# Evolutionary chemical learning in dimerization networks

arXiv: https://arxiv.org/abs/2506.14006 · HTML: https://mlsanity.com/paper/2506.14006/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 41 references that are in the map.
- First posted on arXiv 16 Jun 2025.

## Builds on (most cited first, 5 of 5)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [All-Optical Machine Learning Using Diffractive Deep Neural Networks](https://mlsanity.com/paper/1804.08711/) (2018)
- [Deep physical neural networks enabled by a backpropagation algorithm for arbitrary physical systems](https://mlsanity.com/paper/2104.13386/) (2021)
- [Photonics for artificial intelligence and neuromorphic computing](https://mlsanity.com/paper/2011.00111/) (2020)
- [Backpropagation-free Training of Deep Physical Neural Networks](https://mlsanity.com/paper/2304.11042/) (2023)

## Abstract (arXiv)

We present a framework for chemical learning based on Competitive Dimerization Networks (CDNs) - systems in which multiple molecular species, e.g., proteins, DNA oligomers, or RNA oligomers, reversibly bind to form dimers. We show numerically that these networks can, in principle, be trained in vitro through directed evolution, enabling the implementation of complex learning tasks such as multiclass classification without digital hardware or prior knowledge of all microscopic association constants. Each molecular species functions analogously to a neuron, with binding affinities acting as tunable synaptic weights. A training protocol involving mutation, selection, and amplification of DNA-based components allows CDNs to robustly discriminate among noisy input patterns. The resulting classifiers exhibit strong output contrast and high mutual information between input and output, especially when guided by a contrast-enhancing loss function. Comparative analysis with in silico gradient descent training reveals closely correlated performance. These results establish CDNs as a promising platform for analog physical computation, bridging synthetic biology and machine learning, and advancing the development of adaptive, energy-efficient molecular computing systems.