Rudi Cilibrasi, Ph.D.

Education:

PhD, Computer Science, University of Amsterdam, Holland (2007)

BS, with Honors, Computer Science, Division of Engineering and Applied Science
   California Institute of Technology, Pasadena, CA (1996)

Publications:

• R.L. Cilibrasi, P.M.B. Vitanyi, The Google Similarity Distance, IEEE Trans. Knowledge and Data Engineering, 19:3(2007), 370-383.
• R. Cilibrasi, P.M.B. Vitanyi, A New Quartet Tree Heuristic for Hierarchical Clustering, EU-PASCAL Statistics and Optimization of Clustering Workshop, 5-6 Juli 2005, London, UK.
• R. Cilibrasi, R. de Wolf, P. Vitanyi. Algorithmic clustering of music based on string compression, Computer Music J., 28:4(2004), 49-67.
• R. Cilibrasi, P. Vitanyi. Automatic Extraction of Meaning from the Web. IEEE International Symposium on Information Theory, Seattle, Washington, 2006.
• R. Cilibrasi, Zvi Lotker, Alfredo Navarra, Stephane Perennes, Paul Vitanyi. Lifespan of Peer to Peer Networks: Models and Insight, 10th International Conference On Principles Of Distributed Systems (OPODIS 2006), December 12-15, 2006, Bordeaux Saint-Emilion, France, Lecture Notes in Computer Science, Vol. 4305, Springer Verlag, Berlin, 2006, 290-305
• R. Cilibrasi, P. Vitanyi. Clustering by compression, IEEE Trans. Information Theory, 51:4(2005), 1523 - 1545. http://xxx.lanl.gov/abs/cs.CV/0312044.
• R. Cilibrasi, L. van Iersel, S. Kelk, J. Tromp. On the complexity of several haplotyping problems, to appear in proceedings of WABI2005. http://arxiv.org/pdf/q-bio.GN/0505023.
• R. Cilibrasi, L. van Iersel, S. Kelk, J. Tromp. On the complexity of the Single Individual SNP Haplotyping Problem, Feb 2006: Accepted to appear in Algorithmica. http://arxiv.org/pdf/q-bio.GN/0508012.
• R. Cilibrasi, P. Vitanyi. Similarity of Objects and the Meaning of Words, Proc. 3rd Conf. Theory and Applications of Models of Computation (TAMC), 15-20 May, 2006. http://arxiv.org/pdf/cs.CV/0602065
• R. Cilibrasi Domain Independent Hierarchical Clustering Nieuwsbrief van de Nederlandse Vereniging voor Theoretische Informatica, 2004, nummer 8.
• J. Tromp, R. Cilibrasi, The Limits of Rush-Hour Complexity, March 23, 2006. http://arxiv.org/pdf/cs.CC/0502068.
• T.Roos, T.Heikki, R.Cilibrasi, P.Myllymaki. Compression-based Stemmatology: A Study of the Legend of St. Henry of Finland, (tech. report number HIIT-2005-3), 2005.
• R.Cilibrasi. What is Java, Really? In Linux Journal, October 1996
• R. Cilibrasi gave an expert consultation to D. Butler on consumer grid computing for Nature, published in November 2006: Amazon puts network power online

Work Experience:

CWI research institute PhD research student
Worked with a team of mathematicians to develop cutting-edge universal learning systems. Compression-based statistical approach yielded wide array of popular press attention such as http://homepages.cwi.nl/~paulv/pop.htm

FHP Wireless Contract Developer
Worked with internal developers to create new variant of WEP encryption that accelerated wireless traffic by moving encryption off the wireless card firmware and into the Linux kernel, then subtly modifying the encryption algorithm to allow certain types of precalculations to enable turbo charged demonstrations ahead of critical-path wireless-card hardware availability. (1/02-4/02)

Cranite Systems Lead Software Developer
Worked in a small team of engineers to create a wireless security appliance. Our product consisted of a customized Linux kernel and complementary Windows NDIS intermediate driver to provide for transparent Layer 2 encryption and tunnelling using AES and TLS authentication. We also had several user-level demons running to control access based on a Microsoft RADIUS authentication server and centrally administrated security policies. I contributed code to many areas of this project, but most extensively to the AES encryption core functions and the packet-manipulation primitives in C and C++. (1/01-10/01)

