University Bulletin (2009-2010)

COSI 2a Introduction to Computers
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An introduction to the basic principles underlying computer hardware and software and to the implications of the wider use of computers in society. Topics will include hardware, software, Web page design, applet and servlet programming, the Internet, privacy and security issues, as well as a survey of current research directions, including artificial intelligence and parallel computing. Usually offered every year.
Mr. Hickey

COSI 11a Programming in Java and C
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Open only to students with no previous programing background.
A general introduction to structured programming and problem solving using C and Java in the context of the World Wide Web. Students also learn GUI programming and advanced HTML authoring. There are weekly programming assignments. Usually offered every year.
Staff

COSI 12b Advanced Programming Techniques
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Prerequisite: COSI 11a or programming facility in C.
An introduction to fundamental programming techniques covering basic software engineering, object oriented programming, interfaces, API¿s and abstract classes, with applications to Graphical User Interfaces, web programming, graphics, and other topics. Usually offered every year.
Staff

COSI 21a Data Structures and the Fundamentals of Computing
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Prerequisite: COSI 11a or programming facility in C.
An introduction to the fundamental concepts of computation: discrete structures (sets, relations, functions, sequences, graphs), the fundamental data structures and algorithms for sorting and searching (lists, queues, dequeues, heaps, hashing, binary trees, tries), and the analysis of algorithms (predicate logic,
termination and correctness proofs, computational complexity). Usually offered every year.
Mr. Storer

COSI 21b Structure and Interpretation of Computer Programs
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Prerequisites: COSI 11a or programming facility in C.
An introduction to idioms of programming methodology, and to how programming languages work. Principles of functional programming, data structures and data abstraction; state, imperative and object-oriented programming; lazy data structures; how an interpreter works; metalinguistic abstraction and programming language design; syntax analysis, lexical addressing, continuations and explicit control; continuation-passing style, metacircular and register-machine compilers. Usually offered every year.
Mr. Mairson

COSI 22b Programming Paradigms
Prerequisites: COSI 21a, COSI 22a. Corequisite: COSI 21b. Yields half-course credit (two semester-hour credits).
A practical introduction to the use of appropriate computational paradigms and programming methodologies to solve complex problems. Problem domains vary from year to year but typically include numerical programming, symbolic computation, natural language processing, simulation of physical systems, interpretation and compilation of programming languages. Usually offered every year.
Mr. Mairson

COSI 29a Discrete Structures
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Covers topics in discrete mathematics with applications within computer science. Some of the topics to be covered include graphs and matrices; principles of logic and induction; number theory; counting, summation, and recurrence relations; discrete probability. Usually offered every year.
Mr. Gessel

COSI 30a Introduction to the Theory of Computation
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Prerequisite: COSI 29a.
Formal treatment of models of computation: finite automata and regular languages, pushdown automata and context-free languages, Turing machines, and recursive enumerability. Church's thesis and the invariance thesis. Halting problem and undecidability, Rice's theorem, recursion theorem. Usually offered every year.
Mr. Mairson

COSI 31a Computer System Structures and Organization
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Prerequisites: COSI 21a.
Fundamental structures of a computer system from hardware abstractions through machine and assembly language, to the overall structure of an operating system and key resource management abstractions. Usually offered every year.
Ms. Shrira

COSI 65a Introduction to 3-D Animation
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Covers the fundamental concepts of 3-D animation and teaches both the theory underlying 3-D animation as well as the skills needed to create 3-D movies. Students demonstrate their understanding of the concepts by creating several short animated movies. Usually offered every third year.
Mr. Hickey

COSI 93a Research Internship and Analysis
Provides students with an opportunity to work in a computer science research lab for one semester, pursuing a project that has the potential to produce new scientific results. Students and the faculty member mutually design a project for the semester that supports the research agenda of the group. Students must attend all research group meetings and present their findings in oral and written form at the end of the semester. The project typically includes background research, some lab work, and collaboration with other group members. Course requires signature of the instructor, is subject to the availability of undergraduate research positions, and is typically open only to juniors and seniors.
Staff

