Events

Mar 14 - Mar 20, 2021

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  On Discovering Nature’s Equations from Observations

  Jesper Tegner, Professor, BESE Division, KAUST

  Mar 18, 12:00 - 13:00

  KAUST

  In essence, science is about discovering regularities in Nature. It turns out that such regularities (laws) are written in the language of mathematics. In many cases, such laws are formulated and refined from fundamental “first principles.” Yet, in phenomenological areas such as biology, we have an abundance of data but lack “first principles.” Machine learning and deep learning, in particular, are remarkably successful in classification and prediction tasks. However, such systems, when trained on data, do not, as a rule, provide compact mathematical laws or fundamental first principles. Here we ask how we can identify interpretable compact mathematical laws from complex data-sets when we don’t have access to first principles. I will give an overview of this problem and provide some vignettes of our ongoing work in attacking this problem.

Mar 7 - Mar 13, 2021

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  ArtEmis: Affective Language for Visual Art

  Mohamed Elhoseiny, Associate Professor, Computer Science

  Mar 8, 12:00 - 13:00

  KAUST

  We present a novel large-scale dataset and accompanying machine learning models aimed at providing a detailed understanding of the interplay between visual content, its emotional effect, and explanations for the latter in language. In contrast to most existing annotation datasets in computer vision, we focus on the affective experience triggered by visual artworks and ask the annotators to indicate the dominant emotion they feel for a given image and, crucially, to also provide a grounded verbal explanation for their emotion choice.

Feb 28 - Mar 6, 2021

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  Novel computational models in biological imaging

  Xin Gao, Program Chair, Computer Science

  Mar 1, 12:00 - 13:00

  KAUST

  In this talk, I will introduce our recent efforts on developing novel computational models in the field of biological imaging. I will start with the examples in electron tomography, for which I will introduce a robust and efficient scheme for fiducial marker tracking, and then describe a novel constrained reconstruction model towards higher resolution sub-tomogram averaging. I will then show our work on developing deep learning methods for super-resolution fluorescence microscopy.

Feb 21 - Feb 27, 2021

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  Large-Scale Visualization of Scientific Data

  Markus Hadwiger, Professor, Computer Science

  Feb 23, 15:00 - 16:30

  KAUST

  data visualisation

  "A picture is worth a thousand words", and by going beyond static images, interactive visualization has become crucial to exploring, analyzing, and understanding large-scale scientific data. This is true for many areas of science and engineering, such as high-resolution imaging in neuroscience or materials science, as well as in large-scale fluid simulations of the Earth’s atmosphere and oceans, or of trillion-cell oil reservoirs. However, the fact that the amount of data in data-driven sciences is increasing rapidly toward the petascale, and further, presents a tremendous challenge to interactive visualization and analysis. Nowadays, an important enabler of interactivity is often the parallel processing power of GPUs, which, however, requires well-designed customized data structures and algorithms. Furthermore, scientific data sets do not only get larger, they also get more and more complex, and thus have become very hard to interpret and analyze. In this talk, I will give an overview of the research of my group in large-scale scientific visualization, from data structures and algorithms that enable petascale visualization on GPUs, to novel visual abstractions for interactive analysis of highly complex structures in neuroscience, to novel mathematical techniques that leverage differential geometric methods for the detection and visualization of features in large, complex fluid dynamics data on curved surfaces such as the Earth.
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  Look Here! Guiding Attention in Complex Visualizations

  Manuela Waldner, Assistant Professor at the Research Unit of Computer Graphics of the Institute of Visual Computing and Human-Centered Technology at TU Wien, Austria

  Feb 22, 12:00 - 13:00

  KAUST

  Drawing the user's attention to important items in an image, a complex visualization, or a cluttered graphical user interface is a non-trivial challenge. In the context of visualization, our goal is to effectively attract the user's attention to relevant items in large and complex scenes, while keeping noticeable modifications of the image to a minimum. In this talk, I will give an overview of common highlighting methods and present results from my research on attention guidance in complex, dynamic visualizations.

Feb 14 - Feb 20, 2021

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  Nanovisualization: Depicting the Tiny World Around Us