Weema Technologies Inc. Chief Technology Officer / Lead Software Architect
Created a Linux-based high-scalability TCP/UDP high-reliability streaming media server in several tens of thousands of lines of C++. Made kernel patches against 2.2 and 2.3 Linux kernels to support very high efficiency single threaded live media serving via new socket-send system call. Designed and implemented internal and external cryptographic security solutions, including firewalling, tunnelling, and custom protocol design using RC4, MD5, and other protocols. Developed real world knowledge of network failure modes under very high loads. (1/00-1/01)

Narus Inc., as offsite solution architect. Duties included Unix systems-level redesign, advanced Perl integration, website strategic planning, and miscellaneous consultation. (8/98-9/99)

M.S.Young and Associates, as legacy-systems migration solution architect. Projects included a Unix pseudoterminal based Web WAN replacement system, working in conjunction with DuPont Chemical, AutoImpact , and other strategic partners under a high-value contract. Also created artificial intelligence and simulation-modelling prototyping. Finally, ongoing offsite Linux system administrator. (3/97-7/98)

Idealab, as developer and development manager for very fast-paced internet development projects. Projects included Java and CGI-based websites, data compression, steganography, and adaptive statistical methods. (6/96-2/97)

Tanner Research, a Pasadena-based VLSI software and research company. One of my tasks was to design and implement new advanced techniques for rapid design-rule checking systems. Another duty was to research and critique various strategies for rewriting one of their major software products. Evaluated several container-class framework approaches and solutions, weighing criteria such as run-time efficiency, memory-efficiency, portability, and (most importantly) long-term internal benefits, such as flexibility, safety, and maintainability. (6/95-9/95)

Caltech as Assistant Head TA for CS 1,2, and 3, a series of introductory courses designed to teach the rudiments of C programming (CS 1), data structures (CS 2), and parallel programming (CS 3). Responsibilities included recruiting, interviewing, selecting and hiring a team of 16 TA's. Additionally, designed and implemented course material and labwork, delivered biweekly lectures, and provided hands-on help for students during laboratory periods. (9/95-6/96)

Contract developer / Linux consultant / Private teacher , as time, opportunity, and interest allows. (3/95-present)

Consulted for Bacchus Inc. Primarily developed graphics support tools in C++. Functionality included: file-format conversion from 3D Studio to DEC OFF format; binary space partitioning algorithms using heuristics to minimize polygonal splits; illumination models for shading. (9/94-6/95)

Microsoft as a software developer in the Advanced Technology department, specifically the 4D Graphics Group. My duties included writing a supporting math library in C++, and leading a team to write a real-time interactive 3D graphics demo for Bill Gates. As core programmer, delegated subtasks to other members of the team as appropriate. Postscript review available. (Rating: Outstanding) (6/94-9/94)

Knowledge Adventure Inc. a software company in Pasadena. Knowledge Adventure specializes in multimedia educational games for use on the PC platform. My duties were primarily C++ and C programming tasks. (1/94-6/94)

Green Hills Software in Santa Barbara as a software engineer / technical support representative. Green Hills makes programming tools; Their main products are multiplatform compilers. My duties included determining whether reported bugs were, in fact, bugs in our compiler, or simply a result of customer error. Isolated and aided in fixing bugs. (6/93-9/93)

Special Skills:

Strong grasp of machine learning, artificial intelligence, and scientific computing via extensive research using data compression, Support Vector Machines, neural networks, simulated annealing, optimization, Minimum Description Length theory, and other techniques. Applied to diverse areas such as computational linguistics, music analysis, radio astronomy, bioinformatics, and automated ontological reasoning using Google.

Programming in a variety of languages, including Ruby, Perl, C++, Java, C, Python, BASIC, SQL, Lisp, Pascal, Prolog, and some assembly languages, including 680x0 and 80x86. Experience with UNIX, MS-DOS/MS-Windows, Amiga, and Macintosh operating systems. Experience with most major development environments including Sun's JDK, Microsoft Developer Studio (Visual J++, Visual C++, Visual Basic), Microsoft Access/SQL, most open-source tools, etc.

