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In the past decades, automated high-content microscopy demonstrated its ability to deliver large quantities of image-based data powering the versatility of phenotypic drug screening and systems biology applications. However, as the sizes of image-based datasets grew, it became infeasible for humans to control, avoid and overcome the presence of imaging and sample preparation artefacts in the images. While novel techniques like machine learning and deep learning may address these shortcomings through generative image inpainting, when applied to sensitive research data this may come at the cost of undesired image manipulation. Undesired manipulation may be caused by phenomena such as neural hallucinations, to which some artificial neural networks are prone. To address this, here we evaluate the state-of-the-art inpainting methods for image restoration in a high-content fluorescence microscopy dataset of cultured cells with labelled nuclei. We show that architectures like DeepFill V2 and Edge Connect can faithfully restore microscopy images upon fine-tuning with relatively little data. Our results demonstrate that the area of the region to be restored is of higher importance than shape. Furthermore, to control for the quality of restoration, we propose a novel phenotype-preserving metric design strategy. In this strategy, the size and count of the restored biological phenotypes like cell nuclei are quantified to penalise undesirable manipulation. We argue that the design principles of our approach may also generalise to other applications.

The hearing loss of almost half a billion people is commonly treated with hearing aids. However, current hearing aids often do not work well in real-world noisy environments. We present a deep learning based denoising system that runs in real time on iPhone 7 and Samsung Galaxy S10 (25ms algorithmic latency). The denoised audio is streamed to the hearing aid, resulting in a total delay of around 75ms. In tests with hearing aid users having moderate to severe hearing loss, our denoising system improves audio across three tests: 1) listening for subjective audio ratings, 2) listening for objective speech intelligibility, and 3) live conversations in a noisy environment for subjective ratings. Subjective ratings increase by more than 40%, for both the listening test and the live conversation compared to a fitted hearing aid as a baseline. Speech reception thresholds, measuring speech understanding in noise, improve by 1.6 dB SRT. Ours is the first denoising system that is implemented on a mobile device, streamed directly to users' hearing aids using only a single channel as audio input while improving user satisfaction on all tested aspects, including speech intelligibility. This includes overall preference of the denoised and streamed signal over the hearing aid, thereby accepting the higher latency for the significant improvement in speech understanding.

Stochastic multi-scale modeling and simulation for nonlinear thermo-mechanical problems of composite materials with complicated random microstructures remains a challenging issue. In this paper, we develop a novel statistical higher-order multi-scale (SHOMS) method for nonlinear thermo-mechanical simulation of random composite materials, which is designed to overcome limitations of prohibitive computation involving the macro-scale and micro-scale. By virtue of statistical multi-scale asymptotic analysis and Taylor series method, the SHOMS computational model is rigorously derived for accurately analyzing nonlinear thermo-mechanical responses of random composite materials both in the macro-scale and micro-scale. Moreover, the local error analysis of SHOMS solutions in the point-wise sense clearly illustrates the crucial indispensability of establishing the higher-order asymptotic corrected terms in SHOMS computational model for keeping the conservation of local energy and momentum. Then, the corresponding space-time multi-scale numerical algorithm with off-line and on-line stages is designed to efficiently simulate nonlinear thermo-mechanical behaviors of random composite materials. Finally, extensive numerical experiments are presented to gauge the efficiency and accuracy of the proposed SHOMS approach.

A limited set of tools exist for assessing whether the behavior of quantum machine learning models diverges from conventional models, outside of abstract or theoretical settings. We present a systematic application of explainable artificial intelligence techniques to analyze synthetic data generated from a hybrid quantum-classical neural network adapted from twenty different real-world data sets, including solar flares, cardiac arrhythmia, and speech data. Each of these data sets exhibits varying degrees of complexity and class imbalance. We benchmark the quantum-generated data relative to state-of-the-art methods for mitigating class imbalance for associated classification tasks. We leverage this approach to elucidate the qualities of a problem that make it more or less likely to be amenable to a hybrid quantum-classical generative model.

Accurate activity location prediction is a crucial component of many mobility applications and is particularly required to develop personalized, sustainable transportation systems. Despite the widespread adoption of deep learning models, next location prediction models lack a comprehensive discussion and integration of mobility-related spatio-temporal contexts. Here, we utilize a multi-head self-attentional (MHSA) neural network that learns location transition patterns from historical location visits, their visit time and activity duration, as well as their surrounding land use functions, to infer an individual's next location. Specifically, we adopt point-of-interest data and latent Dirichlet allocation for representing locations' land use contexts at multiple spatial scales, generate embedding vectors of the spatio-temporal features, and learn to predict the next location with an MHSA network. Through experiments on two large-scale GNSS tracking datasets, we demonstrate that the proposed model outperforms other state-of-the-art prediction models, and reveal the contribution of various spatio-temporal contexts to the model's performance. Moreover, we find that the model trained on population data achieves higher prediction performance with fewer parameters than individual-level models due to learning from collective movement patterns. We also reveal mobility conducted in the recent past and one week before has the largest influence on the current prediction, showing that learning from a subset of the historical mobility is sufficient to obtain an accurate location prediction result. We believe that the proposed model is vital for context-aware mobility prediction. The gained insights will help to understand location prediction models and promote their implementation for mobility applications.