  Ivan Viola, Associate Professor, Computer Science

  Feb 17, 11:30 - 13:00

  KAUST

  nanovisualization

  Life at micron-scale is inaccessible to the naked eye. To aid the comprehension of nano- and micro-scale structural complexity, we utilize 3D visualization. Thanks to efficient GPU-accelerated algorithms, we witness a dramatic boost in the sheer size of structures that can be visually explored. As of today an atomistic model of the entire bacterial cell can be displayed interactively. On top of that, advanced 3D visualizations efficiently convey the multi-scale hierarchical architecture and cope with the high degree of structural occlusion which comes with dense packing of biological building blocks. To further scale up the size of life forms that can be visually explored, the rendering pipeline needs to integrate runtime construction of the biological structure. Assembly rules define how a body of a certain biological entity is composed. Such rules need to be applied on-the-fly, depending on where the viewer is currently located in the 3D scene to generate full structural detail for that part of the scene. We will review how to construct membrane-like structures, soluble protein distributions, and fiber strands through parallel algorithms, resulting in a collision-free biologically-valid scene. Assembly rules that define how a life form is structurally built need to be expressed in an intuitive way for the domain scientist, possibly directly in the three-dimensional space. Instead of placing one biological element next to another one for the entire biological structure by the modelers themselves, only assembly rules need to be specified and the algorithm will complete the application of those rules to form the entire biological entity. These rules are derived from current scientific knowledge and from all available experimental observations. The Cryo-EM Tomography is on rising and shows that we can already now reach the near-atomistic detail when employing smart algorithms. Our assembly rules extraction, therefore, needs to integrate with microscopic observations, to create an atomistic representation of specific, observed life forms, instead of generic models thereof. Such models then can be used in whole-cell simulations, and in the context of automated science dissemination.
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  Resilience is the Cybersecurity of the XXI century, and here's why! - 2021-02-15

  Feb 15, 12:00 - 13:00

  KAUST

  In a nutshell, Resilient Computing is a new paradigm based on modelling, architecting and designing computer systems so that: they have built-in baseline defences; such defences cope with virtually any quality of threat, be it accidental faults, design errors, cyber-attacks, or unexpected operating conditions; provide incremental protection of, and automatically adapt to, a dynamic range of threat severity; provide sustainable operation.

Feb 7 - Feb 13, 2021

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  Generative Adversarial Networks and Generative Modeling

  Peter Wonka, Professor, Computer Science

  Feb 8, 12:00 - 13:00

  KAUST

  I will review some background of generative adversarial modeling using GANs and discuss how our group has been using GANs for image editing.
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  Leveraging Readily Available Data for Low Resource Natural Language Processing

  Derry Wijaya, Assistant Professor, Computer Science, Boston University

  Feb 7, 15:00 - 16:00

  KAUST

  Natural Language Processing

  State-of-the-art Natural Language Processing (NLP) systems nowadays are dominated by machine learning and deep learning models. However, most of these models often only work well when there are abundant labeled data for training. Furthermore, as these models typically have a large number of parameters, they require large compute resources to train. For the majority of languages in the world and the researchers working on these languages, however, abundant labeled data are a privilege and so do compute resources. How can we train generalizable NLP models that are effective even when labeled data are scarce and compute resources are limited? In this talk, I will present some of our solutions that leverage unsupervised or few-shot learning and readily available multilingual resources or multimodal data to improve machine translation and nuanced text classification such as news framing under these low resource settings.

Jan 31 - Feb 6, 2021

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  Enabling Accurate and Efficient Simulation in Visual Computing - Graduate Seminar - CS

  Dominik L. Michels, Associate Professor, Computer Science

  Feb 1, 12:00 - 13:00

  KAUST

  The overarching goal of Prof. Michels' Computational Sciences Group within KAUST's Visual Computing Center is enabling accurate and efficient simulations for applications in Scientific and Visual Computing.

Jan 24 - Jan 30, 2021

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  Building Better Datacenters - The Quest for Low Latency

  Simon Peter, Assistant professor, Computer Science, University of Texas, Austin

  Jan 25, 18:30 - 19:30

  KAUST

  In this talk, I focus on the adoption of low latency persistent memory modules (PMMs). PMMs upend the long-established model of remote storage for distributed file systems. Instead, by colocating computation with PMM storage we can provide applications with much higher IO performance, sub-second application failover, and strong consistency. To demonstrate this, I present Assise, a new distributed file system, based on a persistent, replicated coherence protocol that manages client-local PMM as a linearizable and crash-recoverable cache between applications and slower (and possibly remote) storage.
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  Building Latency-Critical Datacenter Systems

  Marios Kogias, Researcher, Computer Science, Microsoft Research, Cambridge

  Jan 24, 10:00 - 11:00

  KAUST

  In the first part of the talk, I will focus on ZygOS[SOSP 2017], a system optimized for μs-scale, in-memory computing on multicore servers. ZygOS implements a work-conserving scheduler within a specialized operating system designed for high request rates and a large number of network connections. ZygOS revealed the challenges associated with serving remote procedure calls (RPCs) on top of a byte-stream oriented protocol, such as TCP. In the second part of the talk, I will present R2P2[ATC 2019]. R2P2 is a transport protocol specifically designed for datacenter RPCs, that exposes the RPC abstraction to the endpoints and the network, making RPCs first-class datacenter citizens. R2P2 enables pushing functionality, such as scheduling, fault-tolerance, and tail-tolerance, inside the transport protocol, making it application-agnostic. I will show how using R2P2 allowed us to offload RPC scheduling to programmable switches that can schedule requests directly on individual cores.

Jan 17 - Jan 23, 2021

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  Building Scalable Network Stacks for Modern Applications

  Ahmed Saeed, Postdoctoral Associate, Computer Science, MIT

  Jan 17, 15:00 - 16:00

  KAUST

  This talk covers two research directions that address the shortcomings of existing network stacks. The first is on scalable software network stacks, solving problems in different components of operating systems and applications to allow a single server to handle data flows for tens of thousands of clients. The second is on Wide Area Network (WAN) congestion control, focusing on network-assisted congestion control schemes, where end-to-end solutions fail. The talk will conclude with a discussion of plans for future research in this area.