Understand UNIX, as user, developer, and system administrator. Experience with shell programming in sh,(t)csh, ksh, and zsh. Fluent with large variety of tools; for software development, autoconf/automake, bison/yacc, (f)lex, svn/cvs/rcs, make, python and m4, to name a few. Clear knowledge of networking from the link layer on up; have used TCP and UDP protocols extensively for fun and profit. Experimented with raw packet analysis and synthesis as a hobby. Built a security tool to monitor a subnet for all active telnet sessions, demultiplex them, and maintain in memory a set of virtual vt100 screens which could be displayed using a curses interface, enabling real-time monitoring of all sessions or eavesdropping. (to demonstrate a good reason to move to ssh)

Deep understanding of computer from VLSI layout / transistor level up to high-level languages; have created layout and simulated a CPU and a floating point processor using the Magic toolset. Have designed and built on wirewrap hardware a 80186 based computer with dynamic memory refresh, keyboard, and serial port. Also created assembly language operating system from scratch. Have worked with device drivers and driver-like software on many platforms, including graphics coprocessor instruction sets on the Amiga computer, hardware ethernet MAC addresses in the Linux kernel (changes incorporated into source tree), terminate-and-stay-resident programs under DOS to intercept keystrokes, etc.

Strong understanding of cryptography - in particular, public and private key encryption, authentication, one-way hash functions, electronic cash, key-exchange protocols, and elliptic curve cryptography. Understand many integer factoring algorithms such as Pollard Rho and Multiple Polynomial Quadratic Sieve. Familiar with theory as well as practice of all popular encryption algorithms. Clear grasp of MD5, RSA, DES, IDEA, RC4, ECC, and others. Sent bug fixes to Bruce Schneier that were incorporated into Applied Cryptography 2nd Edition.

Excellent knowledge of free software with predilection towards GNU tools in general. Specialized knowledge about Linux in particular. Made contributions to the Linux kernel. (v. 1.3.38 and later) Maintain several open-source projects, including
http://complearn.org/, a general-purpose data-mining tool
http://rubysvm.cilibrar.com/, a library for using Support Vector Machines in Ruby
http://mpiruby.sourceforge.net/, MPIRuby, a library for writing supercomputer parallel programs in Ruby

Good understanding of computer graphics. Have implemented several algorithms ranging from ray tracing to binary space partitioning to palette quantization, both for employment and as a hobby. Have also done anti-aliasing transforms, fractals, and vector-based image morphing. Have also done computer music at Microsoft and as a hobby, using waveform synthesis. Have worked with voice synthesis and recognition since 1992.

Data Compression - implemented several ``classical'' data compression algorithms, and wrote some variants of my own. Also took EE150, Data Compression, by Dr. R. J. McEliece, and won a cash prize by creating a compression algorithm slightly better (but much slower) than gzip on an unknown sample file set. Recreated Claude Shannon's famous experiment to determine the entropy of the English language using the internet, and published these results which were later used by a professor at the University of Nevada in a class project.

Automated theorem proving - spent several months researching methods of theorem proving in first-order predicate logic. Experience with many different models for automated deduction, including diverse tasks ranging from game-tree searches with pruning to neural nets. Have also applied genetic algorithms to cryptanalysis of simple substitution cipers with some interesting results regarding the relationship between evolution speed and artificial punctuated population barriers.

Awards:

Appeared in Marquis Who's Who in Science and Engineering, 2006-2007 as a notable figure in science and the creator of the CompLearn open source data mining software.

Won fifth, third, second, and finally first place in successive years in the Association for Computing Machinery programming contest at the regional (Southern California and Nevada) level, as part of a three-person team. (freshman-senior year) Competed in worldwide ACM programming contest representing Caltech in 1996, finally finishing within the top twenty teams in the world that year.

Won $10,000 Microsoft Scholarship in sophomore year. This scholarship was awarded to a single student from each participating school, for merit in computer and computer-related fields.

Won first place in Caltech EE150.2 Data Compression program contest. First prize was $500 cash, paid to the team or individual who wrote the best compression program. The competitors were primarily seniors and graduate-level students. (freshman year) Taught by Dr. McEliece.

Won the Rensselaer Medal, an award given to one junior at each high school for outstanding achievements in science and math.