Russell Sears
Research Publications Classes Resume/CV Public Keys	Research I am a PhD student in Eric Brewer's lab at the University of California, Berkeley. Stasis I am developing an extendible write ahead logging system. It is geared toward high-performance applications that require control over the on-disk layout of their data, or simply are a poor fit for existing storage mechanisms. Unlike past implementations, the library provides fine-grained, layered access to write-ahead-logging components, allowing applications to customize recovery semantics, in-memory layout, logging policies, and eventually distributed storage algorithms. The core interface closely reflects the underlying storage mechanisms, avoiding a number of bottlenecks typical of current systems. I am also interested in using language based techniques such as static analysis, and application-specific optimization strategies to increase the overall reliability and performance of the system. Past Research As an undergraduate, I studied Computer Science at Ohio State University, and worked in Dr. Bo Yuan's bioinformatics research group. Publications Storage Systems Russell Sears, Mark Callaghan, Eric Brewer. Rose: Compressed, log-structured replication, To appear at VLDB, 2008. [pdf] Russell Sears, Catharine van Ingen. Fragmentation in Large Object Repositories, CIDR 2007. [pdf] Russell Sears, Eric Brewer. Stasis: Flexible Transactional Storage, OSDI 2006. [pdf] Russell Sears. A Flexible, Extensible Transaction Framework, HPTS 2005. [ppt] [txt] Russell Sears, Catharine van Ingen, Jim Gray. To BLOB or not to BLOB: Large object storage in a database or filesystem? Microsoft Research technical report, April 2006. [MSR-TR-2006-45] Adversarial Learning Marco Barreno, Blaine Nelson, Russell Sears, and Anthony D. Joseph. User Model Transfer for Email Virus Detection, SysML 2006. [pdf] Blaine Nelson, Marco Barreno, Russell Sears, Anthony D. Joseph and J. D. Tygar. Can Machine Learning be Secure? (Invited paper), ASIACCS 2006. [pdf] Bioinformatics Fred A Wright, William J Lemon, Wei D Zhao, Russell Sears, Degen Zhuo, Jian-Ping Wang, Hee-Yung Yang, Troy Baer, Don Stredney, Joe Spitzner, Al Stutz, Ralf Krahe and Bo Yuan. A Draft Annotation and Overview of the Human Genome, Genome Biol. 2001; 2(7). [pdf] Bo Yuan, Degen Zhuo, Wei D. Zhao, Jian-Ping Wang, Russell Sears, Do-Hun Kwon, David Gordon, Solomon Gibbs, Qing Yang, Ralf Krahe and Fred Wright. Physical Mapping and Functional Annotation of 60,000 Human Genes, Presented at the SC2000 Conference 11/04/2000 - 11/10/2000. Degen Zhuo, Wei D. Zhao, Fred A. Wright, Hee-Yung Yang, Jian-Ping Wang, Russell Sears, Troy Baer, Do-Hun Kwon, David Gordon, Solomon Gibbs, Dean Dai, Qing Yang, Joe Spitzner, Ralf Krahe, Don Stredney, Al Stutz, and Bo Yuan. Assembly, Annotation, and Integration of UNIGENE Clusters into the Human Genome Draft, Genome Research, DOI: 10.1101/gr.GR-1645R. Class projects Here are some of the course projects that I've worked on at Berkeley. Web Traffic Analysis using Latent Dirichlet Allocation of Markov Chains I applied this paper (longer draft copy) to the KDDCUP 2000 gazelle.com dataset, and proposed and tested an extension of the original model. The results were mixed, but the extension to the model may be interesting in other contexts, as the extended model performed well under certain constraints. Aimless Documents Egon Pasztor and I developed a scheme that automatically generates 'glue code' to allow existing software modules to interoperate. It includes a simple query engine and expert system, and an XML-based language that allows end-users and third-party developers to describe interfaces provided by existing software components. A simple bean shell runtime allows the system to be used interactively. Resume [pdf] GPG key [gpg]

Research

I am a PhD student in Eric Brewer's lab at the University of California, Berkeley.