Nov 29 - Dec 5, 2020

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  Modelling and Simulation of Biological Systems - 2020-12-03

  Gabriel Wittum, Professor (former), Applied Mathematics and Computational Science

  Dec 3, 12:00 - 13:00

  KAUST

  Biological systems are distinguished by their enormous complexity and variability. That is why mathematical modeling and computational simulation of those systems is very difficult, in particular thinking of detailed models which are based on first principles. The difficulties start with geometric modeling which needs to extract basic structures from highly complex and variable phenotypes, on the other hand also has to take the statistic variability into account. Moreover, the models of the processes running on these geometries are not yet well established, since these are equally complex and often couple many scales in space and time. Thus, simulating such systems always means to put the whole frame to test, from modelling to the numerical methods and software tools used for simulation. These need to be advanced in connection with validating simulation results by comparing them to experiments.
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  Enabling Accurate and Efficient Simulation in Visual Computing - Public Colloquium

  Dominik L. Michels, Associate Professor, Computer Science

  Nov 30, 14:30 - 16:00

  KAUST

  visual computing

  The overarching goal of Prof. Michels' Computational Sciences Group within KAUST's Visual Computing Center is enabling accurate and efficient simulations for applications in Scientific and Visual Computing. Towards this goal, the group develops new principled computational methods based on solid theoretical foundations. This talk covers a selection of previous and current work presenting a broad spectrum of research highlights ranging from simulating stiff phenomena such as the dynamics of fibers and textiles, over liquids containing magnetic particles, to the development of complex ecosystems and weather phenomena. Moreover, connection points to the growing field of machine learning are addressed and an outlook is provided with respect to selected technology transfer activities.
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  Research at the Image and Video Understanding Lab (IVUL) - Graduate Seminar - CS

  Bernard Ghanem, Professor, Electrical and Computer Engineering

  Nov 30, 12:00 - 13:00

  KAUST

  In this talk, I will give an overview of research done in the Image and Video Understanding Lab (IVUL) at KAUST. At IVUL, we work on topics that are important to the computer vision (CV) and machine learning (ML) communities, with emphasis on three research themes: Theme 1 (Video Understanding), Theme 2 (Visual Computing for Automated Navigation), Theme 3 (Fundamentals/Foundations).

Nov 22 - Nov 28, 2020

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  Towards Accurate Biomedical Genomics Anywhere Anytime - Public Colloquium

  Xin Gao, Program Chair, Computer Science

  Nov 24, 14:00 - 15:30

  KAUST

  In this talk, I will first give an overview of the research activities in Structural and Functional Bioinformatics Group (http://sfb.kaust.edu.sa). I will then focus on our efforts on developing computational methods to tackle key open problems in Nanopore sequencing. In particular, I will introduce our recent works on developing a collection of computational methods to decode raw electrical current signal sequences into DNA sequences, to simulate raw signals of Nanopore, and to efficiently and accurately align electrical current signal sequences with DNA sequences. I will further introduce their applications in biomedicine and healthcare.
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  From a Virtual Red Sea to the Urban Scales of NEOM: A Decade of Progress Driven by Computational Sciences

  Ibrahim Hoteit, Professor, Earth Science and Engineering

  Nov 23, 12:00 - 13:00

  KAUST

  The talk will present our decade-long efforts to build an integrated data-driven modeling system to study and predict the circulation and climate of the Arabian Peninsula at all scales. Starting from a general description of the Virtual Red Sea Initiative at its achievements so far, I will then outline our ongoing research under the KAUST Centre of Excellence for NEOM to develop new tools to seamlessly project and study the environment at the urban scales of NEOM. I will in particular discuss the involved scientific opportunities and challenges in terms of computational Sciences, including our extreme computational requirements, and the handling, analysis and visualization of very large datasets.

Nov 15 - Nov 21, 2020

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  Start your Research Journey at KAUST - Master and Ph.D. degrees in Applied Mathematics, Computer Science, Electrical Engineering and Statistics

  Aigars Ekers, Dean, University of Latvia, Faculty of Science and Technology

  Nov 18, 16:00 - 17:00

  KAUST

  Did you know that courses are taught in English at KAUST? Did you know that the faculty and students are from more than 100 countries? Did you know that you will be fully funded when studying at KAUST? What you will learn from this webinar: Life at KAUST: What are KAUST and CEMSE? Degrees and Academic Programs Research Areas and Lab Facilities Eligibility and Admission Requirements KAUST Fellowship: Benefits of studying at KAUST How to Apply?
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  Federated Learning of a Mixture of Global and Local Models

  Filip Hanzely, Ph.D., Applied Mathematics and Computational Science

  Nov 16, 12:00 - 13:00

  KAUST

  We propose a new optimization formulation for training federated learning models. The standard formulation has the form of an empirical risk minimization problem constructed to find a single global model trained from the private data stored across all participating devices. In contrast, our formulation seeks an explicit trade-off between this traditional global model and the local models, which can be learned by each device from its own private data without any communication. Further, we develop several efficient variants of SGD (with and without partial participation and with and without variance reduction) for solving the new formulation and prove communication complexity guarantees.

