Building AI agents, exploring cognitive science, unraveling bioinformatics

Six ancient questioning techniques map onto the most effective LLM prompting strategies with uncomfortable precision, and what that reveals about these models is more interesting than the performance gains.

How do you verify scientific knowledge when there are 2.9 million papers on arXiv alone, with thousands more added every day? A new paper extracts nearly two million claims from 16,087 manuscripts and compares machine evaluation to human peer review, with 81% agreement.

Over 80% of developers now use AI assistants for code generation, yet at least 62% of AI-generated code contains vulnerabilities. As AI writes code faster than humans can review it, the engineer's primary job shifts from writing code to verifying it through formal methods.

Structure-based and ligand-based drug design evolved as separate fields solving the same problem. ConGLUDe, a contrastive geometric learning model, unifies both approaches and outperforms specialist methods on realistic benchmarks without requiring pre-defined binding pockets.

Google DeepMind's AlphaGenome reads 1 million base pairs of DNA and predicts thousands of regulatory functions at single-nucleotide resolution, beating 25 of 26 specialized models.

AlphaGenome processes 1 million DNA base pairs to predict variant effects across 7,000+ genomic tracks in one second, outperforming specialized models on 25 of 26 VEP benchmarks.

A technical look at AlphaGenome's architecture, its 2D pairwise embeddings for splicing prediction, and what the model means for clinical variant interpretation.

Basecamp Research's EDEN model trains on proprietary environmental metagenomics to design gene-insertion enzymes, antimicrobial peptides, and synthetic microbiomes -- all validated in the wet lab.

A practical guide to selecting genomic foundation models for bioinformatics tasks. Covers ESM-2, DNABERT-2, HyenaDNA, Nucleotide Transformer, scGPT, and Evo with specific recommendations for DNA sequence analysis, protein structure prediction, and single-cell analysis based on hardware requirements, inference speed, and task type.

How TTT-E2E achieves constant inference latency regardless of context length by treating long context as a learning problem rather than an architecture problem.

A technical deep dive into DeepSeek's Engram architecture, which introduces conditional memory as a new axis of sparsity for large language models.

How the same transformer architecture powering GPT learned to predict molecular properties by treating chemistry as a language problem

How researchers adapted BERT for molecular property prediction, turning SMILES strings into drug discovery insights

How generative diffusion models can serve as fast surrogates for expensive biological simulations, achieving 22x speedup while preserving the stochastic diversity that makes these models scientifically useful.

Machine learning models now outperform FDA-approved biomarkers in predicting treatment response, but the best-performing models often resist explanation. Here's how precision oncology is navigating the trade-off between performance and interpretability.