Mohamed Saeed | UCSC OSPO

Final Blog on Using Reproducibility in Machine Learning Education

Wed, 18 Oct 2023 00:00:00 +0000

Welcome back!

In my final blog post for the 2023 Summer of Reproducibility Fellowship, I’ll be sharing my experiences and the materials I’ve created for the Using Reproducibility in Machine Learning Education project. As a quick reminder, my mentor Fraida Fund and I have been working on developing interactive open-source educational resources that teach reproducibility and reproducible research in machine learning. You can find my proposal here.

In this post, I’ll give you a rundown of my experience and share the materials I’ve created. If you haven’t checked out my previous blog posts, definitely take a look before diving into this one. Let’s get started!

Why is this project important 🤔

Reproducibility is an essential aspect of scientific research, and it’s becoming increasingly important in the field of computer science. However, most efforts to promote reproducibility in education focus on students who are actively involved in research, leaving a significant gap in the curriculum for introductory courses. Our project aims to address this issue by incorporating reproducibility experiences into machine learning education.

Why Reproducibility Matters in Education 🎓

There are two primary reasons why we believe reproducibility belongs in the computer science classroom. Firstly, it allows students to experience the process of reproducing research firsthand, giving them a deeper understanding of the scientific method and its importance in the field. This exposure can inspire students to adopt reproducible practices in their future careers, contributing to a more transparent and reliable scientific community.

Source: Fund, Fraida. “We Need More Reproducibility Content Across the Computer Science Curriculum.” Proceedings of the 2023 ACM Conference on Reproducibility and Replicability. 2023.

Secondly, as shown in the figure, involving students in reproducibility efforts can have a significant impact on the reproducibility ecosystem itself. Students can create reproducibility artifacts, such as replicable experiments or data analysis, that can be used by other researchers, including authors and graduate students. Additionally, students can consume reproducibility artifacts created by the research community, provide feedback, and suggest improvements. Authors appreciate this type of engagement, as it adds value to their work and promotes open science.

Focusing on Machine Learning 🧐

Given the growing interest in machine learning and its relevance to reproducibility, our project decided to focus on this area. Machine learning already has a strong culture of reproducibility, with initiatives like Papers with Code and the ML Reproducibility Challenge. These efforts encourage researchers to share their code and reproduce recent machine learning papers, validating their results. By leveraging these existing resources, we can create learning materials that utilize real-world examples and foster hands-on reproducibility experiences for students.

The Interactive Notebooks 📖

We have created two learning materials that focus on machine learning and reproducibility. The first material looks at a paper titled “On Warm Starting Neural Network Training” by Jordan T. Ash and Ryan P. Adams. This paper discusses the concept of warm-starting, which involves using weights from a previously trained model on a subset of the dataset to train a new model. The authors compare the performance of warm-started models with randomly initialized models and find that the warm-started models perform worse as shown in the below figure.

Our material takes students through the process of identifying the different claims made in the paper and finding the corresponding experiments that support them. They will also learn how to use open-source code and available data to reproduce these experiments and understand the computational complexity associated with reproducing each experiment. This material can be found on both github and chameleon where you can use chameleon to run the material on the required resources.

The second material examines the paper “An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale” by Dosovitskiy et al., which introduces a novel way of applying the transformer architecture, which was originally designed for natural language processing, to image recognition tasks. The paper shows that transformers can achieve state-of-the-art results on several image classification benchmarks, such as ImageNet, when trained on large-scale datasets as shown in the following table.

Our material guides students through the process of understanding which claims can and cannot be validated based on the available datasets and how complex it can be to validate each claim. Additionally, they will learn how to use pre-trained models to replicate computationally expensive experiments. Again this material can be on both github and chameleon.

Both materials are designed to be easy to understand and interactive, allowing students to engage with the content and gain a deeper understanding of the concepts. Instructors can use these materials to assess their students’ understanding of machine learning and reproducibility.

Reflecting on the Journey

As we wrap up our journey of creating beginner-friendly learning materials for machine learning using reproducibility, it’s time to reflect on the rewarding experiences and valuable lessons learned along the way. Our deep dive into the world of machine learning and reproducibility not only enriched our knowledge but also provided us with an opportunity to contribute to the community at the UC Open Source Symposium 2023 at UCSC.

The symposium was a memorable event where we presented our work in a poster session. The diversity of the audience, ranging from professors and researchers to students, added depth to our understanding through their valuable feedback and insights. It was intriguing to see the potential applications of our work in various contexts and its capacity to benefit the broader community.

This project has been a personal journey of growth, teaching me much more than just machine learning and reproducibility. It honed my skills in collaboration, communication, and problem-solving. I learned to distill complex ideas into simple, accessible language and create engaging, interactive learning experiences. The most fulfilling part of this journey has been seeing our work come alive and realizing its potential to positively impact many people. The gratification that comes from creating something useful for others is unparalleled, and we are thrilled to share our materials with the world.

