References of "Stefanovic, Darko"
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See detailReservoir Computing with Random Chemical Systems
Nguyen, Hoang; Banda, Peter UL; Stefanovic, Darko et al

in ALIFE 2020: The 2020 Conference on Artificial Life (2020, July 14)

Top-down engineering of biomolecular circuits to perform specific computational tasks is notoriously hard and time-consuming. Current circuits have limited complexity and are brittle and application ... [more ▼]

Top-down engineering of biomolecular circuits to perform specific computational tasks is notoriously hard and time-consuming. Current circuits have limited complexity and are brittle and application-specific. Here we propose an alternative: we design and test a bottom-up constructed Reservoir Computer (RC) that uses random chemical circuits inspired by DNA strand displacement reactions. This RC has the potential to be implemented easily and trained for various tasks. We describe and simulate it by means of a Chemical Reaction Network (CRN) and evaluate its performance on three computational tasks: the Hamming distance and a short- as well as a long-term memory. Compared with the deoxyribozyme oscillator RC model simulated by Yahiro et al., our random chemical RC performs 75.5% better for the short-term and 67.2% better for the long-term memory task. Our model requires an 88.5% larger variety of chemical species, but it relies on random chemical circuits, which can be more easily realized and scaled up. Thus, our novel random chemical RC has the potential to simplify the way we build adaptive biomolecular circuits. [less ▲]

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See detailFeedforward Chemical Neural Network: An In Silico Chemical System That Learns XOR
Blount, Drew; Banda, Peter UL; Teuscher, Christof et al

in Artificial Life (2017), 23(3), 295-317

Inspired by natural biochemicals that perform complex information processing within living cells, we design and simulate a chemically implemented feedforward neural network, which learns by a novel ... [more ▼]

Inspired by natural biochemicals that perform complex information processing within living cells, we design and simulate a chemically implemented feedforward neural network, which learns by a novel chemical-reaction-based analogue of backpropagation. Our network is implemented in a simulated chemical system, where individual neurons are separated from each other by semipermeable cell-like membranes. Our compartmentalized, modular design allows a variety of network topologies to be constructed from the same building blocks. This brings us towards general-purpose, adaptive learning in chemico: wet machine learning in an embodied dynamical system. [less ▲]

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See detailTraining an asymmetric signal perceptron through reinforcement in an artificial chemistry
Banda, Peter UL; Teuscher, Christof; Stefanovic, Darko

in Journal of the Royal Society, Interface (2014), 11(93),

State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be reprogrammed or trained once fabricated. The implementation of adaptive ... [more ▼]

State-of-the-art biochemical systems for medical applications and chemical computing are application-specific and cannot be reprogrammed or trained once fabricated. The implementation of adaptive biochemical systems that would offer flexibility through programmability and autonomous adaptation faces major challenges because of the large number of required chemical species as well as the timing-sensitive feedback loops required for learning. In this paper, we begin addressing these challenges with a novel chemical perceptron that can solve all 14 linearly separable logic functions. The system performs asymmetric chemical arithmetic, learns through reinforcement and supports both Michaelis–Menten as well as mass-action kinetics. To enable cascading of the chemical perceptrons, we introduce thresholds that amplify the outputs. The simplicity of our model makes an actual wet implementation, in particular by DNA-strand displacement, possible. [less ▲]

Detailed reference viewed: 104 (4 UL)