Lamia Youseff

Bio: Lamia Youseff is an academic researcher from University of California, Santa Barbara. The author has contributed to research in topics: Cloud computing & Virtual machine. The author has an hindex of 13, co-authored 21 publications receiving 3678 citations. Previous affiliations of Lamia Youseff include Massachusetts Institute of Technology & Google.

The Eucalyptus Open-Source Cloud-Computing System

Abstract: Cloud computing systems fundamentally provide access to large pools of data and computational resources through a variety of interfaces similar in spirit to existing grid and HPC resource management and programming systems. These types of systems offer a new programming target for scalable application developers and have gained popularity over the past few years. However, most cloud computing systems in operation today are proprietary, rely upon infrastructure that is invisible to the research community, or are not explicitly designed to be instrumented and modified by systems researchers. In this work, we present Eucalyptus -- an open-source software framework for cloud computing that implements what is commonly referred to as Infrastructure as a Service (IaaS); systems that give users the ability to run and control entire virtual machine instances deployed across a variety physical resources. We outline the basic principles of the Eucalyptus design, detail important operational aspects of the system, and discuss architectural trade-offs that we have made in order to allow Eucalyptus to be portable, modular and simple to use on infrastructure commonly found within academic settings. Finally, we provide evidence that Eucalyptus enables users familiar with existing Grid and HPC systems to explore new cloud computing functionality while maintaining access to existing, familiar application development software and Grid middle-ware.

Toward a Unified Ontology of Cloud Computing

Abstract: Progress of research efforts in a novel technology is contingent on having a rigorous organization of its knowledge domain and a comprehensive understanding of all the relevant components of this technology and their relationships. Cloud computing is one contemporary technology in which the research community has recently embarked. Manifesting itself as the descendant of several other computing research areas such as service-oriented architecture, distributed and grid computing, and virtualization, cloud computing inherits their advancements and limitations. Towards the end-goal of a thorough comprehension of the field of cloud computing, and a more rapid adoption from the scientific community, we propose in this paper an ontology of this area which demonstrates a dissection of the cloud into five main layers, and illustrates their interrelations as well as their inter-dependency on preceding technologies. The contribution of this paper lies in being one of the first attempts to establish a detailed ontology of the cloud. Better comprehension of the technology would enable the community to design more efficient portals and gateways for the cloud, and facilitate the adoption of this novel computing approach in scientific environments. In turn, this will assist the scientific community to expedite its contributions and insights into this evolving computing field.

Systematic Analysis of Challenge-Driven Improvements in Molecular Prognostic Models for Breast Cancer

Abstract: Although molecular prognostics in breast cancer are among the most successful examples of translating genomic analysis to clinical applications, optimal approaches to breast cancer clinical risk prediction remain controversial. The Sage Bionetworks–DREAM Breast Cancer Prognosis Challenge (BCC) is a crowdsourced research study for breast cancer prognostic modeling using genome-scale data. The BCC provided a community of data analysts with a common platform for data access and blinded evaluation of model accuracy in predicting breast cancer survival on the basis of gene expression data, copy number data, and clinical covariates. This approach offered the opportunity to assess whether a crowdsourced community Challenge would generate models of breast cancer prognosis commensurate with or exceeding current best-in-class approaches. The BCC comprised multiple rounds of blinded evaluations on held-out portions of data on 1981 patients, resulting in more than 1400 models submitted as open source code. Participants then retrained their models on the full data set of 1981 samples and submitted up to five models for validation in a newly generated data set of 184 breast cancer patients. Analysis of the BCC results suggests that the best-performing modeling strategy outperformed previously reported methods in blinded evaluations; model performance was consistent across several independent evaluations; and aggregating community-developed models achieved performance on par with the best-performing individual models.

Paravirtualization for HPC systems

Abstract: In this work, we investigate the efficacy of using paravirtualizing software for performance-critical HPC kernels and applications. We present a comprehensive performance evaluation of Xen, a low-overhead, Linux-based, virtual machine monitor, for paravirtualization of HPC cluster systems at LLNL. We investigate subsystem and overall performance using a wide range of benchmarks and applications. We employ statistically sound methods to compare the performance of a paravirtualized kernel against three Linux operating systems: RedHat Enterprise 4 for build versions 2.6.9 and 2.6.12 and the LLNL CHAOS kernel. Our results indicate that Xen is very efficient and practical for HPC systems.