COSI 98a Independent Study
Open to exceptional students who wish to study an area of computer science not covered in the standard curriculum. Usually offered every year.
Staff

COSI 98b Independent Study
Open to exceptional students who wish to study an area of computer science not covered in the standard curriculum. Usually offered every year.
Staff

COSI 99d Senior Research
Prerequisites: Open only to seniors. Submission of a thesis proposal during the spring semester of the junior year. This proposal must be signed by a faculty member who has agreed to supervise the thesis.
Research assignments and preparation of a report under the direction of an instructor. Usually offered every year.
Staff

COSI 101a Fundamentals of Artificial Intelligence
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Prerequisites: COSI 21a and COSI 29a. This course may not be repeated for credit by students who have taken COSI 35a in previous years.
Survey course in artificial intelligence. Introduction to Lisp and heuristic programming techniques. Topics include problem solving, planning natural language processing, knowledge representation, and computer vision. Usually offered every year.
Mr. Pollack

COSI 111a Topics in Computational Cognitive Science
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Prerequisite: COSI 101a or 125a, or permission of the instructor.
Focuses on cognitive and social theories of activity that underlie human computer interaction and computer mediated collaboration. Topics include problem solving and skill acquisition, planning and situated activity, distributed cognition, activity theory, collaboration, communication, discourse, and interaction analysis. The laboratory work is designed to give the student practice with the ideas and
techniques under discussion. The content and work of the course are specifically designed for an interdisciplinary class of students from computer science and the social sciences. Usually offered every second year.
Mr. Alterman

COSI 112a Modal, Temporal, and Spacial Logic for Language
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Prerequisites: COSI 21b or 29a and COSI 101a.
Examines the formal and computational properties of logical systems that are used in AI and linguistics. This includes (briefly) propositional logic and first order logic, and then an in-depth study of modal logic, temporal logic, spatial logic, and dynamic logic. Throughout the analyses of these systems, focuses on how they are used in the modeling of linguistic data. Usually offered every second year.
Mr. Pustejovsky

COSI 113b Artificial Life
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Prerequisite: COSI 101a.
A seminar on genetic algorithms, genetic programming, evolutionary programming, blind watchmaking, and related topics, ultimately focusing on co-evolutionary spirals and the automatic construction of agents with complex strategies for games. Usually offered every second year.
Mr. Pollack

COSI 114b Topics in Computational Linguistics
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Prerequisites: COSI 21b or 29a; COSI 101a.
Provides a fundamental understanding of the problems in natural language understanding by computers, and the theory and practice of current computational linguistic systems. Of interest to students of artificial intelligence, algorithms, and the computational processes of comprehension and understanding. Usually offered every year.
Mr. Pustejovsky

COSI 118a Computer-Supported Cooperation
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Prerequisite: COSI 125a or the permission of the instructor.
Covers basic theory and concepts of computer-supported collaborative work and learning. Laboratory work enables the student to practice a set of basic techniques as they apply to the development of computer-mediated collaboration. The content and work of the course are specifically designed for an interdisciplinary class of students from computer science and the social sciences. Usually offered every second year.
Mr. Alterman

COSI 120a Topics in Computer Systems
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Prerequisite: COSI 21a.
Content will vary from year to year. May be repeated for credit. Prerequisites may vary with the topic area; check with instructor for details. Usually offered every third year.
Staff

COSI 123a Statistical Machine Learning
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Prerequisite: MATH 8a, 10a, 15a or familiarity with basic concepts in probability and statistics and differential calculus.
Focuses on learning from data using statistical analysis tools and deals with the issues of designing algorithms and systems that automatically improve with experience. This course is designed to give students a thorough grounding in the methodologies, technologies, mathematics, and algorithms currently needed by research in learning with data. Usually offered every year.
Mr. Hong

