Update README.md

README.md

@@ -452,3 +452,192 @@ configs:
   - split: train
     path: data/Python/train-*
 ---
+
+# Dataset Summary
+
+We develop a new contamination-free multilingual code dataset that facilitates LLM evaluation reproducibility.
+
+# Collection
+
+We collect up to **50,000** public repositories using the [GitHub API](https://docs.github.com/en/rest/search/search?apiVersion=2022-11-28), focusing on *license type*, *star count*, and *creation date*. Repositories with non-permissive licenses are prioritized to reduce contamination, as public code datasets we deduplicate against primarily focus on permissive or no-license repositories. We select repositories created before **April 2024** in decreasing order of their star counts. To handle GitHub rate limits, we use timeouts and pagination during the scraping process.
+
+### Copyleft licenses included in the dataset
+| **License**    | **Family** |
+| :--------: | :-------: |
+| CECILL-1.0 | Weak Copyleft   |
+| CECILL-1.1 |   Weak Copyleft   |
+| CECILL-2.0    | Weak Copyleft   |
+| CECILL-2.1 |   Weak Copyleft   |
+| CECILL-C | Weak Copyleft   |
+| EPL-1.0 | Weak Copyleft   |
+| EPL-2.0 | Weak Copyleft   |
+| LGPL-2.1 | Weak Copyleft   |
+| LGPL-3.0 | Weak Copyleft   |
+| MS-RL | Weak Copyleft   |
+| MPL-2.0 | Weak Copyleft   |
+| GPL-2.0 | Strong Copyleft   |
+| GPL-3.0  | Strong Copyleft   |
+| AGPL-3.0 | Network Copyleft   |
+| EUPL-1.1 | Network Copyleft   |
+| EUPL-1.2 | Network Copyleft   |
+| OSL-3.0 | Network Copyleft   |
+
+The features we extract for each repository are illustrated in the example below.
+
+```json
+  {
+    "id": 126178683,
+    "full_name": "halo-dev/halo",
+    "html_url": "https://github.com/halo-dev/halo",
+    "stargazers_count": 29115,
+    "forks_count": 8985,
+    "watchers_count": 29115,
+    "open_issues_count": 278,
+    "language": "Java",
+    "created_at": "2018-03-21T12:56:52Z",
+    "pushed_at": "2023-10-28T16:29:39Z",
+    "license": {
+      "key": "gpl-3.0",
+      "name": "GNU General Public License v3.0",
+      "spdx_id": "GPL-3.0",
+      "url": "https://api.github.com/licenses/gpl-3.0",
+      "node_id": "MDc6TGljZW5zZTk="
+    },
+    "retrieval_date": "10/30/2023, 3:24:57 PM (Europe/Amsterdam)"
+  }
+
+```
+
+### Repository Fields
+
+- **id**: unique id of the repo
+- **full_name**: complete name of the repo
+- **html_url**: URL to the repo
+- **stargazers_count**: number of stars of the repo
+- **forks_count**: number of forks of the repo
+- **watchers_count**: number of watchers of the repo
+- **open_issues_count**: number of open issues of the repo at the extraction time
+- **language**: main language of the repo
+- **created_at**: creation date of the repo
+- **pushed_at**: date of the most recent push to the repo until the extraction date
+- **license**: license type of the repo
+- **retrieval_date**: date when the repo was scraped from GitHub
+
+We start by retrieving repositories with more than **900** stars using **two-month tumbling windows**. If we hit the **1000** repository limit per window (for a personal GitHub account), we shorten the
+search space to a **one-month window** and restart the iteration. Otherwise, the window advances by two months. Once the timeframe until **April 2024** is covered, we reduce the star search space: between **900** and **100** stars, we decrease the interval by **50** (e.g. search between [900, 850]), between **100** and **10** stars, we decrease the interval by **10**, and for the last **10** stars, we decrease by **1**. Since most repositories fall within the **0-100 star range** (e.g. Figure 1 showcases the distribution of repositories with up to **500** stars for Java), using the **creation date** and **star count** filters helps us avoid API limits and scrape more data by narrowing the search space. 
