Mechanistic Research
Validating causal mechanisms across the sciences.
Mechanistic Validity
Domain-general evidence standards for what warrants a mechanistic claim, how to resolve disputes about underlying mechanisms, and when a finding transfers between systems.
Frameworks 3 papersReproducible Science
Command-line tools that freeze a preregistered plan before it runs, bind every number in a paper to the run that produced it, and check that quoted passages appear in their sources.
Software 1 packageSingle-cell Foundation Models
Foundation model embeddings ranked at chance by 5/5 existing metrics. Derived analytic failure bound and validated replacement metric across 25 tissues.
Evaluation Validity 1 paperRNA/DNA Foundation Models
8/10 foundation models have no structural awareness after controlling for nucleotide composition confound. Graded evaluation across 52 Rfam families.
Evaluation Validity 1 paperPerturbation Biology
Developed a metric for predicting drug mechanism transport across cell lines, tested on transcriptomic, genetic perturbation, and cell painting data.
Mechanism Transport 3 papersSimulated Gene Networks
In 28 simulated Boolean gene regulatory networks, the dynamics create higher-order epistasis three times more often than they destroy it, and no topological feature predicts how much.
Mechanism Transport 1 paperNeural Population Geometry
Session-to-session reliability of 20 geometric metrics on Neuropixels recordings, tested against optogenetic silencing after controlling for neuron count and recording yield.
Evaluation Validity 1 paperMass Spectrometry
None of 54 embedding × metric combinations predicts how well MS/MS spectra transfer between instruments across 101,359 spectra; whether two instruments share a resolution class does.
Mechanism Transport 1 paper