COSI 125a Human-Computer Interaction
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Prerequisite: sophomore standing.
Covers the basic theory and concepts of human-computer interaction. Topics include methodology for designing and testing user interfaces, interaction styles and techniques, design guidelines, and adaptive systems. The laboratory work is designed to give the student practice in a set of basic techniques used in
the area of human-computer interaction. Usually offered every second year.
Mr. Alterman

COSI 127b Database Management Systems
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Prerequisites: COSI 21a and 29a.
Introduces database structure, organization, and languages. Studies relational and object-oriented models, query languages, optimization, normalization, file structures and indexes, concurrency control and recovery algorithms, and distributed databases. Usually offered every second year.
Mr. Cherniack

COSI 128a Modern Database Systems
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Covers advanced topics in database systems such as concurrency control, recovery, security, and data mining. Usually offered every fourth year.
Mr. Cherniack

COSI 133b Internet and Society
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Prerequisite: sophomore standing. This course may not be repeated for credit by students who have taken COSI 33b in previous years.
An interdisciplinary survey of the Internet. Taught by a team of professors from several different departments, the course content will vary from year to year. Some particular topics to be covered are the architecture of the Internet (and the implications this has on its regulation), intellectual property, privacy, censorship, e-commerce, online education, and research. Usually offered every year.
Mr. Hickey

COSI 134a Statistical Approaches to Natural Language Processing
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Prerequisite: COSI 114b. May be taken concurrently with COSI 114b.
An introductory graduate-level course covering fundamental concepts in statistical Natural Language Processing (NLP). Provides an in-depth view of the statistical models and machine-learning methods used in NLP, including methods used in morphological, syntactic, and semantic analysis. Usually offered every year.
Staff

COSI 135b Computational Semantics
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Prerequisites: COSI 11a or permission of the instructor. Open to advanced undergraduate students and first-year graduate students.
A study of the computational treatment of core semantic phenomena in language. After a review of first-order logic and the lambda calculus, the course focuses on three core topics: interrogative structures, including semantics of questions, question-answering systems, dialogue, entailment, commonsense knowledge; meaning update and revision; and computational lexical semantics. Usually offered every year.
Mr. Pustejovsky

COSI 146a Principles of Computer System Design
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Prerequisites: COSI 31a; MATH 10a (MATH 10b recommended).
Topics on the design and engineering of computer systems: techniques for controlling complexity; strong modularity using client-server design; layering; naming; networks; security and privacy; fault-tolerant systems, atomicity and and recovery; performance; impact of computer systems on society. Case studies
of working systems and readings from the current literature provide comparisons and contrast. Usually offered every second year.
Ms. Shrira

COSI 147a Distributed Systems
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Prerequisite: COSI 31a and C/C++/UNIX programming skills.
This course covers abstractions and implementation techniques for the design of distributed systems. Topics include: distributed state sharing, coherence, storage systems, naming systems, security, faulttolerance and replication, scalability and performance. The assigned readings for the course are from current literature. Usually offered every second year.
Ms. Shrira

COSI 155b Computer Graphics
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Prerequisite: COSI 11a.
An introduction to the art of displaying computer-generated images and to the design of graphical user interfaces. Topics include graphic primitives; representations of curves, surfaces, and solids; and the mathematics of two- and three-dimensional transformations. Usually offered every third year.
Mr. Hickey

COSI 160a Parallel Computing and Programming
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Prerequisites: COSI 29a and 31a.
An introduction to parallel computation at the levels of architecture, communication, data structures, algorithms, analysis, programming models, and programming languages. Usually offered every second year.
Staff

COSI 175a Data Compression and Multimedia Processing
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Prerequisites: COSI 21a, 29a, and 31a.
Selected topics in data compression and image and video processing, including adaptive lossless compression, lossy image and video compression, transformations on image and video, multimedia retrieval problems, parallel algorithms. Usually offered every second year.
Mr. Storer