Nov 8 - Nov 14, 2020

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  Exploring Entity Relationship in Pairwise Ranking: Adaptive Sampler and Beyond

  Lu Yu, Ph.D., Computer Science

  Nov 11, 16:00 - 18:00

  KAUST

  Living in the booming age of information, we have to rely on powerful information retrieval tools to seek the unique piece of desired knowledge from such a big data world, like using personalized search engines and recommendation systems. In this thesis, we aim at advancing the development of the methodologies and principles of mining heterogeneous information networks through learning entity relations from a pairwise learning to rank optimization perspective. More specifically we first show the connections of different relation learning objectives modified from different ranking metrics including both pairwise and list-wise objectives. We prove that most of popular ranking metrics can be optimized in the same lower bound. Secondly, we propose the class-imbalance problem imposed by entity relation comparison in ranking objectives, and prove that class-imbalance problems can lead to frequency clustering and gradient vanishment problems. As a response, we indicate out that developing a fast adaptive sampling method is very essential to boost the pairwise ranking model. To model the entity dynamic dependency, we propose to unify the individual-level interaction and union-level interactions, and result in a multi-order attentive ranking model to improve the preference inference from multiple views.
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  Interactive Visual Data Analysis

  Eduard Gröller, Associate Professor of Practical Informatics at the Vienna University of Technology

  Nov 9, 12:00 - 13:00

  KAUST

  Visualization and visual computing use computer-supported, interactive, visual representations of (abstract) data to amplify cognition. In recent years data complexity concerning volume, veracity, velocity, and variety has increased considerably. This is due to new data sources as well as the availability of uncertainty, error, and tolerance information.

Nov 1 - Nov 7, 2020

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  Making RPCs first class datacenter citizens

  Marios Kogias, Researcher, Microsoft Research

  Nov 2, 12:00 - 13:00

  KAUST

  I’ll cover thee different RPC policies implemented on top of R2P2. Specifically, we’ll see how R2P2 enables efficient in-network RPC load balancing based on a novel join-bounded-shortest-queue (JBSQ) policy. JBSQ lowers tail latency by centralizing pending RPCs in the middle box and ensures that requests are only routed to servers with a bounded number of outstanding requests. Then, I’ll talk about SVEN, an SLO-aware RPC admission control mechanism implemented as an R2P2 policy on P4 programmable switches. Finally, I’ll describe HovercRaft, a new approach to building fault-tolerant generic RPC services by integrating state-machine replication in the transport layer.

Oct 25 - Oct 31, 2020

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  Compressed communication in Distributed Deep Learning - A Systems perspective

  Panagiotis Kalnis, Professor, Computer Science

  Oct 26, 12:00 - 13:00

  KAUST

  Deep learning

  Network communication is a major bottleneck in large-scale distributed deep learning. To minimize the problem, many compressed communication schemes, in the form of quantization or sparsification, have been proposed. We investigate them from the Computer Systems perspective, under real-life deployments. We identify discrepancies between the theoretical proposals and the actual implementations, and analyze the impact on convergence.

Oct 18 - Oct 24, 2020

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  Automatic Biomedical Hypothesis Generation by Learning from Dynamic Graphs

  Prof. Xiangliang Zhang

  Oct 18, 14:00 - 15:00

  KAUST

  This talk will introduce two novel models we developed for automatic HG generation in two different settings, positive-negative learning and positive-unlabeled learning. We demonstrate the efficacy of the proposed model on three real-world datasets constructed from biomedical publications.

Oct 11 - Oct 17, 2020

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  Dynamic Programming Multi-Objective Combinatorial Optimization

  Michal A. Mankowski, Postdoctoral Research Fellow, Computer Science

  Oct 13, 15:00 - 16:00

  KAUST

  combinatorial optimization global sequence alignment multi-stage optimization algorithm

  In this dissertation, we consider extensions of dynamic programming for combinatorial optimization. We introduce two exact multi-objective optimization algorithms: the multi-stage optimization algorithm that optimizes the problem relative to the ordered sequence of objectives (lexicographic optimization) and the bi-criteria optimization algorithm that simultaneously optimizes the problem relative to two objectives (Pareto optimization).
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  Visualization and segmentation in Geology and Oil exploration

  Daniel Patel, Bergen University College, Norway

  Oct 12, 12:00 - 13:00

  KAUST

  The talk will consist of two parts. First an introduction to important subsurface structures in relation to hydrocarbon extraction are given, followed by an overview of techniques to segment out and visualize these structures. The talk will include topics such as ground truth visualization of measured seismic data, automated object extraction for getting computer assistance in segmenting important structures in the seismic data such as horizons and faults and creation, and visualizing and visual fusion of multiattribute seismic data using the GPU.

