Programming adaptive behaviors at the cellular level is a long-standing goal that raises the question of how probabilistic computation can be implemented in biochemical systems. Chemical reaction networks (CRNs) provide such a substrate and have been shown to realize probabilistic models, including hidden Markov models and factor graphs, with dynamics reproducing Bayesian inference and belief propagation. However, encoding these algorithms typically requires prohibitively large reaction networks, and classical CRN reduction techniques do not directly apply. By recovering the factor graph structure encoded in Napp--Adams-compiled CRNs, we transport recent factor-graph reduction results to their chemical implementations, obtaining significantly smaller CRNs while preserving the belief-propagation fixed points on surviving variables.
This paper develops a categorical framework -- Learning in Infinitesimal Non-Compositional Sketches (LINCS) -- as the repair of non-compositionality: failures of diagrams to factor through quotient sketches lifted to the tangent category setting. Machine learning problems are spe…
Agentic systems increasingly improve themselves by editing skills: prompts, rubrics, plans, tool contracts, examples, validators, and traces. Skill edits are not independent coordinates in a vector space: they are local repairs to structured artifacts whose effects are observed o…
Mapping a chemical reaction network, the graph of minima and transition states (TS) and the elementary reactions connecting them, is the natural language of chemistry, from catalysis to combustion to the origin of life. Constructing such a reaction network for a given chemistry h…
Reaction mechanisms consist of the step-by-step sequences of elementary reactions that explain chemical transformations. Learning the mechanism logic is therefore essential for enhancing the fundamental chemical intelligence of large language models (LLMs). The stepwise deduction…
Forecasting the outcomes of transition-metal-catalyzed reactions is notoriously complex due to the interplay of diverse physical and chemical variables. A persistent computational bottleneck has been effectively merging broad electronic descriptors with the localized, three-dimen…
False alarms remain a major barrier to deploying network intrusion detection systems (NIDS). In high-volume environments, even a sub-1% false positive rate can generate tens of thousands of daily alerts. Filter-based feature selection is attractive because it operates upstream of…