COSI 178a Computational Molecular Biology
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Open to advanced undergraduate students and graduate students.
Information and computing technologies are becoming indispensable to modern biological research due to the significant advances of high-throughput experimental technologies in recent years. This course presents an overview of the systematic development and application of computing systems and computational algorithms/techniques to the analysis of biological data, such as sequences, gene
expression, protein expression, and biological networks. Hand-on training will be provided. Usually offered every other year.
Mr. Hong

COSI 180a Algorithms
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Prerequisites: COSI 21a,b, and 29a. This course may not be repeated for credit by students who have taken COSI 30b in previous years.
Basic concepts in the theory of algorithm design and analysis, including advanced data structures and algorithms, parallel algorithms, and specialized topics. Usually offered every second year.
Staff

COSI 190a Introduction to Programming Language Theory
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Prerequisite: COSI 21a or familiarity with a functional programming language, set theory, and logic.
An introduction to the mathematical semantics of functional programming languages. Principles of denotational semantics; lambda calculus and its programming idiom; Church-Rosser theorem and Böhm's theorem; simply typed lambda calculus and its model theory: completeness for the full type frame,
Statman's 1-section theorem and completeness of beta-eta reasoning; PCF and full abstraction with parallel operations; linear logic, proofnets, context semantics and geometry of interaction, game semantics, and full abstraction. Usually offered every second year.
Mr. Mairson

COSI 200a Readings
Specific sections for individual faculty members as requested.
Staff

COSI 200b Readings
Specific sections for individual faculty members as requested.
Staff

COSI 210a Independent Study
Usually offered every year.
Staff

COSI 215a Advanced Topics in Computer Supported Cooperation
Topics vary from year to year. The course may be repeated with the approval of the instructor. Usually offered every second year.
Staff

COSI 216a Topics in Natural Language Processing
Prerequisite: COSI 101a.
Reviews recent trends in computational approaches to linguistics, semantics, knowledge representation for language, and issues in parsing and inferences. Usually offered every fourth year.
Mr. Pustejovksy

COSI 217a Topics in Adaptive Systems
Prerequisite: COSI 101a.
In nature, systems with greater complexity than any designed by humans arise without a designer. The central question explored is: How can complex modular organization arise without an intelligent designer? The class reads about theories of organization in different settings and scales (cells, brains, minds, behavior, society, economies), and studies papers, models, and algorithms from a variety of fields that might shed light on the issue. Usually offered every third year.
Mr. Pollack

COSI 217b Natural Language Processing Systems
Prerequisite: COSI 114b or permission of the instructor.
This course looks at building coherent systems designed to tackle real applications in computational linguistics. Particular topics will vary from year to year, but each call will consider some of the following: machine (aided) translation, speech interfaces, information retrieval/extraction, natural language question answering systems, dialogue systems, summarization, computer-assisted language learning, language documentation/linguistics hypothesis testing, and handwriting recognition. Usually offered every year.
Staff

COSI 220a Advanced Topics in Systems
Prerequisite: COSI 31a.
Covers selected areas in advanced computer systems and engages students in top-flight systems research. The class is based on a discussion of important research papers and a research project. Usually offered every second year.
Ms. Shrira

COSI 227b Advanced Topics in Database Systems
Prerequisite: COSI 127b.
An in-depth treatment of advanced topics in database management systems. Topics vary from year to year and may include distributed databases, query processing, transaction processing, and Web-based data management. Usually offered every second year.
Mr. Cherniack

COSI 228a Topics in Distributed Systems
Advanced topics in networked information systems and internet-scale data management. Usually offered every third year.
Ms. Papaemmauouil

COSI 230a Topics in Computational Biology
This course aims to transcend traditional departmental boundaries and facilitate communications between experimental biologists and computational scientists. Through reading literature and small research projects, students will be introduced to problems in computational biology and learn the methods for studying them.
Mr. Hong

COSI 235a IT Entrepreneurship
Covers the fundamental concepts needed to transform an idea for a software application into a viable IT business. The focus of the course is on software-based IT enterprises and the specific challenges and opportunities they present. Usually offered every year.
Mr. Colon Osorio

