ALPyNA: Acceleration of Loops in Python for Novel Architectures

We present ALPyNA, an automatic loop parallelization framework for Python, which analyzes data dependences within nested loops and dynamically generates CUDA kernels for GPU execution. The ALPyNA system applies classical dependence analysis techniques to discover and exploit potential parallelism. The skeletal structure of the dependence graph is determined statically (if possible) or at runtime; this is combined with type and bounds information discovered at runtime, to auto-generate high-performance kernels for offload to GPU. We demonstrate speedups of up to 1000x relative to the native CPython interpreter across four array-intensive numerical Python benchmarks. Performance improvement is related to both iteration domain size and dependence graph complexity. Nevertheless, this approach promises to bring the benefits of manycore parallelism to application developers

Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

Bioimage Data Analysis Workflows ‒ Advanced Components and Methods

This open access textbook aims at providing detailed explanations on how to design and construct image analysis workflows to successfully conduct bioimage analysis. Addressing the main challenges in image data analysis, where acquisition by powerful imaging devices results in very large amounts of collected image data, the book discusses techniques relying on batch and GPU programming, as well as on powerful deep learning-based algorithms. In addition, downstream data processing techniques are introduced, such as Python libraries for data organization, plotting, and visualizations. Finally, by studying the way individual unique ideas are implemented in the workflows, readers are carefully guided through how the parameters driving biological systems are revealed by analyzing image data. These studies include segmentation of plant tissue epidermis, analysis of the spatial pattern of the eye development in fruit flies, and the analysis of collective cell migration dynamics. The presented content extends the Bioimage Data Analysis Workflows textbook (Miura, Sladoje, 2020), published in this same series, with new contributions and advanced material, while preserving the well-appreciated pedagogical approach adopted and promoted during the training schools for bioimage analysis organized within NEUBIAS – the Network of European Bioimage Analysts. This textbook is intended for advanced students in various fields of the life sciences and biomedicine, as well as staff scientists and faculty members who conduct regular quantitative analyses of microscopy images

Slideflow: Deep Learning for Digital Histopathology with Real-Time Whole-Slide Visualization

Deep learning methods have emerged as powerful tools for analyzing histopathological images, but current methods are often specialized for specific domains and software environments, and few open-source options exist for deploying models in an interactive interface. Experimenting with different deep learning approaches typically requires switching software libraries and reprocessing data, reducing the feasibility and practicality of experimenting with new architectures. We developed a flexible deep learning library for histopathology called Slideflow, a package which supports a broad array of deep learning methods for digital pathology and includes a fast whole-slide interface for deploying trained models. Slideflow includes unique tools for whole-slide image data processing, efficient stain normalization and augmentation, weakly-supervised whole-slide classification, uncertainty quantification, feature generation, feature space analysis, and explainability. Whole-slide image processing is highly optimized, enabling whole-slide tile extraction at 40X magnification in 2.5 seconds per slide. The framework-agnostic data processing pipeline enables rapid experimentation with new methods built with either Tensorflow or PyTorch, and the graphical user interface supports real-time visualization of slides, predictions, heatmaps, and feature space characteristics on a variety of hardware devices, including ARM-based devices such as the Raspberry Pi

Bioinformatics

This book is divided into different research areas relevant in Bioinformatics such as biological networks, next generation sequencing, high performance computing, molecular modeling, structural bioinformatics, molecular modeling and intelligent data analysis. Each book section introduces the basic concepts and then explains its application to problems of great relevance, so both novice and expert readers can benefit from the information and research works presented here

