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Paper with Ryan McIntyre to appear in the Journal of Discrete Algorithms

Happy to announce that Ryan McIntyre’s masters thesis results, An improved upper bound and algorithm for clique covers (prelim), will be published as our joint paper in Journal of Discrete Algorithms.

Our paper is on indeterminate strings, which are important for their applicability in bioinformatics. (They have been considered, for example, in Christodoulakis 2015  and Helling 2017.)

An interesting feature of indeterminate strings is the natural correspondence with undirected graphs. One aspect of this correspondence is the fact that the minimal alphabet size of indeterminates representing any given undirected graph corresponds to the size of the minimal clique cover of this graph. This paper first considers a related problem proposed in Helling 2017: characterize $latex\Theta_n(m)$, which is the size of the largest possible minimal clique cover (i.e., an exact upper bound), and hence alphabet size of the corresponding indeterminate, of any graph on $latex n$ vertices and $latex m$ edges. We provide improvements to the known upper bound for $latex \Theta_n(m)$. Helling 2017 also presents an algorithm which finds clique covers in polynomial time. We build on this result with an original heuristic for vertex sorting which significantly improves their algorithm’s results, particularly in dense graphs.

This work was the result of building on Helling 2017 (see this post) and of a year of research undertaken by Ryan McIntyre under my (Michael Soltys) supervision at the California State University Channel Islands.

An article from the CSUCI news center about this work can be found here.

National Engineers Week Banquet @CSUCI

It was a great pleasure to Emcee the National Engineers Week of Ventura and Santa Barbara Counties banquet at CSU Channel Islands (CI). This was the 45th annual engineering week dinner, and the second year (in a row) that it took place at CI.

Thank you to my colleagues Jason Isaacs and Houman Dallali, and their students Adan Sanchez, Alexandra Collette and Nicole Dubin for a display of the student engineering projects at CI. We were delighted to announce that we are welcoming the first cohort of Mechatronics students in the fall of this year (2018). It was especially appropriate to welcome engineers from the local businesses and the local Navy bases at CI, as we pursue three interdependent missions:

  • Scholarship
  • Teaching
  • Engagement in the community

The pièce de résistance event of the evening was a keynote address by  Dr. Adam Steltzner, NASA Engineer with Jet Propulsion Laboratory. Dr. Steltzer is a renowned engineer who led the team responsible for the Curiosity Rover’s successful landing on Mars (the EDL: Entry, Descent, Landing system); the famous 7 Minutes of Terror. Last year Dr. Steltzer was named to the National Academy of Engineering.

It was a great honor to meet Dr. Steltzer and listen to a first hand account of the mission.

Why is it called the 7 Minutes of Terror? In just seven minutes, NASA’s six-wheeled rover called Curiosity, must go from 13,000 mph as it enters the Martian atmosphere to a dead stop on the surface.

During those seven minutes, the rover is on its own. Earth is too far away for radio signals to make it to Mars in time for ground controllers to do anything. Everything in the EDL system must work perfectly, or Curiosity will not so much land as go splat. The team that invented the EDL system, led by Dr. Steltzer, has spent nearly 10 years perfecting it.

Computer Science at CI is hiring a Lab Technician

The job posting can be found here: https://www.csuci.edu/careers/ and select the “Staff Position” button, and once there do the following search:

While the position is temporary until June, the expectation is that it will become a permanent position after that, following a second round of interviews – of course, the first successful candidate would be expected to reapply for the permanent position.

Here is the position description:

Support lab activities and instruction for the Computer Science, Information Technology and Mechatronics Engineering programs. Ensuring safe and effective operation of all Computer Science, Information Technology and Mechatronics Engineering lab facilities. Responsible for complex work in the purchase, installation and maintenance of computer science laboratory equipment and software. This position will also be responsible for supporting equipment and instrumentation of teaching laboratories for Computer Science, Information Technology and Mechatronics.

Maintains the equipment in the general Computer Science, Information Technology and Mechatronics Engineering labs, and in the specialized labs (e.g., networks, robotics, and embedded systems). Perform periodic preventative maintenance as necessary. Set up and operate basic complex electronic equipment and instrumentation such as computers and peripherals, data acquisition hardware and software, electronic imaging, 3d printers, robots, power supplies, etc. Maintains all equipment, cleans and arranges for returns of devices to manufacturer or other repair facilities or for a field engineer to come to the campus for onsite repair in the event of major problems. Analyzes and gives advice on selection and purchase of new equipment, computers, components and software and assists in the selection and set up of vendors. System Administration for Computer Science, Information Technology, and Mechatronics Engineering programs, coordinate and consult, acting as the liaison between the Computer Science, Information Technology, and Mechatronics Engineering with the Division of Technology & Innovation.