An operating system for multicore and clouds: mechanisms and implementation

Abstract: Cloud computers and multicore processors are two emerging classes of computational hardware that have the potential to provide unprecedented compute capacity to the average user. In order for the user to effectively harness all of this computational power, operating systems (OSes) for these new hardware platforms are needed. Existing multicore operating systems do not scale to large numbers of cores, and do not support clouds. Consequently, current day cloud systems push much complexity onto the user, requiring the user to manage individual Virtual Machines (VMs) and deal with many system-level concerns. In this work we describe the mechanisms and implementation of a factored operating system named fos. fos is a single system image operating system across both multicore and Infrastructure as a Service (IaaS) cloud systems. fos tackles OS scalability challenges by factoring the OS into its component system services. Each system service is further factored into a collection of Internet-inspired servers which communicate via messaging. Although designed in a manner similar to distributed Internet services, OS services instead provide traditional kernel services such as file systems, scheduling, memory management, and access to hardware. fos also implements new classes of OS services like fault tolerance and demand elasticity. In this work, we describe our working fos implementation, and provide early performance measurements of fos for both intra-machine and inter-machine operations.

Machine Learning in Medicine.

Abstract: Spurred by advances in processing power, memory, storage, and an unprecedented wealth of data, computers are being asked to tackle increasingly complex learning tasks, often with astonishing success. Computers have now mastered a popular variant of poker, learned the laws of physics from experimental data, and become experts in video games - tasks that would have been deemed impossible not too long ago. In parallel, the number of companies centered on applying complex data analysis to varying industries has exploded, and it is thus unsurprising that some analytic companies are turning attention to problems in health care. The purpose of this review is to explore what problems in medicine might benefit from such learning approaches and use examples from the literature to introduce basic concepts in machine learning. It is important to note that seemingly large enough medical data sets and adequate learning algorithms have been available for many decades, and yet, although there are thousands of papers applying machine learning algorithms to medical data, very few have contributed meaningfully to clinical care. This lack of impact stands in stark contrast to the enormous relevance of machine learning to many other industries. Thus, part of my effort will be to identify what obstacles there may be to changing the practice of medicine through statistical learning approaches, and discuss how these might be overcome.

The Eucalyptus Open-Source Cloud-Computing System

Abstract: Cloud computing systems fundamentally provide access to large pools of data and computational resources through a variety of interfaces similar in spirit to existing grid and HPC resource management and programming systems. These types of systems offer a new programming target for scalable application developers and have gained popularity over the past few years. However, most cloud computing systems in operation today are proprietary, rely upon infrastructure that is invisible to the research community, or are not explicitly designed to be instrumented and modified by systems researchers. In this work, we present Eucalyptus -- an open-source software framework for cloud computing that implements what is commonly referred to as Infrastructure as a Service (IaaS); systems that give users the ability to run and control entire virtual machine instances deployed across a variety physical resources. We outline the basic principles of the Eucalyptus design, detail important operational aspects of the system, and discuss architectural trade-offs that we have made in order to allow Eucalyptus to be portable, modular and simple to use on infrastructure commonly found within academic settings. Finally, we provide evidence that Eucalyptus enables users familiar with existing Grid and HPC systems to explore new cloud computing functionality while maintaining access to existing, familiar application development software and Grid middle-ware.

Achieving Secure, Scalable, and Fine-grained Data Access Control in Cloud Computing

Abstract: Cloud computing is an emerging computing paradigm in which resources of the computing infrastructure are provided as services over the Internet. As promising as it is, this paradigm also brings forth many new challenges for data security and access control when users outsource sensitive data for sharing on cloud servers, which are not within the same trusted domain as data owners. To keep sensitive user data confidential against untrusted servers, existing solutions usually apply cryptographic methods by disclosing data decryption keys only to authorized users. However, in doing so, these solutions inevitably introduce a heavy computation overhead on the data owner for key distribution and data management when fine-grained data access control is desired, and thus do not scale well. The problem of simultaneously achieving fine-grainedness, scalability, and data confidentiality of access control actually still remains unresolved. This paper addresses this challenging open issue by, on one hand, defining and enforcing access policies based on data attributes, and, on the other hand, allowing the data owner to delegate most of the computation tasks involved in fine-grained data access control to untrusted cloud servers without disclosing the underlying data contents. We achieve this goal by exploiting and uniquely combining techniques of attribute-based encryption (ABE), proxy re-encryption, and lazy re-encryption. Our proposed scheme also has salient properties of user access privilege confidentiality and user secret key accountability. Extensive analysis shows that our proposed scheme is highly efficient and provably secure under existing security models.

Mesos: a platform for fine-grained resource sharing in the data center

Abstract: We present Mesos, a platform for sharing commodity clusters between multiple diverse cluster computing frameworks, such as Hadoop and MPI. Sharing improves cluster utilization and avoids per-framework data replication. Mesos shares resources in a fine-grained manner, allowing frameworks to achieve data locality by taking turns reading data stored on each machine. To support the sophisticated schedulers of today's frameworks, Mesos introduces a distributed two-level scheduling mechanism called resource offers. Mesos decides how many resources to offer each framework, while frameworks decide which resources to accept and which computations to run on them. Our results show that Mesos can achieve near-optimal data locality when sharing the cluster among diverse frameworks, can scale to 50,000 (emulated) nodes, and is resilient to failures.