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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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.

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.

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.

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).

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.

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.

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.

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.

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.

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).

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.

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.