scientific visualization | UCSC OSPO

Mediglot

Tue, 04 Feb 2025 00:00:00 +0000

PolyPhy is a GPU-oriented agent-based system for reconstructing and visualizing optimal transport networks defined over sparse data. Rooted in astronomy and inspired by nature, we have used an early prototype called Polyphorm to reconstruct the Cosmic web structure, but also to discover network-like patterns in natural language data. You can see an instructive overview of PolyPhy in our workshop and more details about our research here. Recent projects, such as Polyglot and Mediglot have focused on using PolyPhy to better visualize language embeddings.

Medicinal Language Embeddings

Topics: Large Language Models NLP Embeddings Medicine
Skills: Python, JavaScript, Data Science, Technical Communication
Difficulty: Challenging
Size: Large (350 hours)
Mentors: Oskar Elek, Kiran Deol

This project aims to refine and enhance Mediglot, a web application for visualizing 3D medicinal embeddings, which extends the Polyglot app and leverages the PolyPhy toolkit for network-inspired data science. Mediglot currently enables users to explore high-dimensional vector representations of medicines (derived from their salt compositions) in a 3D space using UMAP, as well as analyze similarity through the innovative Monte-Carlo Physarum Machine (MCPM) metric. Unlike traditional language data, medicinal embeddings do not have an inherent sequential structure. Instead, we must work with the salt compositions of each medicine to create embeddings that are faithful to the intended purpose of each medicine.

This year, we would like to focus on exploring and integrating state-of-the-art AI techniques and algorithms to improve Mediglot’s clustering capabilities and its representation of medicinal data in 3D. The contributor will experiment with advanced large language models (LLMs) and cutting-edge AI methods to develop innovative approaches for refining clustering and extracting deeper insights from medicinal embeddings. Beyond LLMs, we would like to experiment with more traditional language processing methods to design novel embedding procedures. Additionally, we would like to experiment with other similarity metrics. While the similarity of two medicines depends on the initial embedding, we would like to examine the effects of different metrics on the kinds of insights a user can extract. Finally, the contributor is expected to evaluate and compare different algorithms for dimensionality reduction to enhance the faithfulness of the visualization and its interpretability.

The ideal contributor for this project has experience with Python (and common scientific toolkits such as NumPy, Pandas, SciPy). They will also need some experience with JavaScript and web development (MediGlot is distributed as a vanilla JS web app). Knowledge of embedding techniques for language processing is highly recommended.

Specific tasks:

Closely work with the mentors to understand the context of the project and its detailed requirements in preparation for the proposal.
Become acquainted with the tooling (PolyPhy, PolyGlot, Mediglot) prior to the start of the project period.
Explore different embedding techniques for medicinal data (including implementing novel embedding procedures).
Explore different dimensionality reduction techniques, with a focus on faithful visualizations.
Document the process and resulting findings in a publicly available report.

Enhancing PolyPhy Web Application

Topics: Web Development UI/UX Design Full Stack Development JavaScript Next.js Node.js
Skills: Full Stack Web Development, UI/UX Design, JavaScript, Next.js, Node.js, Technical Communication
Difficulty: Challenging
Size: Medium (175 hours)
Mentors: Oskar Elek, Kiran Deol

This project aims to revamp and enhance the PolyPhy web platform to better support contributors, users, and researchers. The goal is to optimize the website’s UI/UX, improve its performance, and integrate Mediglot to provide users with a seamless experience in visualizing both general network structures and 3D medicinal embeddings.

The contributor will be responsible for improving the website’s overall look, feel, and functionality, ensuring a smooth and engaging experience for both contributors and end-users. This includes addressing front-end and back-end challenges, optimizing the platform for better accessibility, and ensuring seamless integration with Mediglot.

The ideal candidate should have experience in full-stack web development, particularly with Next.js, JavaScript, and Node.js, and should be familiar with UI/UX design principles. A strong ability to communicate effectively, both in writing and through code, is essential for this role.

Specific tasks:

Collaborate with mentors to understand the project’s goals and the specific requirements for the website improvements.
UI/UX Redesign:
- Redesign and enhance the website’s navigation, layout, and visual elements to create an intuitive and visually engaging experience.
- Improve mobile responsiveness for broader accessibility across devices.
Website Performance & Stability:
- Identify and resolve performance bottlenecks, bugs, or issues affecting speed, stability, and usability.
Mediglot Integration:
- Integrate the Mediglot web application with PolyPhy, ensuring seamless functionality and a unified user experience for visualizing medicinal data alongside general network reconstructions.
Documentation:
- Document the development process, challenges, and solutions in a clear and organized manner, ensuring transparent collaboration with mentors and the community.

PolyPhy

Mon, 01 Jan 2024 00:00:00 +0000

PolyPhy is a GPU oriented agent-based system for reconstructing and visualizing optimal transport networks defined over sparse data. Rooted in astronomy and inspired by nature, we have used an early prototype called Polyphorm to reconstruct the Cosmic web structure, but also to discover network-like patterns in natural language data. You can see an instructive overview of PolyPhy in our workshop and more details about our research here.

