Krešimir Josić́

Hyeontae Jo, Krešimir Josić, Jae Kyoung Kim

Non-autonomous differential equations are crucial for modeling systems influenced by external signals, yet fitting these models to data becomes particularly challenging when the signals change abruptly. To address this problem, we propose a novel parameter estimation method utilizing functional approximations with artificial neural networks. Our approach, termed Harmonic Approximation of Discontinuous External Signals using Neural Networks (HADES-NN), operates in two iterated stages. In the first stage, the algorithm employs a neural network to approximate the discontinuous signal with a smooth function. In the second stage, it uses this smooth approximate signal to estimate model parameters. HADES-NN gives highly accurate and precise parameter estimates across various applications, including circadian clock systems regulated by external light inputs measured via wearable devices and the mating response of yeast to external pheromone signals. HADES-NN greatly extends the range of model systems that can be fit to real-world measurements.

Sorena Sarmadi, James J. Winkle, Razan N. Alnahhas et al.

Our work targets automated analysis to quantify the growth dynamics of a population of bacilliform bacteria. We propose an innovative approach to frame-sequence tracking of deformable-cell motion by the automated minimization of a new, specific cost functional. This minimization is implemented by dedicated Boltzmann machines (stochastic recurrent neural networks). Automated detection of cell divisions is handled similarly by successive minimizations of two cost functions, alternating the identification of children pairs and parent identification. We validate the proposed automatic cell tracking algorithm using (i) recordings of simulated cell colonies that closely mimic the growth dynamics of E. coli in microfluidic traps and (ii) real data. On a batch of 1100 simulated image frames, cell registration accuracies per frame ranged from 94.5% to 100%, with a high average. Our initial tests using experimental image sequences (i.e., real data) of E. coli colonies also yield convincing results, with a registration accuracy ranging from 90% to 100%.