Creating a platform for the democratisation of Deep Learning in microscopy

One of the major technological success stories of the last decade has been the advent of deep learning (DL), which has touched almost every aspect of modern life after a breakthrough performance in an image detection challenge in 2012. The bioimaging community quickly recognised the prospect of the automated ability to make sense of image data with near-human performance as potentially ground-breaking. In the decade since, hundreds of publications have used this technology to tackle many problems related to image analysis, such as labelling or counting cells, identifying cells or organelles of interest in large image datasets, or removing noise or improving the resolution of images. However, the adoption of DL tools in large parts of the bioimaging community has been slow, and many tools have remained in the hands of developers. In this project, I have identified key barriers which have prevented many bioimage analysts and microscopists from accessing existing DL technology in their field and have, in collaboration with colleagues, developed the ZeroCostDL4Mic platform, which aims to address these barriers. This project is inspired by the observation that the most significant impact technology can have in science is when it becomes ubiquitous, that is, when its use becomes essential to address the community’s questions. This work represents one of the first attempts to make DL tools accessible in a transparent, code-free, and affordable manner for bioimage analysis to unlock the full potential of DL via its democratisation for the bioimaging community

Masivně paralelní implementace algoritmů počítačové grafiky

Computer graphics, since its inception in the 1960s, has made great progress. It has become part of everyday life. We can see it all around us, from smartwatches and smartphones, where graphic accelerators are already part of the chips and can render not only interactive menus but also demanding graphic applications, to laptops and personal computers as well as to high-performance visualization servers and supercomputers that can display demanding simulations in real time. In this dissertation we focus on one of the most computationally demanding area of computer graphics and that is the computation of global illumination. One of the most widely used methods for simulating global illumination is the path tracing method. Using this method, we can visualize, for example, scientific or medical data. The path tracing method can be accelerated using multiple graphical accelerators, which we will focus on in this work. We will present a solution for path tracing of massive scenes on multiple GPUs. Our approach analyzes the memory access pattern of the path tracer and defines how the scene data should be distributed across up to 16 GPUs with minimal performance impact. The key concept is that the parts of the scene that have the highest number of memory accesses are replicated across all GPUs. We present two methods for maximizing the performance of path tracing when dealing with partially distributed scene data. Both methods operate at the memory management level, and therefore the path tracing data structures do not need to be redesigned. We implemented this new out-of-core mechanism in the open-source Blender Cycles path tracer, which we also extended with technologies that support running on supercomputers and can take advantage of all accelerators allocated on multiple nodes. In this work, we also introduce a new service that uses our extended version of the Blender Cycles renderer to simplify sending and running jobs directly from Blender.Počítačová grafika od svého vzniku v 60. letech 20. století udělala velký pokrok. Stala se součástí každodenního života. Můžeme ji vidět všude kolem nás, od chytrých hodinek a smartphonů, kde jsou grafické akcelerátory již součástí čipů a dokáží vykreslovat nejen interaktivní menu, ale i náročné grafické aplikace, přes notebooky a osobní počítače až po výkonné vizualizační servery nebo superpočítače, které dokáží zobrazovat náročné simulace v reálném čase. V této disertační práci se zaměříme na jednu z výpočetně nejnáročnějších oblastí počítačové grafiky, a tou je výpočet globálního osvětlení. Jednou z nejpoužívanějších metod pro simulaci globálního osvětlení je metoda sledování cesty. Pomocí této metody můžeme vizualizovat např. vědecká nebo lékařská data. Metodu sledování cest lze urychlit pomocí několika grafických akcelerátorů, na které se v této práci zaměříme. Představíme řešení pro vykreslování masivních scén na více GPU. Náš přístup analyzuje vzory přístupů k paměti a definuje, jak by měla být data scény rozdělena mezi grafickými akcelerátory s minimální ztrátou výkonu. Klíčovým konceptem je, že části scény, které mají nejvyšší počet přístupů do paměti, jsou replikovány na všech grafických akcelerátorech. Představíme dvě metody pro maximalizaci výkonu vykreslování při práci s částečně distribuovanými daty scény. Obě metody pracují na úrovni správy paměti, a proto není třeba datové struktury přepracovávat. Tento nový out-of-core mechanismus jsme implementovali do open-source path traceru Blender Cycles, který jsme také rozšířili o technologie podporující běh na superpočítačích a schopné využít všechny akcelerátory alokované na více uzlech. V této práci také představíme novou službu, která využívá naši rozšířenou verzi Blender Cycles a zjednodušuje odesílání a spouštění úloh přímo z programu Blender.96220 - Laboratoř pro výzkum infrastrukturyvyhově