+The creation date window can be reduced even further (week or day level), in order to extract more data. After retrieving the repositories, we extract all the files corresponding to each language. We extend the programming languages extension list used for [The Stack](https://gist.github.com/ppisarczyk/43962d06686722d26d176fad46879d41) with 4 languages: EJS, Raku, Starlark, and WebAssembly. 
+
+The final dataset structure is shown in the example below.
+
+```json
+{
+    "file_name": "Font.java",
+    "file_path": ".../lateralgm/resources/Font.java",
+    "content": "*/ package org.lateralgm.resources; import java.util.EnumMap; import org.lateralgm.main.Prefs; ...",
+    "file_size": 1,985,
+    "language": "Java",
+    "extension": ".java",
+    "repo_name": "lwizchz/GameMaker-HTML5-Player",
+    "repo_stars": 22,
+    "repo_forks": 9,
+    "repo_open_issues": 0,
+    "repo_created_at": "2011-09-10T16:05:20Z",
+    "repo_pushed_at": "2013-05-06T23:00:17Z",
+    "sha": "00046809b218b2c058f4be7...",
+    "exact_duplicates_stackv1": False,
+    "exact_duplicates_stackv2": True,
+    "near_duplicates_stackv1": True,
+    "near_duplicates_stackv2": False,
+     ....
+ 
+  } 
+
+```
+
+### Dataset Fields
+
+- **file_name**: name of the file extracted from its repo
+- **file_path**: path to the file in its repo
+- **content**: content of the file
+- **file_size**: size of the file
+- **language**: language of the file
+- **extension**: language extension of the file
+- **repo_name**: complete name of the file's repo
+- **repo_stars**: number of stars of the file's repo
+- **repo_forks**: number of forks of the file's repo
+- **repo_open_issues**: number of open issues of the file's repo at the extraction date
+- **repo_created_at**: creation date of the file's repo
+- **repo_pushed_at**: date of the most recent push to the file's repo until the extraction date
+- **sha**: sha value of the file's content
+- **exact_duplicates_stackv1**: boolean flag stating if there are any exact duplicate files from The Stack 
+
+<!-- ![image/png](https://cdn-uploads.huggingface.co/production/uploads/66a89f0fd6625ead0411af50/fctcChY0DRwxMeXazUWUV.png) -->
+<div style="text-align: center;">
+    <img src=https://cdn-uploads.huggingface.co/production/uploads/66a89f0fd6625ead0411af50/fctcChY0DRwxMeXazUWUV.png alt="Figure 1: Distribution of scraped repositories with at most 500 stars." style="display: block; margin: 0 auto; width: 600px; height: auto;" />
+    <p><b>Figure 1:</b> Distribution of scraped repositories with at most 500 stars.</p>
+</div>
+
+
+# Cleaning
+
+The next stage in our dataset pipeline is the cleaning procedure. We exclude Java files **larger than 50 MB** and those with **fewer than 10 words**.
+
+# Deduplication
+
+The final stage of our dataset pipeline is the deduplication process. Firstly, we remove any potential duplicated repositories obtained due to the pagination process. We then perform **exact deduplication** between **our dataset and the Java-Stack v2**, and **within our dataset itself**, using the **sha256** function to generate hashes for each file.
+We choose this hash function because it provides a uniform distribution of hash values, minimizes collisions, and ensures even distribution across the hash space.
+For **near-deduplication**, we use the **MinHashLSH** algorithm from the [*datasketch1*](https://ekzhu.com/datasketch/lsh.html) library. To calculate the minhashes, we use the same hash function as above, but we extract the first 16 bytes to generate 128-bit hash values. 
+This approach balances the need for a strong hash function with the efficiency of a shorter hash length. 
+
+Additionally, we use **128** file permutations for LSH, with weights of **0.4** for **precision** and **0.6** for **recall**. We generate **7-character shingles** after [lowercasing the file content and removing whitespace](http://infolab.stanford.edu/~ullman/mmds/book.pdf). 
