Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, our large international expert consortium created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool, which also provides a point of access to explore weaknesses, strengths and specific recommendations for the most common validation metrics. The broad applicability of our framework across domains is demonstrated by an instantiation for various biological and medical image analysis use cases.
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Difficult, in particular NP-complete, optimization problems are traditionally solved approximately using search heuristics. These are usually slowed down by the rugged landscapes encountered, because local minima arrest the search process. Cover-encoding maps were devised to circumvent this problem by transforming the original landscape to one that is free of local minima and enriched in near-optimal solutions. By definition, these involve the mapping of the original (larger) search space into smaller subspaces, by processes that typically amount to a form of coarse-graining. In this paper, we explore the details of this coarse-graining using formal arguments, as well as concrete examples of cover-encoding maps, that are investigated analytically as well as computationally. Our results strongly suggest that the coarse-graining involved in cover-encoding maps bears a strong resemblance to that encountered in renormalisation group schemes. Given the apparently disparate nature of these two formalisms, these strong similarities are rather startling, and suggest deep mathematical underpinnings that await further exploration.
We collect robust proposals given in the field of regression models with heteroscedastic errors. Our motivation stems from the fact that the practitioner frequently faces the confluence of two phenomena in the context of data analysis: non--linearity and heteroscedasticity. The impact of heteroscedasticity on the precision of the estimators is well--known, however the conjunction of these two phenomena makes handling outliers more difficult. An iterative procedure to estimate the parameters of a heteroscedastic non--linear model is considered. The studied estimators combine weighted $MM-$regression estimators, to control the impact of high leverage points, and a robust method to estimate the parameters of the variance function.
Organoids are self-organized 3D cell clusters that closely mimic the architecture and function of in vivo tissues and organs. Quantification of organoid morphology helps in studying organ development, drug discovery, and toxicity assessment. Recent microscopy techniques provide a potent tool to acquire organoid morphology features, but manual image analysis remains a labor and time-intensive process. Thus, this paper proposes a comprehensive pipeline for microscopy analysis that leverages the SegmentAnything to precisely demarcate individual organoids. Additionally, we introduce a set of morphological properties, including perimeter, area, radius, non-smoothness, and non-circularity, allowing researchers to analyze the organoid structures quantitatively and automatically. To validate the effectiveness of our approach, we conducted tests on bright-field images of human induced pluripotent stem cells (iPSCs) derived neural-epithelial (NE) organoids. The results obtained from our automatic pipeline closely align with manual organoid detection and measurement, showcasing the capability of our proposed method in accelerating organoids morphology analysis.
We study single-image super-resolution algorithms for photons at collider experiments based on generative adversarial networks. We treat the energy depositions of simulated electromagnetic showers of photons and neutral-pion decays in a toy electromagnetic calorimeter as 2D images and we train super-resolution networks to generate images with an artificially increased resolution by a factor of four in each dimension. The generated images are able to reproduce features of the electromagnetic showers that are not obvious from the images at nominal resolution. Using the artificially-enhanced images for the reconstruction of shower-shape variables and of the position of the shower center results in significant improvements. We additionally investigate the utilization of the generated images as a pre-processing step for deep-learning photon-identification algorithms and observe improvements in the case of training samples of small size.
SCONE-GAN presents an end-to-end image translation, which is shown to be effective for learning to generate realistic and diverse scenery images. Most current image-to-image translation approaches are devised as two mappings: a translation from the source to target domain and another to represent its inverse. While successful in many applications, these approaches may suffer from generating trivial solutions with limited diversity. That is because these methods learn more frequent associations rather than the scene structures. To mitigate the problem, we propose SCONE-GAN that utilises graph convolutional networks to learn the objects dependencies, maintain the image structure and preserve its semantics while transferring images into the target domain. For more realistic and diverse image generation we introduce style reference image. We enforce the model to maximize the mutual information between the style image and output. The proposed method explicitly maximizes the mutual information between the related patches, thus encouraging the generator to produce more diverse images. We validate the proposed algorithm for image-to-image translation and stylizing outdoor images. Both qualitative and quantitative results demonstrate the effectiveness of our approach on four dataset.