Oct 4 - Oct 10, 2020

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  Extensions of Dynamic Programming for Combinatorial Optimization and Data Mining - 2020

  Mikhail Moshkov, Professor, Applied Mathematics and Computational Science

  Oct 5, 12:00 - 13:00

  KAUST

  We developed extensions of dynamic programming which allow us (i) to describe the set of objects under consideration, (ii) to perform a multi-stage optimization of objects relative to different criteria, (iii) to count the number of optimal objects, (iv) to find the set of Pareto optimal points for the bi-criteria optimization problem, and (v) to study the relationships between two criteria.

Sep 27 - Oct 3, 2020

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  Personalized, Predictive and Preventive Visual Analytics for Cancer Treatment

  Renata Raidou, Assistant Professor (Tenure Track) in Medical Visualization and Visual Analytics, and a Rosalind Franklin Fellow at the Bernoulli Institute of the University of Groningen, Netherlands

  Sep 28, 12:00 - 13:00

  KAUST

  The term P4 medicine has been coined almost a decade ago to indicate novel ways of early detection and prevention of diseases. P4 stands for personalized, predictive, preventive, and participatory, to indicate that a diagnosis or treatment is tailored to each individual patient, risk factors are identified early and addressed before manifestation, and individuals are actively involved into all processes. Often, P4 approaches are accompanied by the acquisition of large and complex medical imaging data, and demanding computational processes–especially, when it comes to cancer radiotherapy, which is a data heavy and visual computing rich process.

Sep 20 - Sep 26, 2020

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  Data-sparse Algorithms for Large-scale Applications on Emerging Architectures

  David Keyes, Professor, Applied Mathematics and Computational Science

  Sep 21, 12:00 - 13:00

  KAUST

  A traditional goal of algorithmic optimality, squeezing out operations, has been superseded because of evolution in architecture. Algorithms must now squeeze memory, data transfers, and synchronizations, while extra operations on locally cached data cost relatively little time or energy. Hierarchically low-rank matrices realize a rarely achieved combination of optimal storage complexity and high-computational intensity in approximating a wide class of formally dense operators that arise in exascale applications. They may be regarded as algebraic generalizations of the fast multipole method.

Sep 13 - Sep 19, 2020

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  Automating Guidance in Nanovisualization - Graduate Seminar

  Ivan Viola, Professor, Computer Science

  Sep 14, 12:00 - 13:00

  KAUST

  Research in visualization and computer graphics has developed techniques to geometrically model objects from our everyday life, or from various branches of industry and science, including modeling life-forms that are of submicron in size. These are not visible to the naked eye and most of us are unfamiliar with structures that form life organized in an assembly of biomolecules. Here visualization techniques can be of tremendous help to guide the viewers to familiarize themselves with what they see and make the engaging visual exploration of these complex structures to an intellectual enrichment.
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  Learning from Scholarly Attributed Graphs for Scientific Discovery

  Uchenna Akujuobi, Ph.D., Computer Science

  Sep 14, 11:30 - 12:30

  KAUST

  Research and experimentation in various scientific fields are based on the knowledge and ideas from scholarly literature. The advancement of research and development has, thus, strengthened the importance of literary analysis and understanding. However, in recent years, researchers have been facing massive scholarly documents published at an exponentially increasing rate. Analyzing this vast number of publications is far beyond the capability of individual researchers. This dissertation is motivated by the need for large scale analyses of the exploding number of scholarly literature for scientific knowledge discovery and information retrieval. In the first part of this dissertation, the interdependencies between scholarly literature are studied. First, I develop Delve -- a data-driven search engine supported by our designed semi-supervised edge classification method. This system enables users to search and analyze the relationship between datasets and scholarly literature. Based on the Delve system, I propose to study information extraction as a node classification problem in attributed networks. Specifically, if we can learn the research topics of documents (nodes in a network), we can aggregate documents by topics and retrieve information specific to each topic (e.g., top-k popular datasets).

Sep 6 - Sep 12, 2020

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  On Studying Computer Science - 2020-09-07

  Peter Wonka, Professor, Computer Science

  Sep 7, 12:00 - 13:00

  KAUST

  Computer science

  The talk will be pre-recorded and a youtube link will be provided to seminar participants. During the seminar time, Prof. Wonka will mainly answer some questions from the audience.