COSI 236b Software Development for IT Entrepreneurship
Prerequisite: COSI 235a or permission of the instructor.
This course teaches the fundamentals of software engineering and emphasizes rapid prototyping, unit testing, usability testing, and collaborative software development principles. Students apply these concepts by building a complex software system in small teams of programmers/developers. Usually offered every year.
Mr. Colon Osorio

COSI 240b Computational Logic
Prerequisite: Some previous exposure to logic, computation theory, and functional programming.
An introduction to logic and computation from a syntactic perspective. Lambda calculus: programming idiom, Church-Rosser and Böhm's theorems, standardization theorem, Krivine machine and head reduction; sequent calculus and Gentzen's cut-elimination theorem; simply-typed lambda calculus:
intuitionistic logic, Curry-Howard correspondence, normalization theorems, complexity of deciding equality; polymorphic lambda calculus: programming idiom, strong normalization, realizability of total functions, "Dialectica" interpretation, incompleteness; linear logic: proofnets, correctness criteria and complexity, complexity of normalization, geometry of interaction and translation of lambda calculus, optimal reduction; computational classical logic: double-negation translations and continuations; games and provability; differential lambda calculus and reinterpretation of Taylor's theorem. Usually offered every second year.
Mr. Mairson

COSI 293a Graduate Research Internship
Permission of the graduate advising head required. Yields half-course credit; may be repeated for credit.
Offers graduate students a opportunity to engage in industrial research in computer science by completing a paid or unpaid internship of at least ten weeks duration approved and monitored by a faculty member.
Staff

COSI 300a Master's Project
Usually offered every year.
Staff

COSI 300b Master's Project
Usually offered every year.
Staff

COSI 310a Seminar in Artificial Intelligence
Usually offered every second year.
Staff

COSI 315b Current Topics in Learning and Neural Nets
Usually offered every second year.
Staff

COSI 320a IT Entrepreneurship Practicum I
Prerequisites: COSI 235a, 236b, and permission of the faculty advisor.
This course guides students through the process of developing a marketable prototype of an original software application and helps them prepare a business plan for that application. Usually offered every year.
Staff

COSI 320b IT Entrepreneurship Practicum II
Prerequisite: COSI 320a.
Staff

COSI 340a Seminar in Programming Languages
Usually offered every second year.
Staff

COSI 390a Seminar in Theory of Computation
Usually offered every second year.
Staff

COSI 400d Dissertation Research
Specific sections for individual faculty members as requested.
Staff

ANTH 138a Social Relations in Cyberspace
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Provides an introduction to various forms of computer-mediated communication (e.g., instant messaging, blogging, social networking, online dating) and the ways in which people interact in these different contexts of cyberspace. Students are expected to do online research. Usually offered every year.
Mr. Jacobson

ANTH 174b Virtual Communities
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Prerequisite: ANTH 138a or permission of the instructor.
A research seminar dealing with a selected problem in the social organization of online communities. Possible topics include impression formation in cyberspace, social control in virtual communities, the concept of presence in computer-mediated communication, and the transition between online and offline relationships. Students will do online fieldwork. Usually offered every third year.
Mr. Jacobson

BCHM 170b Bioinformatics
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Prerequisites: Familiarity with computing is necessary and a basic biochemistry course is recommended. A joint offering between Brandeis University and Wellesley College.
Familiarizes students with the basic tools of bioinformatics and provides a practical guide to biological sequence analysis. Topics covered include an introduction to probability and statistics; sequence alignments; database searches; alignments and phylogenetic trees; sequence pattern discovery; structure determination by secondary structure prediction; and three-dimensional structure prediction by homology modeling. In all cases, the strengths and limitations of the methods will be discussed. Usually offered every third year.
Ms. Ringe

BIOL 135b The Principles of Biological Modeling
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Prerequisite: MATH 10a or 10b.
With examples from neuroscience, cell biology, ecology, evolution, and physiology, dynamical concepts of significance throughout the biological world are discusses. Simple computational and mathematical models are used to demonstrate important roles of the exponential function, feedback, stability, oscillations, and randomness. Usually offered every second year.
Mr. Miller

