Krešimir Josić

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.

Nicholas W. Barendregt, Joshua I. Gold, Krešimir Josić et al.

To survive in dynamic and uncertain environments, individuals must develop effective decision strategies that balance information gathering and decision commitment. Models of such strategies often prioritize either optimizing tangible payoffs, like reward rate, or gathering information to support a diversity of (possibly unknown) objectives. However, our understanding of the relative merits of these two approaches remains incomplete, in part because direct comparisons have been limited to idealized, static environments that lack the dynamic complexity of the real world. Here we compared the performance of normative reward- and information-seeking strategies in a dynamic foraging task. Both strategies show similar transitions between exploratory and exploitative behaviors as environmental uncertainty changes. However, we find subtle disparities in the actions they take, resulting in meaningful performance differences: whereas reward-seeking strategies generate slightly more reward on average, information-seeking strategies provide more consistent and predictable outcomes. Our findings support the adaptive value of information-seeking behaviors that can mitigate risk with minimal reward loss.

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%.