Aug 30 - Sep 5, 2020

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  Machine Learning Models for Biomedical Ontology Integration and Analysis

  Fatima Zohra Smaili, Ph.D. Student, Computer Science

  Sep 3, 16:00 - 17:00

  KAUST

  Biological knowledge is widely represented in the form of ontologies and ontology-based annotations. The structure and information contained in ontologies and their annotations make them valuable for use in machine learning, data analysis and knowledge extraction tasks. In this thesis, we propose the first approaches that can exploit all of the information encoded in ontologies, both formal and informal, to learn feature embeddings of biological concepts and biological entities based on their annotations to ontologies by applying transfer learning on the literature. To optimize learning that combines ontologies and natural language data such as the literature, we also propose a new approach that uses self-normalization with a deep Siamese neural network to improve learning from both the formal knowledge within ontologies and textual data. We validate the proposed algorithms by applying them to generate feature representations of proteins, and of genes and diseases.
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  Large-Scale Visualization of Scientific Data: Volume Data and Flow Fields - 2020-08-31

  Markus Hadwiger, Professor, Computer Science

  Aug 31, 12:00 - 13:00

  KAUST

  ‌ Abstract Welcome to the new semester! This talk will give an overview of the research of the High-Performance Visualization research group (vccvisualization.org) at the KAUST Visual Computing Center (VCC). Interactive visualization is crucial to exploring, analyzing, and understanding large-scale scientific data, such as the data acquired in medicine or neurobiology using computed tomography or electron microscopy, and data resulting from large-scale simulations such as fluid flow in the Earth’s atmosphere and oceans. The amount of data in data-driven science is increasing rapidly toward the

Jul 5 - Jul 11, 2020

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  Maximizing I/O Bandwidth for Out-of-Core HPC Applications on Heterogeneous Large-Scale Systems

  Tariq Alturkestani, Ph.D. Student, Computer Science

  Jul 9, 16:00 - 17:00

  KAUST

  Out-of-Core simulation systems often produce a massive amount of data that cannot fit on the aggregate fast memory of the compute nodes, and they also require to read back these data for computation. As a result, I/O data movement can be a bottleneck in large-scale simulations. Advances in memory architecture have made it feasible to integrate hierarchical storage media on large-scale systems, starting from the traditional Parallel File Systems to intermediate fast disk technologies (e.g., node-local and remote-shared NVMe and SSD-based Burst Buffers) and up to CPU’s main memory and GPU’s High Bandwidth Memory. However, while adding additional and faster storage media increases I/O bandwidth, it pressures the CPU, as it becomes responsible for managing and moving data between these layers of storage. Simulation systems are thus vulnerable to being blocked by I/O operations. The Multilayer Buffer System (MLBS) proposed in this research demonstrates a general method for overlapping I/O with computation that helps to ameliorate the strain on the processors through asynchronous access. The main idea consists in decoupling I/O operations from computational phases using dedicated hardware resources to perform expensive context switches. By continually prefetching up and down across all hardware layers of the memory/storage subsystems, MLBS transforms the original I/O-bound behavior of evaluated applications and shifts it closer to a memory-bound or compute-bound regime.

May 3 - May 9, 2020

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  Modeling and Automated Storytelling of Mesoscale Molecular Models

  Ivan Viola, Professor, Computer Science

  May 4, 12:00 - 13:00

  KAUST

  multi-scale 3D visualization biological models

  In my talk, I will present techniques that allow biologists to model a mesocale entity in a rapid way in the timeframe of a few minutes to hours. This way we have created the first complete atomistic model of the SARS-CoV-2 virion that we are these days sharing with the worldwide scientific community. Mesoscale represents a scalar gap that is currently not possible to accurately image with neither microscopy nor X-ray crystallography approaches. For this purpose, scientists characterize it by observations from the surrounding nanoscale and the microscale. From this information, it is possible to reconstruct a three-dimensional model of a biological entity with a full atomistic model. The problem is that these models are enormously large and are not possible to model with traditional methods from computer graphics within a reasonable time.

Apr 26 - May 2, 2020

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  A New Approach to Quad Mesh Processing for Computational Design and Fabrication

  Apr 27, 12:00 - 13:00

  KAUST

  computational design fabrication

  In this talk, we will discuss a new way of computing with quad meshes. It is based on the checkerboard pattern of parallelograms one obtains by subdividing a quad mesh at its edge midpoints. The new approach is easy to understand and implement. It simplifies the transfer from the familiar theory of smooth surfaces to the discrete setting of quad meshes. This is illustrated with applications to constrained editing of 3D models, mesh design for architecture and digital modeling of shapes which can be fabricated by bending flat pieces of inextensible sheet material.

Apr 19 - Apr 25, 2020

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  Simulation of Neuronal Signal Processing - 2020-04-20

  Gabriel Wittum, Professor (former), Applied Mathematics and Computational Science

  Apr 20, 12:00 - 13:00

  KAUST

  Neuronal ensembles

  In the lecture, we present a three-dimensional model for the simulation of signal processing in neurons. Part of this approach is a method to reconstruct the geometric structure of neurons from data measured by 2-photon microscopy. Being able to reconstruct neural geometries and network connectivities from measured data is the basis of understanding coding of motoric perceptions and long term plasticity which is one of the main topics of neuroscience. Other issues are compartment models and upscaling.

