently released under Apache License 2.0
+
+---

metadata/T1.csv

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processed/dna_embeddings/T1/dna_embeddings.h5

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