Estimating a prediction function is a fundamental component of many data analyses. The Super Learner ensemble, a particular implementation of stacking, has desirable theoretical properties and has been used successfully in many applications. Dimension reduction can be accomplished by using variable screening algorithms, including the lasso, within the ensemble prior to fitting other prediction algorithms. However, the performance of a Super Learner using the lasso for dimension reduction has not been fully explored in cases where the lasso is known to perform poorly. We provide empirical results that suggest that a diverse set of candidate screening algorithms should be used to protect against poor performance of any one screen, similar to the guidance for choosing a library of prediction algorithms for the Super Learner.
Imaging through perturbed multimode fibres based on deep learning has been widely researched. However, existing methods mainly use target-speckle pairs in different configurations. It is challenging to reconstruct targets without trained networks. In this paper, we propose a physics-assisted, unsupervised, learning-based fibre imaging scheme. The role of the physical prior is to simplify the mapping relationship between the speckle pattern and the target image, thereby reducing the computational complexity. The unsupervised network learns target features according to the optimized direction provided by the physical prior. Therefore, the reconstruction process of the online learning only requires a few speckle patterns and unpaired targets. The proposed scheme also increases the generalization ability of the learning-based method in perturbed multimode fibres. Our scheme has the potential to extend the application of multimode fibre imaging.
We present a hierarchical Bayesian pipeline, BP3M, that measures positions, parallaxes, and proper motions (PMs) for cross-matched sources between Hubble~Space~Telescope (HST) images and Gaia -- even for sparse fields ($N_*<10$ per image) -- expanding from the recent GaiaHub tool. This technique uses Gaia-measured astrometry as priors to predict the locations of sources in HST images, and is therefore able to put the HST images onto a global reference frame without the use of background galaxies/QSOs. Testing our publicly-available code in the Fornax and Draco dSphs, we measure accurate PMs that are a median of 8-13 times more precise than Gaia DR3 alone for $20.5<G<21~\mathrm{mag}$. We are able to explore the effect of observation strategies on BP3M astrometry using synthetic data, finding an optimal strategy to improve parallax and position precision at no cost to the PM uncertainty. Using 1619 HST images in the sparse COSMOS field (median 9 Gaia sources per HST image), we measure BP3M PMs for 2640 unique sources in the $16<G<21.5~\mathrm{mag}$ range, 25% of which have no Gaia PMs; the median BP3M PM uncertainty for $20.25<G<20.75~\mathrm{mag}$ sources is $0.44~$mas/yr compared to $1.03~$mas/yr from Gaia, while the median BP3M PM uncertainty for sources without Gaia-measured PMs ($20.75<G<21.5~\mathrm{mag}$) is $1.16~$mas/yr. The statistics that underpin the BP3M pipeline are a generalized way of combining position measurements from different images, epochs, and telescopes, which allows information to be shared between surveys and archives to achieve higher astrometric precision than that from each catalog alone.
Generating high-quality and person-generic visual dubbing remains a challenge. Recent innovation has seen the advent of a two-stage paradigm, decoupling the rendering and lip synchronization process facilitated by intermediate representation as a conduit. Still, previous methodologies rely on rough landmarks or are confined to a single speaker, thus limiting their performance. In this paper, we propose DiffDub: Diffusion-based dubbing. We first craft the Diffusion auto-encoder by an inpainting renderer incorporating a mask to delineate editable zones and unaltered regions. This allows for seamless filling of the lower-face region while preserving the remaining parts. Throughout our experiments, we encountered several challenges. Primarily, the semantic encoder lacks robustness, constricting its ability to capture high-level features. Besides, the modeling ignored facial positioning, causing mouth or nose jitters across frames. To tackle these issues, we employ versatile strategies, including data augmentation and supplementary eye guidance. Moreover, we encapsulated a conformer-based reference encoder and motion generator fortified by a cross-attention mechanism. This enables our model to learn person-specific textures with varying references and reduces reliance on paired audio-visual data. Our rigorous experiments comprehensively highlight that our ground-breaking approach outpaces existing methods with considerable margins and delivers seamless, intelligible videos in person-generic and multilingual scenarios.
The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.
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