Conventional and electron microscopy visualize structures in the micrometer to nanometer range, and such visualizations contribute decisively to our understanding of biological processes. Due to different factors in recording processes, microscopy images are subject to noise. Especially at their respective resolution limits, a high degree of noise can negatively effect both image interpretation by experts and further automated processing. However, the deteriorating effects of strong noise can be alleviated to a large extend by image enhancement algorithms. Because of the inherent high noise, a requirement for such algorithms is their applicability directly to noisy images or, in the extreme case, to just a single noisy image without a priori noise level information (referred to as blind zero-shot setting). This work investigates blind zero-shot algorithms for microscopy image denoising. The strategies for denoising applied by the investigated approaches include: filtering methods, recent feed-forward neural networks which were amended to be trainable on noisy images, and recent probabilistic generative models. As datasets we consider transmission electron microscopy images including images of SARS-CoV-2 viruses and fluorescence microscopy images. A natural goal of denoising algorithms is to simultaneously reduce noise while preserving the original image features, e.g., the sharpness of structures. However, in practice, a tradeoff between both aspects often has to be found. Our performance evaluations, therefore, focus not only on noise removal but set noise removal in relation to a metric which is instructive about sharpness. For all considered approaches, we numerically investigate their performance, report their denoising/sharpness tradeoff on different images, and discuss future developments. We observe that, depending on the data, the different algorithms can provide significant advantages or disadvantages in terms of their noise removal vs. sharpness preservation capabilities, which may be very relevant for different virological applications, e.g., virological analysis or image segmentation.

Latent variable models (LVMs) represent observed variables by parameterized functions of latent variables. Prominent examples of LVMs for unsupervised learning are probabilistic PCA or probabilistic sparse coding which both assume a weighted linear summation of the latents to determine the mean of a Gaussian distribution for the observables. In many cases, however, observables do not follow a Gaussian distribution. For unsupervised learning, LVMs which assume specific non-Gaussian observables (e.g., Bernoulli or Poisson) have therefore been considered. Already for specific choices of distributions, parameter optimization is challenging and only a few previous contributions considered LVMs with more generally defined observable distributions. In this contribution, we do consider LVMs that are defined for a range of different distributions, i.e., observables can follow any (regular) distribution of the exponential family. Furthermore, the novel class of LVMs presented here is defined for binary latents, and it uses maximization in place of summation to link the latents to observables. In order to derive an optimization procedure, we follow an expectation maximization approach for maximum likelihood parameter estimation. We then show, as our main result, that a set of very concise parameter update equations can be derived which feature the same functional form for all exponential family distributions. The derived generic optimization can consequently be applied (without further derivations) to different types of metric data (Gaussian and non-Gaussian) as well as to different types of discrete data. Moreover, the derived optimization equations can be combined with a recently suggested variational acceleration which is likewise generically applicable to the LVMs considered here. Thus, the combination maintains generic and direct applicability of the derived optimization procedure, but, crucially, enables efficient scalability. We numerically verify our analytical results using different observable distributions, and, furthermore, discuss some potential applications such as learning of variance structure, noise type estimation and denoising.

We combine two popular optimization approaches to derive learning algorithms for generative models: variational optimization and evolutionary algorithms. The combination is realized for generative models with discrete latents by using truncated posteriors as the family of variational distributions. The variational parameters of truncated posteriors are sets of latent states. By interpreting these states as genomes of individuals and by using the variational lower bound to define a fitness, we can apply evolutionary algorithms to realize the variational loop. The used variational distributions are very flexible and we show that evolutionary algorithms can effectively and efficiently optimize the variational bound. Furthermore, the variational loop is generally applicable (“black box”) with no analytical derivations required. To show general applicability, we apply the approach to three generative models (we use Noisy-OR Bayes Nets, Binary Sparse Coding, and Spike-and-Slab Sparse Coding). To demonstrate effectiveness and efficiency of the novel variational approach, we use the standard competitive benchmarks of image denoising and inpainting. The benchmarks allow quantitative comparisons to a wide range of methods including probabilistic approaches, deep deterministic and generative networks, and non-local image processing methods. In the category of “zero-shot” learning (when only the corrupted image is used for training), we observed the evolutionary variational algorithm to significantly improve the state-of-the-art in many benchmark settings. For one well-known inpainting benchmark, we also observed state-of-the-art performance across all categories of algorithms although we only train on the corrupted image. In general, our investigations highlight the importance of research on optimization methods for generative models to achieve performance improvements.

We investigate how the neural processing in auditory cortex is shaped by the statistics of natural sounds. Hypothesising that auditory cortex (A1) represents the structural primitives out of which sounds are composed, we employ a statistical model to extract such components. The input to the model are cochleagrams which approximate the non-linear transformations a sound undergoes from the outer ear, through the cochlea to the auditory nerve. Cochleagram components do not superimpose linearly, but rather according to a rule which can be approximated using the max function. This is a consequence of the compression inherent in the cochleagram and the sparsity of natural sounds. Furthermore, cochleagrams do not have negative values. Cochleagrams are therefore not matched well by the assumptions of standard linear approaches such as sparse coding or ICA. We therefore consider a new encoding approach for natural sounds, which combines a model of early auditory processing with maximal causes analysis (MCA), a sparse coding model which captures both the non-linear combination rule and non-negativity of the data. An efficient truncated EM algorithm is used to fit the MCA model to cochleagram data. We characterize the generative fields (GFs) inferred by MCA with respect to in vivo neural responses in A1 by applying reverse correlation to estimate spectro-temporal receptive fields (STRFs) implied by the learned GFs. Despite the GFs being non-negative, the STRF estimates are found to contain both positive and negative subfields, where the negative subfields can be attributed to explaining away effects as captured by the applied inference method. A direct comparison with ferret A1 shows many similar forms, and the spectral and temporal modulation tuning of both ferret and model STRFs show similar ranges over the population. In summary, our model represents an alternative to linear approaches for biological auditory encoding while it captures salient data properties and links inhibitory subfields to explaining away effects.

We establish a link between evolutionary algorithms (EAs) and learning of probabilistic generative models with binary hidden variables. Learning is formulated as approximate maximum likelihood optimization using variational expectation maximization. When choosing truncated posteriors as variational distributions, the variational parameters take the form of sets of latent states. By (A) identifying these sets with populations of genomes, and by (B) defining the fitness of individuals as the joint probability of the chosen generative model, the sets of latent states can be optimized using EAs. We obtain scalable learning algorithms that effectively improve the tractable free energy objective of truncated posteriors. While this novel approach is applicable to any model with binary latents and tractable joint probability, as a proof of concept, we here apply it to the optimization of parameters of noisy-OR Bayes Nets (modeling binary data) and Binary Sparse Coding (modelling continuous data). We find that the data likelihood is efficiently improved by employing genetic algorithms with point mutations and single-point cross-over as EAs. In general we believe that, with the novel link established here, standard as well as recent results in evolutionary optimization can be leveraged to address the difficult problem of parameter optimization in generative models.