Under the hood, PolyPhy uses a richer 3D scalar field representation of the reconstructed network, instead of a typical discrete representation like a graph or a mesh. The ultimate purpose of PolyPhy is to become a toolkit for a range of specialists across different disciplines: astronomers, neuroscientists, data scientists and even artists and designers. PolyPhy aspires to be a tool for discovering connections between different disciplines by creating quantitatively comparable structural analytics.

PolyPhy Web Presence

Topics: Web Development UX Social Media
Skills: full stack web development, Javascript, good communicator
Difficulty: Challenging
Size: Large (350 hours)
Mentors: Oskar Elek, Ezra Huscher

The online presentation of a software project is without a doubt one of the core ingredients of its success. This project aims to develop a sustainable web presentce for PolyPhy, catering to interested contributors, active collaborators, and users alike.

Specific tasks:

Closely work with the mentors on understanding the context of the project and its detailed requirements in preparation of the proposal.
Port the existing website into a more modern Javascript framework (such as Next.js) that provides a user-friendly CMS and admin interface.
Update the contents of the website with new information from the repository repository page as well as other sources as directed by the mentors.
Develop a simple functional system for posting updates about the project to selected social media and other communication platforms (LinkedIn, Twitter/X or Mastodon, mailing list) which will also be reflected on the website.
Optional: improve the UX of the website where needed.
Optional: implement website analytics (visitor stats etc).

Data Visualization and Analysis with PolyPhy/Polyglot

Topics: Data Science Data Visualization Point Clustering 3D Neural Embeddings
Skills: data science, Python, Javascript, statistics, familiarity with AI and latent embedding spaces a big plus
Difficulty: Challenging
Size: Large (350+ hours)
Mentors: Oskar Elek, Kiran Deol

The aim of this project is to explore a novel data-scientific usecase using PolyPhy and its associated web visualization interface PolyGlot. The contributor is expected to identify a dataset they are already well familiar with, and that fits the application scope of the PolyPhy/PolyGlot tooling: a complex point cloud arising from a 3D or a higher dimensional process which will benefit from latent pattern identification and a subsequent visual as well as quantitative analysis. The contributor needs to have the rights for using the dataset - either by owning the copyright or via the open-source nature of the data.

Specific tasks:

Closely work with the mentors on understanding the context of the project and its detailed requirements in preparation of the proposal.
Become acquainted with the tooling (PolyPhy, PolyGlot) prior to the start of the project period.
Document the nature of the target dataset and define the complete data pipeline with assistance of the mentors, including the specific analytic tasks and objectives.
Implement the data pipeline in PolyPhy and PolyGlot.
Document the process and resulting findings in a publicly available report.

Polyphorm / PolyPhy

Thu, 15 Dec 2022 00:00:00 +0000

PolyPhy infrastructure engineering and practices

Topics: DevOps Code Refactoring CI/CD
Skills: fluidity in Python, experience with OOP, experience with building and packaging libraries, understanding GitHub and its tools ecosystem
Difficulty: Challenging
Size: 350+ hours
Mentors: Oskar Elek, Anisha Goel
Contributor(s): Prashant Jha

Your responsibility in this project will be developing new infrastructure of the PolyPhy project as well as maintaining the existing codebases. This is a multifaceted role that will require coordination with the team and active approach to understanding the technical needs of the community.

Specific tasks:

Work with the technical lead to develop effective interfaces for PolyPhy, providing access to its functionality on the level of both Python/Jupyter code and the command line.
Maintain the existing codebase and configure it according to the team’s needs.
Develop and extend the current CI/CD functionality and related code metrics.
Document the best practices related to the above.

Write PolyPhy’s technical story and content

Topics: Writing Documentation Storytelling
Skills: experienced writing structured text, well read, technical or scientific education, webdev basics (preferably NodeJS)
Difficulty: Moderate
Size: 350 hours
Mentors: Oskar Elek, Ezra Huscher

Integral to PolyPhy’s presentation is a “story” - a narrative understanding - that the users and the project contributors can relate to. Your responsibility will be to develop the written part of that understanding, as well as major portions of technical documentation that match it.

Specific tasks:

Work with mentors on understanding the context of the project.
Write and edit diverse pages of the project website.
Work with mentors to improve project’s written community practices (diversity, communication).
Write and edit narrative and explanatory parts of PolyPhy’s documentation.
Create tutorials that present core functionality of the toolkit.

Community engagement and management

Topics: Community Management Social Media Networking
Skills: documented experience with current social media landscape, social and well spoken, ability to communicate technical concepts
Difficulty: Moderate
Size: 175 or 350 hours
Mentors: Oskar Elek, Ezra Huscher

Your responsibility will be to build and engage the community around PolyPhy. This includes its standing team and stakeholders, current expert users, potential adopters as well as the general public. The scope (size) of the project depends on the level of commitment during and beyond the Summer and is negotiable upfront.

Specific tasks:

Manage the team’s communication channels (Slack, Zoom, email) and maintain active presence therein.
Develop social media presence for PolyPhy on Twitter, LinkedIn and other selected social media platforms.
Manage and extend the online presence for the project, including its website, mailing list, and other applicable outreach activities.
Research and engage with new communities that would benefit from PolyPhy, both as its expert users and contributors.