Organize and update inventory for the Computer Science, Information Technology, and Mechatronics Engineering labs and prepare these labs for students when necessary. Order needed parts and supplies and maintain budget and purchase records. Responsible for cleaning the equipment in the computer labs.

Requires a minimum of a bachelor’s degree and one year of experience with computer equipment or technical training in electronics or electrical engineer. Experience in an academic environment required. Rudimentary knowledge of hardware, and basic knowledge of network and system security. Excellent written and verbal communications skills, excellent technical communication skills, personal and professional integrity.

Highly desirable skills:
Linux server administration (especially Apache, MySQL, Subversion, and deployments of Ubuntu in both desktop and server), Mac OS X server administration, Windows server administration and Windows and Mac desktop administration. Familiarity with every software package used in any of the Computer Science, Information Technology, and Mechatronics Engineering courses. Network administration (knowledge of DHCP, DNS, TFTP, FTP, SSH/SFTP, TCP/IP; basic knowledge of Open Directory/OpenLDAP and some knowledge of Active Directory).

The lab technician will have to be proactive with the Information Technology needs of the department and possess the ability to work with others to implement solutions. Ability to work independently and be adaptable to new situations is required.

Physical Demands: Frequent/ Continuous reaching within arm’s distance, frequent sitting in office chair, up to 5-7 hours at the time. Occasional lifting /carrying of up to 15 pounds at waist level with office area, continuous use of hands to operate telephone, computer system, filing and writing activities, occasional reaching at or above waist and shoulder level, occasional bending and/or stooping at the waist, continuous use of hands for grasping, fine manipulation and ability to stand/walk up to 20 minutes at a time.

 

Speaking at the Camarillo Chamber of Commerce

my remarks

  • Thank you for the opportunity to tell you about Computer Science at CI
  • We are a fast growing Dept – we doubled our majors to 400 in the last 3 years
  • We are starting a new engineering program in Mechatronics (Mechanical & Engineering) this fall – after years of preparation.
  • We have a program in IT, one Computer Science, and the new Mechatronics program. Also programs in Cybersecurity, robotics, and Game design.
  • We work with the local community: with IT & Manufacturing companies, with Navy, HTTF, and we started an Advisory Board consisting of heads of local business & industry.
  • To give you an idea about our work, I will talk about 3 directions, but there are many more:
    • Houman Dallali – Mechatronics – he was the first targeted Mechatronics hire, and he works in intelligent prosthetics. Cheap Controllers (Raspberry Pi’s) and 3D printers have revolutionized our field, but ours is still an expensive endeavor and we rely on the community – for example, companies such as Advanced Motion or Amgen have given us equipment.
    • Jason Isaacs – Swarmathon – Jason has a PhD in engineering from UCSB, like most of our faculty has years of industrial experience, but loves the University setting and has come back. NASA wants to go to Mars, and Jason and his student are participating in one aspect of that endeavor: a swarm of robots that will be released on Mars to collect raw components to make fuel for the journey back home. We took 3rd place at the competition at Cape Canaveral in Florida in 2017.
    • I work in Algorithms generally speaking, they are the snippets of ideas that become code that run your computers. But I also work, and consult, in Cybersecurity, and we have an ongoing collaboration with HTTF. Set up by the Secret Service and the FBI to aid local law enforcement in dealing with the sophisticated digital crime, they have a lab in Camarillo, at a secret location, and our students have worked on several R&D projects for them, for example SEAKER last summer.
  • Today I have brought two students with me Vlad Synnes and Samuel Decanio who will tell you a little bit about themselves, and a little bit about “Voyager” a project that we did for the HTTF.

C language completes comeback in programming popularity

The once-declining C language has completed a comeback in the monthly Tiobe Index of language popularity, winning the 2017 Programming Language of the Year designation from Tiobe as the biggest gainer in share.

Although the language only grew 1.69 percentage points in its rating year over year in the January index, that was enough beat out runners-up Python (1.21 percent gain) and Erlang (0.98 percent gain). Just five months ago, C was at its lowest-ever rating, at 6.477 percent; this month, its rating is 11.07 percent, once again putting it in second place behind Java (14.215 percent)—although Java dropped 3.05 percent compared to January 2017. C’s revival is possibly being fueled by its popularity in manufacturing and industry, including the automotive market, Tiobe believes.

The Tiobe Programming Language of the Year for 2016 was Google’s Go language (Golang). Tiobe, which provides software quality services, bases its rankings on a formula assessing searches on languages in popular search engines such as Google, Bing, and Wikipedia.

Other languages that saw jumps in 2017 included R, which rose from 16th to 8th place; Kotlin, which jumped to 39th place after being in 89th a year earlier, and Erlang, which placed 23rd after being in 44th place a year ago.

