Blog Posts
Welcome to my collection of blog posts on genomics, generative modeling, and bioinformatics research.
Recent Posts
Squidiff: Conditional Diffusion for Single-Cell Development and Perturbation Prediction
April 11, 2026
A synthesis of Squidiff, a conditional diffusion model for predicting single-cell transcriptomes along developmental trajectories and under perturbations, with semantic latent conditioning, DDIM sampling, and critical discussion of evidence strength, OOD masking experiments, and reproducibility (code, PyPI, checkpoints, license hygiene).
Topics covered:
- Semantic-conditioned diffusion and diffusion-autoencoder motivation
- Datasets: differentiation, gene and drug perturbation, organoids, irradiation
- Comparisons to scGen, GEARS, and the broader VAE / OT / GNN landscape
- Evaluation metrics, limitations, and practical validation strategies
A Synthesis of Multimodal Reasoning in Genomics: Analyzing BioReason and Genome-Bench in the Context of GWAS
September 27, 2025
An exploration of the paradigm shift in computational genomics from statistical associations to mechanistic biological understanding. This post examines how BioReason and Genome-Bench are advancing the field beyond traditional GWAS approaches.
Topics covered: - Evolution of genomic analysis approaches - From GWAS to multimodal reasoning - The BioReason architecture - Genome-Bench evaluation framework - Future directions in computational genomics
Comparative Analysis: DNA-Diffusion and DiscDiff in Genomic Sequence Generation
August 19, 2025
An in-depth comparison of two cutting-edge diffusion models for genomic sequence generation: DNA-Diffusion and DiscDiff. This analysis explores their architectures, performance metrics, and implications for the future of generative modeling in genomics.
Topics covered: - Diffusion models in genomics - Architecture comparison of DNA-Diffusion and DiscDiff - Performance evaluation and benchmarks - Applications in genomic research - Future directions in generative genomics
AlphaGenome Evolution: Advancing Regulatory Variant Prediction and Genomic Modeling
August 2, 2025
A comprehensive exploration of AlphaGenome’s capabilities in regulatory variant prediction and its integration with advanced DNA language models for enhanced genomic modeling. This post synthesizes insights from two key papers on AlphaGenome’s evolution and its applications in genomic prediction.
Topics covered: - Regulatory variant effect prediction - Integration with advanced DNA language models for enhanced genomic modeling - Multi-scale genomic modeling approaches - Clinical and research applications - Future directions in genomic prediction
More posts coming soon!