+We find that 7-shingles provide a reasonable trade-off between the number of shingles and the data processed, being small enough to keep the number of unique shingles manageable yet large enough to provide meaningful comparisons. 
+It was shown that the number of shingles should be large enough to ensure a low probability of shingles appearing across documents, with **k = 5** suggested for smaller documents such as [emails](http://infolab.stanford.edu/~ullman/mmds/book.pdf). 
+However, Java files usually contain a **larger dictionary** of characters than emails, including arithmetic and comparison operators which are less frequent in emails. 
+Thus, given the increased **complexity** and **size** of Java files, we consider 7-shingles to be appropriate to capture sufficient context, ensuring uniqueness and **reducing false positives**, which smaller shingles such as k = 5 might fail to achieve. 
+Furthermore, **k = 9** was shown to be a safe choice for [large research articles](http://infolab.stanford.edu/~ullman/mmds/book.pdf), however, for our needs, 7-shingles strike a balance between accuracy and
+computational efficiency, crucial for handling the **Java-Stack v2’s size** of over **222 M** files. This choice provides better computational efficiency by reducing the number of comparisons while maintaining a manageable shingle space.
+Lastly, we use a **Jaccard similarity threshold** of **0.7**, which proved to be efficient for both [SantaCoder](https://arxiv.org/abs/2301.03988) and [StarCoder](https://arxiv.org/abs/2305.06161) models. Such a high threshold
+reduces false positives, leading to fewer unnecessary comparisons and lower computational overhead. Moreover, this standard threshold value has been shown to be [robust for duplicate detection](https://dl.acm.org/doi/10.1145/3359591.3359735). 
+
+Instead of removing near-duplicates, we introduce a new feature to our dataset, called *near_dups_stkv2_idx*. This feature is a list of IDs of the near-duplicate files from the Java-Stack v2 corresponding to the current file in our dataset.
+The table below shows the number of files removed by each preprocessing method and the final number of files we are left with in the end (excluding near-duplicates). 
+Starting with **7.8 M** files, we are left with about **2.13 M** after applying all pre-processing methods (this includes near-duplicates). 
+Of the removed files, approximately **5.63 M** are exact duplicates (including about **0.87 M** from Java-Stack v2), and **0.8 M** are near-duplicates from Java-Stack v2. 
+This implies that training any LLM on Stack v2 will breach copy-left code licenses, despite the dataset creators’ claim that files under such licenses were removed.
+
+### Files removed by each pre-processing method
+| **Method**    | **#Files** |
+| :--------: | :-------: |
+| Raw dataset  | 7.80 M    |
+| Auto-generated |   0.04 M   |
+| Exact-deduplication    | 5.63 M    |
+| Near-deduplication |    0.80 M    |
+| Final dataset | 1.33 M |
+
+
+# Usage 
+
+By default, the dataset includes near-duplicate entries from Java-Stack v2, with their IDs listed in the *near_dups_stkv2_idx* field. 
+*An entry with an empty list in this field indicates that no near-duplicate files were found in Java-Stack v2 for that specific file.* 
+
+Near-duplicates can be removed as shown in the example below.
+
+```python
+from datasets import load_dataset
+
+# Load dataset
+dataset = load_dataset("LaughingLogits/Stackless_Java_V2")
+
+# Load train split (only one split available)
+dataset = load_dataset("LaughingLogits/Stackless_Java_V2", split="train")
+
+# Dataset streaming
+data = load_dataset("LaughingLogits/Stackless_Java_V2", split="train", streaming= True)
+for sample in iter(data):
+    print(sample["content"])
+
+# Filter dataset to not include near-duplicates from Java-Stack v2
+dataset = load_dataset("LaughingLogits/Stackless_Java_V2", split="train")
+near_deduplicated_dataset = dataset.filter(lambda sample: len(sample["near_dups_stkv2_idx"]) == 0)
+
+```