Eric J Ma's Website

In part 1 of a three-part series on protein language models, I do a deep dive into the fascinating world of protein language models (PLMs) for protein engineering, drawing parallels between PLMs and GenAI models like GPT-4. I explore three distinct applications: patent-breaking, prioritized deep mutational scans, and candidate expansion via natural mimicry, highlighting the goal of generating plausible protein sequences for diversification. I also touch upon the potential of PLMs for optimization, using mutational effect scores for predictive purposes. How can PLMs revolutionize protein engineering and what lies ahead in this promising field?

In this blog post, I share my enriching experience at SciPy 2024, from attending insightful tutorials on Quarto, LLMs, Anywidget, and handling large datasets, to delivering talks on fostering an open-source culture and LlamaBot. I also highlight the vibrant lightning talks, the collaborative sprints, and the engaging social activities that made this conference memorable. Not to forget, the delicious Tacoma cuisine that added flavor to the whole experience. Curious to know which tutorial inspired me to recreate my talks just for fun?

In this blog post, I share a cautionary tale from my work experience about the pitfalls of using pickle files for data storage, particularly highlighting their dependency on the computing environment and specific package versions. I encountered an issue when a notebook failed to run due to a pickle file not being compatible with the updated version of pandas. This experience led me to advocate for using native formats over pickles for better stability and reproducibility, and underscored the importance of software skills like continuous testing. How can we ensure our data storage methods don't become obsolete with evolving dependencies?

In this blog post, I reflect on two years of running quarterly docathons at work, dedicated two-day events focused on writing high-quality documentation. I discuss what docathons are, their purpose, and the simple yet effective way to organize them, emphasizing the importance of food, documentation, and optional workshops. Based on both cost and the invaluable benefits of improved documentation practices, I also discuss the significant return on investment these docathons have yielded. How can such a straightforward event substantially enhance the quality of documentation and team engagement? Read on to find out.

In this blog post, I share insights from a co-op performance calibration, highlighting the crucial difference between conversational and communication skills in the hiring process. I recount an experience where a candidate's excellent conversational abilities masked their technical skills, leading to a dilemma on whether to hire them. Drawing from Andy Grove's 'High Output Management,' I emphasize the importance of using interviews to gauge technical abilities effectively, advocating for code reviews as a high-bandwidth method to assess candidates' skills. This approach minimizes the risk of being misled by mere conversational charm. How can we better distinguish between conversational prowess and genuine communication skills in interviews?

In this blog post, I explore the importance of reproducibility and portability in data science, focusing on data access patterns. I introduce pins, an open-source tool that enables data scientists to reference data from a central source of truth and manage data versions explicitly. By using pins, we can avoid common pitfalls like non-reproducible analyses and streamline the process of accessing and versioning data. This approach not only enhances productivity but also ensures that data is accessed in a consistent and error-free manner. Curious about how pins and analogous tools can robustify your data science workflow?

In this blog post, I do a deep dive into the paper 'The Continuous Language of Protein Structure' by Billera et al., which explores generating protein backbones using autoregressive models and the von Mises mixture model for sampling dihedral angles. This approach challenges the traditional discrete output of autoregressive models by producing continuous values, specifically for modeling protein structures. I discuss the technical and scientific premises, the role of the von Mises distribution, and the potential issue of non-identifiability in mixture models. How does this method open new avenues in protein structural modeling? Read on to find out.

In this blog post, I share how to resolve CUDA backend initialization issues when installing JAX with CUDA, specifically addressing outdated cuDNN versions. I detail a method using Conda environments to manage CUDA installations and set environment variables correctly, offering two solutions: configuring LD_LIBRARY_PATH through Conda's activate.d and deactivate.d scripts, or directly within a Python session using a .env file. Both approaches aim to ensure that JAX utilizes the correct CUDA libraries, but each has its tradeoffs regarding portability. Curious about which method might work best for your setup?

In this blog post, I explore multi-modality deep learning based on two papers from the biomedical world, in which we explore the definition of data modalities, what fusion is and how it takes place within a model, and possible training objectives. In this post, I also considers how to utilize these models with only one input modality available, highlighting the potential for protein function prediction and sequence generation. How can multi-modal deep learning transform our approach to complex data analysis?

In this blog post, I share my journey of learning to script PyMOL directly from Jupyter notebooks, a skill I picked up with the help of GPT-4. I detail the process of installing PyMOL, setting up the environment, and scripting to process and visualize protein structures, specifically nanobody VHH structures. I also demonstrate how to plot these structures in a grid using matplotlib. But the more important lesson here is how quickly I was able to pick it up, thanks to GPT-4! Are you able to leverage LLMs as a skill-learning hack?