The forecasting and computation of the stability of chaotic systems from partial observations are tasks for which traditional equation-based methods may not be suitable. In this computational paper, we propose data-driven methods to (i) infer the dynamics of unobserved (hidden) chaotic variables (full-state reconstruction); (ii) time forecast the evolution of the full state; and (iii) infer the stability properties of the full state. The tasks are performed with long short-term memory (LSTM) networks, which are trained with observations (data) limited to only part of the state: (i) the low-to-high resolution LSTM (LH-LSTM), which takes partial observations as training input, and requires access to the full system state when computing the loss; and (ii) the physics-informed LSTM (PI-LSTM), which is designed to combine partial observations with the integral formulation of the dynamical system's evolution equations. First, we derive the Jacobian of the LSTMs. Second, we analyse a chaotic partial differential equation, the Kuramoto-Sivashinsky (KS), and the Lorenz-96 system. We show that the proposed networks can forecast the hidden variables, both time-accurately and statistically. The Lyapunov exponents and covariant Lyapunov vectors, which characterize the stability of the chaotic attractors, are correctly inferred from partial observations. Third, the PI-LSTM outperforms the LH-LSTM by successfully reconstructing the hidden chaotic dynamics when the input dimension is smaller or similar to the Kaplan-Yorke dimension of the attractor. This work opens new opportunities for reconstructing the full state, inferring hidden variables, and computing the stability of chaotic systems from partial data.

Deep neural operators (DNOs) have been utilized to approximate nonlinear mappings between function spaces. However, DNOs face the challenge of increased dimensionality and computational cost associated with unaligned observation data. In this study, we propose a hybrid Decoder-DeepONet operator regression framework to handle unaligned data effectively. Additionally, we introduce a Multi-Decoder-DeepONet, which utilizes an average field of training data as input augmentation. The consistencies of the frameworks with the operator approximation theory are provided, on the basis of the universal approximation theorem. Two numerical experiments, Darcy problem and flow-field around an airfoil, are conducted to validate the efficiency and accuracy of the proposed methods. Results illustrate the advantages of Decoder-DeepONet and Multi-Decoder-DeepONet in handling unaligned observation data and showcase their potentials in improving prediction accuracy.

TraitLab is a software package for simulating, fitting and analysing tree-like binary data under a stochastic Dollo model of evolution. The model also allows for rate heterogeneity through catastrophes, evolutionary events where many traits are simultaneously lost while new ones arise, and borrowing, whereby traits transfer laterally between species as well as through ancestral relationships. The core of the package is a Markov chain Monte Carlo (MCMC) sampling algorithm that enables the user to sample from the Bayesian joint posterior distribution for tree topologies, clade and root ages, and the trait loss, catastrophe and borrowing rates for a given data set. Data can be simulated according to the fitted Dollo model or according to a number of generalized models that allow for heterogeneity in the trait loss rate, biases in the data collection process and borrowing of traits between lineages. Coupled pairs of Markov chains can be used to diagnose MCMC mixing and convergence and to debias MCMC estimators. The raw data, MCMC run output, and model fit can be inspected using a number of useful graphical and analytical tools provided within the package or imported into other popular analysis programs. TraitLab is freely available and runs within the Matlab computing environment with its Statistics and Machine Learning toolbox, no other additional toolboxes are required.

In light of the increasing adoption of edge computing in areas such as intelligent furniture, robotics, and smart homes, this paper introduces HyperSNN, an innovative method for control tasks that uses spiking neural networks (SNNs) in combination with hyperdimensional computing. HyperSNN substitutes expensive 32-bit floating point multiplications with 8-bit integer additions, resulting in reduced energy consumption while enhancing robustness and potentially improving accuracy. Our model was tested on AI Gym benchmarks, including Cartpole, Acrobot, MountainCar, and Lunar Lander. HyperSNN achieves control accuracies that are on par with conventional machine learning methods but with only 1.36% to 9.96% of the energy expenditure. Furthermore, our experiments showed increased robustness when using HyperSNN. We believe that HyperSNN is especially suitable for interactive, mobile, and wearable devices, promoting energy-efficient and robust system design. Furthermore, it paves the way for the practical implementation of complex algorithms like model predictive control (MPC) in real-world industrial scenarios.