Your time and interest in our work are greatly appreciated! Hope you enjoyed this blog!

Learning Machine Learning by Reproducing Vision Transformers

Fri, 06 Oct 2023 00:00:00 +0000

Hello again!

In this blog post, I will be discussing the second material I created for the 2023 Summer of Reproducibility Fellowship. As you may recall from my first post, I am working on the Using Reproducibility in Machine Learning Education project with Fraida Fund as my mentor. My goal is to create interactive open-source educational resources that teach reproducibility and reproducible research in machine learning (ML), as outlined in my proposal.

In this post, I will share with you my second material, and how it can be helpful in machine learning class to teach students about vision transformers and reproducibility at the same time. If you haven’t seen my first work, be sure to check out my previous blog post. Without further ado, let’s dive in!

Reproducing “An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale”

This material is a reproduction of Dosovitskiy et al.‘s 2020 paper, “An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale”. This paper introduces the Vision Transformer (ViT), a novel architecture that applies the transformer model, originally designed for natural language processing tasks, to image recognition. The ViT model achieves state-of-the-art performance on several image classification benchmarks, demonstrating the potential of transformers for computer vision tasks.

The figure illustrates the key idea behind ViT, which is to treat an image as a sequence of patches, similar to how a transformer treats a sentence as a sequence of words. Each patch is flattened into a vector and fed into the transformer encoder, which learns to capture the complex relationships between these patches. The resulting representation is then fed into an MLP head, which produces a final prediction for the image. This approach allows ViT to handle large input images and capture both global context and fine-grained details. ViT models can also be pre-trained on large datasets and fine-tuned on smaller datasets for improved performance.

To reproduce this paper, I followed a systematic approach to ensure reliable results:

Critically analyze the paper’s qualitative and quantitative claims.
Identify the necessary experiments to verify each claim.
Determine the required data, code, and hyperparameters for each experiment.
Utilize pre-trained models for validating claims that require high computational resources.
Investigate resources shared by the authors, such as code, data, and models.
Assess the feasibility of verifying different types of claims.
Design new experiments for validating qualitative claims when certain models or datasets are unavailable.

I utilized Chameleon as my platform for conducting and documenting my reproduction experiments. Chameleon is a large-scale, reconfigurable experimental environment that supports computer science systems research. It enables users to create and share Jupyter notebooks capable of running Python code on Chameleon’s cloud servers. For this work, a GPU with 24GB or more memory is required to run the notebooks on GPU, which Chameleon offers in its variety of GPUs.

I have set up a GitHub repository where you can access all of my reproduction work. The repository contains interactive Jupyter notebooks that will help you learn more about machine learning and the reproducibility of machine learning research. These notebooks provide a hands-on approach to understanding the concepts and techniques presented in my reproduction work.

Challenges

Reproducing a paper can be a challenging task, and I encountered several obstacles during the process, including:

The unavailability of pretraining datasets and pretrained models
Inexact or unspecified hyperparameters
The need for expensive resources for some hyperparameters
The use of different frameworks for baseline CNNs and Vision Transformers

These issues posed significant difficulties in replicating the following table, a key result from the Vision Transformer paper that demonstrates its superiority over prior state-of-the-art models.

To overcome these challenges, I used the same models mentioned in the paper but pretrained on different datasets, experimented with various hyperparameter combinations to achieve the best results, and wrote my own code to ensure that both the baseline and Vision Transformer were fine-tuned using the same framework. I also faced other challenges, which I discussed in my notebooks along with the solutions I applied.

How to use this material?

This material consists of a series of notebooks that guide you through the paper, its claims, experiments, and results. You will learn how to analyze, interpret, and validate the authors’ claims. To get started, I recommend briefly skimming the original paper to gain an understanding of the main ideas and public information. This will help you see how the authors could have been more transparent and clear in certain sections. The notebooks provide clear instructions and explanations, as well as details on how I addressed any missing components.

Conclusion

In this blog post, I’ve walked you through the contents of this material and the insights users can gain from it. This material is particularly intriguing as it replicates a paper that has significantly influenced the field of computer vision. The interactive nature of the material makes it not only educational but also engaging and enjoyable. I believe users will find this resource both fun and beneficial.

I hope you found this post informative and interesting. If you have any questions or feedback, please feel free to contact me. Thank you for reading and stay tuned for more updates!

Introducing Levels of Reproduction and Replication in Machine Learning

Wed, 02 Aug 2023 00:00:00 +0000

Hello again,

I am Mohamed Saeed and this is my second blog post for the 2023 Summer of Reproducibility Fellowship. As you may recall from my previous post, I am working on the Using Reproducibility in Machine Learning Education project with Fraida Fund as my mentor. My goal is to create interactive open educational resources that teach reproducibility and reproducible research in machine learning (ML) as I proposed.

In this post, I will share with you some of the progress I have made so far, as well as some of the challenges I have faced and how I overcame them. I will also highlight some of the specific accomplishments that I am proud of and what I plan to do next.