Apr 12 - Apr 18, 2020

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  Extensions of Dynamic Programming for Combinatorial Optimization and Data Mining

  Mikhail Moshkov, Professor, Applied Mathematics and Computational Science

  Apr 13, 12:00 - 13:00

  KAUST

  data mining Dynamic programming combinatorial optimization

  Dynamic programming is an efficient technique to solve optimization problems. It is based on decomposing the initial problem into simpler ones and solving these sub-problems beginning from the simplest ones. A conventional dynamic programming algorithm returns an optimal object from a given set of objects. We developed extensions of dynamic programming which allow us (i) to describe the set of objects under consideration, (ii) to perform a multi-stage optimization of objects relative to different criteria, (iii) to count the number of optimal objects,(iv) to find the set of Pareto optimal points for the bi-criteria optimization problem, and (v) to study the relationships between two criteria.

Apr 5 - Apr 11, 2020

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  Predicting Single Gene Loss of Function Phenotypes

  Maxat Kulmanov, Research Scientist, Bio-Ontology Research Group

  Apr 6, 19:30 - 21:30

  KAUST

  We developed and expanded novel methods for representation learning, predicting protein functions and their loss of function phenotypes. We use deep neural network algorithm and combine them with symbolic inference into neural-symbolic algorithms. Our work significantly improves previously developed methods for predicting protein functions through methodological advances in machine learning, incorporation of broader data types that may be predictive of functions, and improved systems for neural-symbolic integration. The methods we developed are generic and can be applied to other domains in which similar types of structured and unstructured information exist. In future, our methods can be applied to prediction of protein function for metagenomic samples in order to evaluate the potential for discovery of novel proteins of industrial value. Also our methods can be applied to the prediction of loss of function phenotypes in human genetics and incorporate the results in a variant prioritization tool that can be applied to diagnose patients with Mendelian disorders.
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  Deep Continual Learning

  Mohamed Elhoseiny, Associate Professor, Computer Science

  Apr 6, 12:00 - 13:00

  KAUST

  Deep learning

  In this seminar, I will present some of the work I have done on Continual Deep Learning, among the research topics at the Vision-CAIR group. Continual learning aims to learn new tasks without forgetting previously learned ones. This is especially challenging when one cannot access data from previous tasks and when the model has a fixed capacity as adopted in modern deep learning techniques. Decreasing the gap towards human-level continual learning, we extended continual deep learning from multiple perspectives. The Hebb's learning theory from biology can be famously summarized as “Cells that fire together wire together.". Inspired by this theory from biology, we proposed Memory Aware Synapses (ECCV18) to quantify and reduce machine forgetting in a way that enables leveraging unlabeled data, which was not possible in former techniques. We later developed a Bayesian approach appearing at ICLR2020, where we explicitly modeled uncertainty parameters to orchestrates forgetting in continual learning. We showed in our ICLR2019 and ACCV18 works that task descriptors/ language can operate in continual learning visual tasks to improve learning efficiency and enable zero-shot task transfer. Beyond computer vision tasks, we recently developed an approach appearing at ICLR2020 we call "Compositional Language Continual Learning". We showed that disentangling syntax from semantics enables better compositional Seq2Seq learning and can significantly alleviate forgetting of tasks like machine translation. In the talk, I will go over these techniques and shed some light on future research possibilities.

Mar 29 - Apr 4, 2020

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  Breaking Shackles: Hardware Acceleration Beyond the CPU

  Suhaib Fahmy, Reader, School of Engineering, University of Warwick, UK

  Apr 1, 12:00 - 13:00

  KAUST

  This talk discusses a body of work on exploiting the DSP Blocks in modern FPGAs to construct high-performance datapaths including the concept of FPGA overlays. It outlines work that established FPGAs as a viable virtualized cloud acceleration platform, and how the industry has adopted this model. Finally, it discusses recent work on incorporating accelerated processing in network controllers and the emerging concept of in-network computing with FPGAs. These strands of work come together to demonstrate the value of thinking about computing beyond the CPU-centric view that still dominates.
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  EE+CS Graduate Seminar: Deep Graph Convolutional Networks

  Bernard Ghanem, Professor, Electrical and Computer Engineering

  Mar 29, 12:00 - 13:00

  KAUST

  Deep learning GCN

  In this talk, I will present a line of work done at the Image and Video Understanding Lab (IVUL), which focuses on developing deep graph convolutional networks (DeepGCNs). A GCN is a deep learning network that processes generic graph inputs, thus extending the impact of deep learning to irregular grid data including 3D point clouds and meshes, social graphs, protein interaction graphs, etc. By adapting architectural operations from the CNN realm and reformulating them for graphs, we were the first to show that GCNs can go as deep as CNNs. Developing such a high capacity deep learning platform for generic graphs opens up many opportunities for exciting research, which spans applications in the field of computer vision and beyond, architecture design, and theory. In this talk, I will showcase some of the GCN research done at IVUL and highlight some interesting research questions for future work.

Mar 22 - Mar 28, 2020

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  How to Preserve Privacy in Learning?

