Eric J Ma's Website

In this blog post, I explore the challenges biotech teams face when integrating public datasets with internal data for machine learning. Despite initial excitement, issues like data compatibility, missing variables, domain shifts, and biological complexity often arise. I suggest a shift from a machine learning perspective to a decision support approach, advocating for separate models and a decision fusion layer that incorporates human expertise. This method respects the complexity of biological systems and aids in effective decision-making. How can we better navigate these challenges to accelerate biotech discoveries?

When typing became physically demanding, I discovered that dictation tools could do more than just help me write – they could fundamentally change how I capture and develop ideas. Using Better Dictation and VoicePal, combined with AI assistance, I found a way to write that matches the natural flow of thought. This isn't just about accessibility or working around limitations; it's about finding a better way to translate the nonlinear, rapid-fire nature of our thoughts into written words. I share my approach to preserving authentic voice while using AI tools, and why sometimes constraints push us toward unexpected improvements in how we work.

In this post, I share a practical approach to managing secrets in data science workflows, learned from personal experience with both successes and mistakes. I cover essential tools like direnv and .env files for local development, strategies for secure secret handling in Jupyter notebooks, and crucial version control practices including pre-commit hooks to catch accidental API key commits. I also discuss team collaboration approaches for secret sharing, platform-specific secrets management features, and what to do when secrets accidentally get committed to repositories. While tools like AWS Secrets Manager exist for enterprise needs, I focus on practical, accessible methods that create robust security through layered defenses, following proven software development principles that apply equally well to data science work.

In this blog post, I explore what defines an LLM agent, highlighting its goal-oriented non-determinism, decision-making flow control, and natural language interfaces. I also discuss when to use agents, emphasizing the importance of variable scope inputs and constrained actions. By examining industry perspectives from Anthropic and Google, I also explore how agents can effectively handle diverse inputs while maintaining defined action boundaries. Real-world examples, like a bill calculation bot and a literature research assistant, illustrate these principles. How can these insights transform your approach to designing agent applications?

In this blog post, I reflect on my year-long challenge of writing a blog post every week, surpassing my goal with 53 posts. This journey taught me the power of consistency, improved my ability to communicate complex ideas, and helped me develop AI-assisted tools to streamline my workflow. I also explored the intersection of life sciences and computation, aiming to accelerate scientific discovery. How did these experiences shape my approach to integrating AI into creative processes and what insights can you gain from my journey?

In this blog post, I explore the challenges of extracting structured text from PDFs, especially when dealing with equations, tables, and figures. I discuss two tools, Nougat-OCR by Facebook Research and Docling by IBM, which I found effective for this task. Nougat-OCR excels at handling equations and tables, while Docling excels on extracting figures. By combining these tools, we can develop a workflow that captures all critical components of a PDF. Want to know how to retain valuable knowledge from complex PDFs?

In this blog post, I explore how to navigate and thrive during organizational changes. I share personal insights and practical strategies, such as focusing on meaningful relationships with colleagues, consistently delivering great work, and proactively building your career path. I also emphasize the importance of staying present and cultivating a 'career committee' of trusted advisors. Change is inevitable in any organization, but how we respond can transform these shifts into growth opportunities. Curious about how to build your own resilience in changing times?

In this blog post, I provide an overview of retrieval methods for Retrieval-Augmented Generation (RAG), exploring various methods like human-curated, exact keyword search, fuzzy keyword search, vector similarity search, and knowledge graph-based retrieval. Each method is dissected to reveal its unique strengths and ideal use cases, providing insights into how they can enhance RAG systems' performance. Curious about how these strategies can be combined for even more robust results?

In this blog post, I explore the innovative features of LlamaBot's new AgentBot, designed to simplify complex task automation. These agents operate with goal-oriented non-determinism, decision-making flow control, and natural language interfaces, making them powerful yet user-friendly. I also provide real-world examples, including a detailed walkthrough of a stock market analysis. Curious about how these agents can streamline your workflows and enhance the flexibility of your LLM applications?

Building data platforms at biotechs often fails because we ask scientists to change their workflow and manually catalog data. This leads to poor adoption, wasted engineering effort, and continued data accessibility problems. Instead of building new systems, I propose automatically capturing data sharing patterns that already exist. This approach:

• Reduces implementation costs by 60-80% compared to traditional platforms
• Requires zero change in scientist behavior
• Creates an automatically-maintained data catalog
• Enables rapid data discovery through social connections
• Can be implemented incrementally, showing value within 3-6 months