Reproducing “On Warm Starting Neural Network Training”

This material is a reproduction of the paper “On Warm Starting Neural Network Training” by Jordan T. Ash and Ryan P. Adams (2020). This paper investigates the effect of warm-starting neural networks, which means using the weights of previous models trained on a subset of the data, to train on a new dataset that has more data.

The figure illustrates how the new model uses the weights from the previous model as its initial values. This allows the new model to train on both the “Original” data, which it has already seen, and the new data, which it has not encountered before. In contrast, the randomly initialized model treats the entire data as unfamiliar and starts from scratch.

The paper also shows that this method can lead to lower test accuracy than starting from scratch with random weights, even though the training loss is similar. The paper also proposes a simple way to improve the test accuracy of warm-starting by adding some noise to the previous weights.

To reproduce this paper, I followed a systematic approach that ensured reliable results. This approach involved:

Reading the paper and its main claims carefully.
Finding out what resources the authors shared, such as code, data, and models.
Looking for additional materials online that could help me save time and fill in the gaps left by the authors.
Setting up the environment and dependencies needed to run the code smoothly.
Writing code and updating any outdated functions that might cause errors.
Running the code and verifying that it matched the results reported in the paper.
Analyzing and interpreting the results and comparing them with the paper’s findings.

I used Chameleon as my platform for running and documenting my reproduction experiments. Chameleon is a large-scale, reconfigurable experimental platform that supports computer science systems research. It allows users to create and share Jupyter notebooks that can run Python code on Chameleon’s cloud servers.

I created a GitHub repository where you can find all related to my reproduction work in the form of interactive jupyter notebooks that will help you learn more about machine learning and reproducibility of machine learning research.

Challenges

Reproducing a paper is not an easy task. I faced several challenges along the way. One of the biggest challenges was the lack of code and pretrained models from the authors. This is a common problem for many reproducibility projects. Fortunately, I found a previous reproducibility publication for this paper on ReScience journal. I used some of their code and added some new functions and modifications to match the original paper’s descriptions. I also encountered other challenges that I discussed in the notebooks with the solutions that I applied.

How to use this material?

This material is a series of notebooks that walk you through the paper and its claims, experiments, and results. You will learn how to analyze, explain, and validate the authors’ claims. To get started, I suggest you skim the original paper briefly to get the main idea and the public information. This will help you understand how the authors could have been more clear and transparent in some sections. I have given clear instructions and explanations in the notebooks, as well as how I dealt with the missing components. You can use this material for self-learning or as an assignment by hiding the final explanation notebook.

Conclusion and Future Work

In this blog post, I have shared with you some of my work on reproducing warm starting neural network training. I have learned a lot from this experience and gained a deeper understanding of reproducibility and reproducible research principles in ML.

I am very happy with what I have achieved so far, but I still have more work to do. I am working on reproducing the Vision Transformer: An Image is Worth 16x16 Words paper by Alexey Dosovitskiy et al. This time my approach is to use the available pretrained models provided by the authors to verify the claims made in the paper. However, there are some challenges that I face in reproducing the paper. For example, some of the datasets and code that the authors used are not publicly available, which makes it hard to replicate their experiments exactly. These challenges are common in reproducing research papers, especially in computer vision. Therefore, it is important to learn how to deal with them and find ways to validate some of the claims.

I hope you enjoyed reading this blog post and found it informative and interesting. If you have any questions or feedback, please feel free to contact me. Thank you for your attention and stay tuned for more updates!

Introducing Levels of Reproduction and Replication in Machine Learning

Thu, 01 Jun 2023 00:00:00 +0000

Greetings everyone,

I am Mohamed Saeed and I am delighted to be part of the 2023 Summer of Reproducibility program, where I am contributing to the Using Reproducibility in Machine Learning Education project.

My proposal was accepted, and I am fortunate to have Fraida Fund as my mentor. The objective of my project is to develop highly interactive open educational resources that can be utilized by instructors teaching graduate or undergraduate machine learning courses. These resources will focus on integrating instruction on reproducibility and reproducible research principles.

Understanding and practicing reproducibility in machine learning (ML) research is of utmost importance in today’s scientific and technological landscape. Reproducibility ensures the reliability, transparency, and credibility of ML findings and discoveries. By learning the principles of reproducibility, students from different levels can validate research results, test introduced methodologies, and understand level of reproducibilty of research.

My contribution will involve developing interactive educational resources that encompass code examples, writing exercises, and comprehensive explanations of key concepts of reproducing ML research. These resources will be carefully crafted to assist students at various levels of expertise. Our aim is for these resources to be widely adopted by instructors teaching graduate or undergraduate machine learning courses, as they seek to enhance the understanding of reproducibility and reproducible research principles.

I think this is a great opportunity to learn more about ML research reproducibility. I’ll be posting regular updates and informative blogs throughout the summer, so stay tuned!