  Di Wang, Ph.D. Student, Computer Science and Engineering, State University of New York at Buffalo

  Mar 24, 15:00 - 16:00

  KAUST

  In this talk, I will use the Empirical Risk Minimization (ERM) problem as an example and show how to overcome these challenges. Particularly, I will first talk about how to overcome the high dimensionality challenge from the data for Sparse Linear Regression in the local DP (LDP) model. Then, I will discuss the challenge from the non-interactive LDP model and show a series of results to reduce the exponential sample complexity of ERM. Next, I will present techniques on achieving DP for ERM with non-convex loss functions. Finally, I will discuss some future research along these directions.
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  Building Compilers for High Performance Code Generation

  Riyadh Baghdadi, Postdoctoral Associate, Computer Science, MIT

  Mar 22, 15:00 - 16:00

  KAUST

  This talk is about building compilers for high-performance code generation. It has three parts. The first part is about Tiramisu (http://tiramisu-compiler.org/), a polyhedral compiler designed for generating highly efficient code for multicores and GPUs. It is the first polyhedral compiler that can match the performance of highly hand-optimized industrial libraries such as Intel MKL and cuDNN. The second part is about applying Tiramisu to accelerate deep learning (DNN) inference. In comparison to other DNN compilers, Tiramisu has two unique features: (1) it supports sparse DNNs; and (2) it can express and optimize general RNNs (Recurrent Neural Networks). The third part will present recent work on the problem of automatic code optimization. In particular, it will focus on using deep learning to build a cost model to explore the search space of code optimizations.

Mar 15 - Mar 21, 2020

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  On Studying Computer Science - 2020-03-16

  Peter Wonka, Professor, Computer Science

  Mar 16, 12:00 - 13:00

  KAUST

  Computer science

  In this talk, I will discuss a wide range of ideas on studying computer science and doing research in computer science. Peter Wonka is the program chair of the computer science program. His research interests are deep learning, computer graphics, computer vision, and remote sensing.

Mar 1 - Mar 7, 2020

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  Knowledge-based methods in life sciences

  Robert Hoehndorf, Associate Professor, Computer Science

  Mar 3, 10:00 - 11:30

  B9 L2 H2 R2325

  Computer science bioinformatics knowledge representation

  In my research I aim to understand how formalized knowledge bases can be used to systematically structure and integrate biological knowledge, and how to utilize these formalized knowledge bases as background knowledge to improve scientific discovery in biology and biomedicine. To achieve these aims, I develop methods for representing, integrating, and analyzing data and knowledge with the specific aim to make the combination of data and formalized knowledge accessible to data analytics and machine learning in bioinformatics. Biomedicine, and life sciences in general, are an ideal domain for knowledge-driven data analysis methods due to the large number of formal knowledge bases that have been developed to capture the broad, diverse, and heterogeneous data and knowledge.
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  Data-sparse Methods for Large-scale Applications on Emerging Architectures

  David Keyes, Professor, Applied Mathematics and Computational Science

  Mar 2, 12:00 - 13:00

  B9 L2 H1 R2322

  hierarchical computations

  A traditional goal of algorithmic optimality, squeezing out operations, has been superseded because of evolution in architecture. Arithmetic operations no longer serve as a reasonable proxy for all aspects of complexity. Instead, algorithms must now squeeze memory, data transfers, and synchronizations, while extra operations on locally cached data represent only small costs in time and energy. Hierarchically low-rank matrices realize a rarely achieved combination of optimal storage complexity and high-computational intensity in approximating a wide class of formally dense operators that arise in applications for which exascale computers are being constructed. We describe modules of a KAUST-built software toolkit, Hierarchical Computations on Manycore Architectures (HiCMA), that illustrate these features and are building blocks of KAUST mission applications, such as matrix-free higher-order methods in optimization and large-scale spatial statistics. Early modules of this open-source project have undergone industrial-rigor testing are distributed in the software libraries of major vendors.

Feb 23 - Feb 29, 2020

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  Multi-layer Red Team vs. Blue Team Methods towards Secure Cyber-Physical Energy Systems

  Charalambos (Harrys) Konstantinou, Assistant Professor of Electrical and Computer Engineering with Florida A&M University and Florida State University (FAMU-FSU) College of Engineering

  Feb 24, 12:00 - 13:00

  B9 L2 H1

  cybersecurity Cyber attacks and defenses

  Election hacking, power grid cyber-attacks, troll farms, fake news, ransomware, and other terms have entered our daily vocabularies and are here to stay. Cybersecurity touches nearly every part of our daily lives. Most importantly, national security and economic vitality rely on a safe, resilient, and stable cyber-space. We rely on cyber-physical systems with hardware devices, software platforms, and network systems to connect, travel, communicate, power our homes, provide health care, run our economy, etc. However, cyber-threats and attacks have grown exponentially over the past years, exposing both corporate and personal data, disrupting critical operations, causing a public health and safety impact, and imposing high costs on the economy. In this talk, we will focus on cyber-physical energy systems (CPES) as the backbone of critical infrastructure, and provide a research perspective and present red team security threats, challenges, and blue team countermeasures. We will discuss recent approaches on developing low-budget targeted cyberattacks against CPES, designing resilient methods against false data, and the need for an accurate assessment environment achieved through the inclusion of hardware-in-the-loop testbeds.