But promising languages such as Julia, Hack, Rust, and Kotlin were not able to reach the top 20 or even the top 30, Tiobe pointed out. “Becoming part of the top 10 or even the top 20 requires a large ecosystem of communities and evangelists including conferences,” said Paul Jansen, Tiobe managing director and compiler of the index. “This is not something that can be developed in one year’s time.”

The top-rated languages in the index this month were as follows:

Java (14.215 percent)
C (11.037 percent)
C++ (5.603 percent)
Python (4.678 percent)
C# (3.754 percent)
JavaScript (3.465 percent)
Visual Basic .Net (3.261 percent)
R (2.549 percent)
PHP (2.532 percent)
Perl (2.419 percent)

Source: C language completes comeback in programming popularity | InfoWorld

1932: Polish Cipher Bureau Success!

1 December 1932: Polish Cipher Bureau first solved ENIGMA message. (Read an article in our Cryptologic Bytes Archives about Poland’s Overlooked Enigma Codebreakers.”)

Polish mathematicians from the University of Poznan (from left): Marian Rejewski, Jerzy Rozycki, and Henryk Zygalski broke the Enigma code, the most important encryption machine used by Nazi Germany. The success of the Polish cryptologists from the Cryptology Bureau enabled the British to read encrypted German correspondences during World War II, contributing to the wartime success of the allies.

In 1928, when the German military began using the cipher machine, Enigma, the Polish Cipher Bureau began its efforts to break it. They hired the three mathematicians in 1932 to do just that! The team worked for months to determine the wiring of the rotors. Using a mathematical equation and key lists acquired from a German traitor, they determined the three rotors’ internal wiring. They discovered three ways of deciphering Enigma readings. The Polish team then exploited some of the Germans’ standardized methods and successfully read many of the encrypted messages. They read the first one on December 1, 1932. They were in business…at least for a time…Seven years later, just before war broke out, the Poles handed over their knowledge of the Enigma codes, as well as Polish-built replicas of the machines, to British and French Intelligence officers near Warsaw.

The government official said that in recognition of the trio’s efforts, the upper house of Poland’s parliament has passed a resolution in their honor to ‘restore justice’. The resolution reads: ‘In both popular literature and official information, the public was told that the breaking of the Enigma codes was due to the work of the British Intelligence services to the complete omission of the work of Polish scientists.’

Source: National Cryptologic Foundation

Poland’s Overlooked Enigma Codebreakers

Posted on 07/08/2014

Poland’s Overlooked Enigma Codebreakers

By Gordon Corera
BBC News, Warsaw
4 July 2014
Read the article and see more photos online HERE.

The first breakthrough in the battle to crack Nazi Germany’s Enigma code was made not in Bletchley Park but in Warsaw. The debt owed by British wartime codebreakers to their Polish colleagues was acknowledged this week at a quiet gathering of spy chiefs. Continue reading “1932: Polish Cipher Bureau Success!”

I will be giving a talk on Cybersecurity for small businesses on December 8

Detective Kimo Hildreth and I will be giving a talk at a breakfast event on Cybersecurity for Small Businesses on Friday December 8, 2017, at 8:30am. To RSVP and view more event details click here. The event is organized by  Assemblymember Jacqui Irwin, and it will take place at 2100 Thousand Oaks Blvd, in the “Oak and Park Room”.

msoltys-talk-dec8-2017

Research position is available in the Department of Computer Science at the University of Pisa

A 20-month research position is available in the Department of Computer Science at the University of Pisa.

Research program:
Development of a novel software framework for processing compressed data structures, pattern matching and discovery, and their applications on biological sequence collections

Research areas include (but are not limited to):
– string algorithms,
– text indexing for big data,
– indexes for approximate pattern matching,
– text compression and compressed text indexing,
– external memory indexes,
– space efficient data structures, and
– shared memory parallel computing.

* Application deadline: 6th December 2017
* Potential starting dates: January/February 2018 (or as soon thereafter)
* Duration: 20 months
* Expected qualification: Master’s Degree or PhD.

The annual gross salary of the grant is EUR 25,200.00, which is approximately EUR 1,500.00 net per month after tax and mandatory retirement/superannuation contributions (for those having other mandatory retirement schemes other than INPS, the annual gross salary is EUR 23,930.46).  If you have family, you can also considerably increase your annual salary.

Candidates with expertise in string/parallel algorithms, combinatorics, software development and/or NGS bioinformatics are strongly encouraged to apply.

For more details on the job description and how to apply, please find the official competition call (both in Italian and English languages):
https://www.unipi.it/ateneo/bandi/assegni/pra2017/inf/20dic2017/index.htm