Stasis

I am developing an extendible write ahead logging system. It is geared toward high-performance applications that require control over the on-disk layout of their data, or simply are a poor fit for existing storage mechanisms. Unlike past implementations, the library provides fine-grained, layered access to write-ahead-logging components, allowing applications to customize recovery semantics, in-memory layout, logging policies, and eventually distributed storage algorithms. The core interface closely reflects the underlying storage mechanisms, avoiding a number of bottlenecks typical of current systems.

I am also interested in using language based techniques such as static analysis, and application-specific optimization strategies to increase the overall reliability and performance of the system.

Past Research

As an undergraduate, I studied Computer Science at Ohio State University, and worked in Dr. Bo Yuan's bioinformatics research group.

Publications

Storage Systems

Russell Sears, Mark Callaghan, Eric Brewer. Rose: Compressed, log-structured replication, To appear at VLDB, 2008. [pdf]

Russell Sears, Catharine van Ingen. Fragmentation in Large Object Repositories, CIDR 2007. [pdf]

Russell Sears, Eric Brewer. Stasis: Flexible Transactional Storage, OSDI 2006. [pdf]

Russell Sears. A Flexible, Extensible Transaction Framework, HPTS 2005. [ppt] [txt]

Russell Sears, Catharine van Ingen, Jim Gray. To BLOB or not to BLOB: Large object storage in a database or filesystem? Microsoft Research technical report, April 2006. [MSR-TR-2006-45]

Adversarial Learning

Marco Barreno, Blaine Nelson, Russell Sears, and Anthony D. Joseph. User Model Transfer for Email Virus Detection, SysML 2006. [pdf]

Blaine Nelson, Marco Barreno, Russell Sears, Anthony D. Joseph and J. D. Tygar. Can Machine Learning be Secure? (Invited paper), ASIACCS 2006. [pdf]

Bioinformatics

Fred A Wright, William J Lemon, Wei D Zhao, Russell Sears, Degen Zhuo, Jian-Ping Wang, Hee-Yung Yang, Troy Baer, Don Stredney, Joe Spitzner, Al Stutz, Ralf Krahe and Bo Yuan. A Draft Annotation and Overview of the Human Genome, Genome Biol. 2001; 2(7). [pdf]

Bo Yuan, Degen Zhuo, Wei D. Zhao, Jian-Ping Wang, Russell Sears, Do-Hun Kwon, David Gordon, Solomon Gibbs, Qing Yang, Ralf Krahe and Fred Wright. Physical Mapping and Functional Annotation of 60,000 Human Genes, Presented at the SC2000 Conference 11/04/2000 - 11/10/2000.

Degen Zhuo, Wei D. Zhao, Fred A. Wright, Hee-Yung Yang, Jian-Ping Wang, Russell Sears, Troy Baer, Do-Hun Kwon, David Gordon, Solomon Gibbs, Dean Dai, Qing Yang, Joe Spitzner, Ralf Krahe, Don Stredney, Al Stutz, and Bo Yuan. Assembly, Annotation, and Integration of UNIGENE Clusters into the Human Genome Draft, Genome Research, DOI: 10.1101/gr.GR-1645R.

Class projects

Here are some of the course projects that I've worked on at Berkeley.

Web Traffic Analysis using Latent Dirichlet Allocation of Markov Chains

I applied this paper (longer draft copy) to the KDDCUP 2000 gazelle.com dataset, and proposed and tested an extension of the original model. The results were mixed, but the extension to the model may be interesting in other contexts, as the extended model performed well under certain constraints.

Aimless Documents

Egon Pasztor and I developed a scheme that automatically generates 'glue code' to allow existing software modules to interoperate. It includes a simple query engine and expert system, and an XML-based language that allows end-users and third-party developers to describe interfaces provided by existing software components. A simple bean shell runtime allows the system to be used interactively.

Resume

[pdf]

GPG key

[gpg]