CHEM 144a Computational Chemistry
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Prerequisites: A satisfactory grade in CHEM 11a, 15a and CHEM 11b, 15b or equivalent; MATH 10a,b or equivalent; PHYS 11a,b or 15a,b or equivalent. Organic chemistry is also recommended.
Topics in computational chemistry: applications of quantum mechanics to structural and spectroscopic analysis of small molecules; molecular dynamics and Monte Carlo simulations of biomacromolecules. Standard computational programs are used by students to perform homework exercises. Usually offered every other year.
Mr. Jordan

LING 130a Formal Semantics: Truth, Meaning, and Language
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Prerequisite: LING 100a or permission of the instructor. LING 8b or LING 120b recommended.
Explores the semantic structure of language in terms of the current linguistic theory of model-theoretic semantics. Topics include the nature of word meanings, categorization, compositionality, and plurals and mass terms. Usually offered every year.
Ms. Malamud

MATH 30a Introduction to Algebra, Part I
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Prerequisite: MATH 23b and MATH 22a, or permission of the instructor.
An introduction to the basic notions of modern algebra-rings, fields, and linear algebra. Usually offered every year.
Mr. Igusa (fall)

MATH 30b Introduction to Algebra, Part II
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Prerequisite: MATH 30a or permission of the instructor.
A continuation of MATH 30a, culminating in Galois theory. Usually offered every second year.
Staff (spring)

MATH 36a Probability
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Prerequisite: MATH 20a or 22b.
Sample spaces and probability measures, elementary combinatorial examples. Random variables, expectations, variance, characteristic, and distribution functions. Independence and correlation. Chebychev's inequality and the weak law of large numbers. Central limit theorem. Markov and Poisson processes. Usually offered every year.
Mr. Adler (fall)

MATH 38b Number Theory
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Prerequisites: MATH 23b and either MATH 22a or permission of the instructor.
Congruences, finite fields, the Gaussian integers, and other rings of numbers. Quadratic reciprocity. Such topics as quadratic forms or elliptic curves will be covered as time permits. Usually offered every second year.
Mr. Bellaiche (spring)

MATH 39a Introduction to Combinatorics
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Prerequisites: COSI 29a or MATH 23b.
Topics include graph theory (trees, planarity, coloring, Eulerian and Hamiltonian cycles), combinatorial optimization (network flows, matching theory), enumeration (permutations and combinations, generating functions, inclusion-exclusion), and extremal combinatorics (pigeonhole principle, Ramsey's theorem). Usually offered every second year.
Staff (fall)

PHIL 106b Mathematical Logic
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Prerequisite: One course in logic or permission of the instructor.
Covers in detail several of the following proofs: the Gödel Incompleteness Results, Tarski's Undefinability of Truth Theorem, Church's Theorem on the Undecidability of Predicate Logic, and Elementary Recursive Function Theory. Usually offered every year.
Staff

PHYS 29a Electronics Laboratory I
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Prerequisites: PHYS 10a and 10b or PHYS 15a and 15b; and PHYS 18a and 18b or PHYS 19a and 19b.
Introductory laboratory in analog electronics. Topics to be covered are DC circuits, AC circuits, complex impedance analysis, diodes, transistors, and amplifiers. Usually offered every year.
Mr. Kirsch

PHYS 29b Electronics Laboratory II
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Prerequisite: PHYS 29a.
Introductory laboratory in digital electronics. Topics to be covered are Boolean algebra, combinational logic, sequential logic, state machines, digital-analog conversion, and microprocessors. The last part of the semester is spent on individual design projects. Usually offered every year.
Mr. Kirsch

PHYS 32b Microprocessor Laboratory
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Prerequisite: PHYS 29a or b.
Study of microprocessor design and use as controller for other devices. Topics include architecture of microcomputers, interfacing, digital control, analog control, and software development. Usually offered every second year.
Mr. Kirsch