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Planktonic organisms are key components of aquatic ecosystems and respond quickly to changes in the environment, therefore their monitoring is vital to understand the changes in the environment. Yet, monitoring plankton at appropriate scales still remains a challenge, limiting our understanding of functioning of aquatic systems and their response to changes. Modern plankton imaging instruments can be utilized to sample at high frequencies, enabling novel possibilities to study plankton populations. However, manual analysis of the data is costly, time consuming and expert based, making such approach unsuitable for large-scale application and urging for automatic solutions. The key problem related to the utilization of plankton datasets through image analysis is plankton recognition. Despite the large amount of research done, automatic methods have not been widely adopted for operational use. In this paper, a comprehensive survey on existing solutions for automatic plankton recognition is presented. First, we identify the most notable challenges that that make the development of plankton recognition systems difficult. Then, we provide a detailed description of solutions for these challenges proposed in plankton recognition literature. Finally, we propose a workflow to identify the specific challenges in new datasets and the recommended approaches to address them. For many of the challenges, applicable solutions exist. However, important challenges remain unsolved: 1) the domain shift between the datasets hindering the development of a general plankton recognition system that would work across different imaging instruments, 2) the difficulty to identify and process the images of previously unseen classes, and 3) the uncertainty in expert annotations that affects the training of the machine learning models for recognition. These challenges should be addressed in the future research.

A nonlinear sea-ice problem is considered in a least-squares finite element setting. The corresponding variational formulation approximating simultaneously the stress tensor and the velocity is analysed. In particular, the least-squares functional is coercive and continuous in an appropriate solution space and this proves the well-posedness of the problem. As the method does not require a compatibility condition between the finite element space, the formulation allows the use of piecewise polynomial spaces of the same approximation order for both the stress and the velocity approximations. A Newton-type iterative method is used to linearize the problem and numerical tests are provided to illustrate the theory.

In this work we begin a theoretical and numerical investigation on the spectra of evolution operators of neutral renewal equations, with the stability of equilibria and periodic orbits in mind. We start from the simplest form of linear periodic equation with one discrete delay and fully characterize the spectrum of its monodromy operator. We perform numerical experiments discretizing the evolution operators via pseudospectral collocation, confirming the theoretical results and giving perspectives on the generalization to systems and to multiple delays. Although we do not attempt to perform a rigorous numerical analysis of the method, we give some considerations on a possible approach to the problem.

We study the 2D Navier-Stokes equation with transport noise subject to periodic boundary conditions. Our main result is an error estimate for the time-discretisation showing a convergence rate of order (up to) 1/2. It holds with respect to mean square error convergence, whereas previously such a rate for the stochastic Navier-Stokes equations was only known with respect to convergence in probability. Our result is based on uniform-in-probability estimates for the continuous as well as the time-discrete solution exploiting the particular structure of the noise.

Hawkes processes are a popular framework to model the occurrence of sequential events, i.e., occurrence dynamics, in several fields such as social diffusion. In real-world scenarios, the inter-arrival time among events is irregular. However, existing neural network-based Hawkes process models not only i) fail to capture such complicated irregular dynamics, but also ii) resort to heuristics to calculate the log-likelihood of events since they are mostly based on neural networks designed for regular discrete inputs. To this end, we present the concept of Hawkes process based on controlled differential equations (HP-CDE), by adopting the neural controlled differential equation (neural CDE) technology which is an analogue to continuous RNNs. Since HP-CDE continuously reads data, i) irregular time-series datasets can be properly treated preserving their uneven temporal spaces, and ii) the log-likelihood can be exactly computed. Moreover, as both Hawkes processes and neural CDEs are first developed to model complicated human behavioral dynamics, neural CDE-based Hawkes processes are successful in modeling such occurrence dynamics. In our experiments with 4 real-world datasets, our method outperforms existing methods by non-trivial margins.

Matrix recovery from sparse observations is an extensively studied topic emerging in various applications, such as recommendation system and signal processing, which includes the matrix completion and compressed sensing models as special cases. In this work we propose a general framework for dynamic matrix recovery of low-rank matrices that evolve smoothly over time. We start from the setting that the observations are independent across time, then extend to the setting that both the design matrix and noise possess certain temporal correlation via modified concentration inequalities. By pooling neighboring observations, we obtain sharp estimation error bounds of both settings, showing the influence of the underlying smoothness, the dependence and effective samples. We propose a dynamic fast iterative shrinkage thresholding algorithm that is computationally efficient, and characterize the interplay between algorithmic and statistical convergence. Simulated and real data examples are provided to support such findings.

In neural networks, task-relevant information is represented jointly by groups of neurons. However, the specific way in which this mutual information about the classification label is distributed among the individual neurons is not well understood: While parts of it may only be obtainable from specific single neurons, other parts are carried redundantly or synergistically by multiple neurons. We show how Partial Information Decomposition (PID), a recent extension of information theory, can disentangle these different contributions. From this, we introduce the measure of "Representational Complexity", which quantifies the difficulty of accessing information spread across multiple neurons. We show how this complexity is directly computable for smaller layers. For larger layers, we propose subsampling and coarse-graining procedures and prove corresponding bounds on the latter. Empirically, for quantized deep neural networks solving the MNIST and CIFAR10 tasks, we observe that representational complexity decreases both through successive hidden layers and over training, and compare the results to related measures. Overall, we propose representational complexity as a principled and interpretable summary statistic for analyzing the structure and evolution of neural representations and complex systems in general.

We present a new approach, the Topograph, which reconstructs underlying physics processes, including the intermediary particles, by leveraging underlying priors from the nature of particle physics decays and the flexibility of message passing graph neural networks. The Topograph not only solves the combinatoric assignment of observed final state objects, associating them to their original mother particles, but directly predicts the properties of intermediate particles in hard scatter processes and their subsequent decays. In comparison to standard combinatoric approaches or modern approaches using graph neural networks, which scale exponentially or quadratically, the complexity of Topographs scales linearly with the number of reconstructed objects. We apply Topographs to top quark pair production in the all hadronic decay channel, where we outperform the standard approach and match the performance of the state-of-the-art machine learning technique.

Previous research has shown that fully-connected networks with small initialization and gradient-based training methods exhibit a phenomenon known as condensation during training. This phenomenon refers to the input weights of hidden neurons condensing into isolated orientations during training, revealing an implicit bias towards simple solutions in the parameter space. However, the impact of neural network structure on condensation has not been investigated yet. In this study, we focus on the investigation of convolutional neural networks (CNNs). Our experiments suggest that when subjected to small initialization and gradient-based training methods, kernel weights within the same CNN layer also cluster together during training, demonstrating a significant degree of condensation. Theoretically, we demonstrate that in a finite training period, kernels of a two-layer CNN with small initialization will converge to one or a few directions. This work represents a step towards a better understanding of the non-linear training behavior exhibited by neural networks with specialized structures.

The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations. NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides. This doctoral thesis provides an in-depth survey of the field. Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions). Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation). We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.