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Indiana University, Fall 2024

This course studies the fundamental ideas for efficiently analyzing large amounts of data, such as DNA sequence databases and geographic information. These fundamental ideas come in two kinds: algorithms and data structures. Algorithms are instructions for solving problems and data structures are strategies for organizing information on computers. Efficient algorithms require appropriate data structures, and vice versa, so the study of algorithms and data structures is tightly linked. In this course we learn about the algorithms and data structures that form the building blocks for many of Today's large-scale computer systems. We apply these ideas to solve challenging problems in bioinformatics and geographic information systems. Warning: a possible side-effect of taking this course is doing better on job interview questions.

Lecture

  • Section 7280, Mondays and Wednesdays 9:45am-11:00am, Wendell W. Wright Education Building (ED), Room 1084.

Labs

  • Section 7326, Fridays 10:20am-12:15pm, Ballantine Hall (BH) 241

Expect at least one quiz per month during lab time.

  • 15 minutes, at the end of a lab session
  • The scope of each quiz is everything turned in prior to the quiz, including homework and lab assignments

Instructors

  • Jeremy Siek (jsiek), office hours Mondays 1-2pm, Wednesdays 3-4pm, Luddy Room 3014, make a reservation

Teaching Assistants

  • Aaron Olson (aarolson)
  • Calvin Josenhans (cjosenha)

Office Hours

Office hours with TAs are in Luddy Hall Room 0121. Office hours with Jeremy are in Luddy Hall Room 3014.

Time | Monday | Tuesday | Wednesday | Thursday | Friday 11am | | | | | 12pm | | | | | 1pm | Jeremy | | Calvin | Calvin | 2pm | | | | | 3pm | | | Jeremy | | Aaron 4pm | | | | | Aaron 5pm | | | | |

Textbook

Data Structures and Algorithm Analysis in Java, 3rd Ed. by Mark A. Weiss

Slack (communicating with instructors and other students)

Workspace (signup)

Schedule

Day | Lecture Topic | Reading Due | Assignments and Due Dates | Link Aug. 26 | Introduction | | | Aug. 28 | Arrays, Rotation, Testing | Ch. 1 | | Aug. 30 | | | Lab: Array Search and Testing | code, test Sep. 2 | Labor Day no class Sep. 3 | | | Lab Array Search due Sep. 4 | Algorithm Analysis (video) | Ch. 2 | Sep. 6 | | | Lab: Work on FloodIt! Project | code Sep. 9 | Algorithm Analysis, continued (video) | | FloodIt! Project due | Sep. 11 | Introduction to Deduce and Linked Lists Sep. 13 | | | Lab: Linked Lists (Quiz in Lab) Sep. 16 | Writing Proofs in Deduce | | Lab due Sep. 18 | More about Proofs, Correctness of Insertion Sort | Ch.7 Sec. 1-2 Sep. 19 | | | Homework: Proof Exercises due Sep. 20 | | | Lab: Insertion Sort Sep. 23 | Code Review (Flood It!), Quicksort | Ch.7 Sec. 7 | Insertion Sort due Sep. 25 | Java Interfaces | Ch. 3 Sep. 27 | | | Lab: Quicksort | code, test Sep. 30 | Sorting in Linear Time | Ch. 7 Sec. 11| Quicksort due Oct. 2 | Binary Trees | Ch. 4 Sec. 1-2 Oct. 4 | | | Lab: Next Prev Binary Tree | code, test Oct. 7 | Review for Midterm Exam | | Next Prev Binary Tree due Oct. 9 | Midterm Exam (in class) Oct. 11 | Fall Break | | No Lab Oct. 14 | Binary Search Trees | Ch. 4 Sec. 3 Oct. 16 | Balanced Search Trees (AVL) | Ch. 4 Sec. 4 Oct. 18 | | | Lab: Segment Intersection | code, test Oct. 21 | Recipes for Time Analysis | | Segment Intersection due Oct. 23 | Hash Tables | Ch. 5 sec.1-6 Oct. 25 | | | Lab: Hash Table | code, test Oct. 28 | Heaps and Priority Queues | Ch. 6 sec. 1-4,9 | Hash Table due Oct. 30 | Code Review (Segment Intersection) Nov. 1 | | | Lab: Huffman Coding (Heap Implementation) | code, test Nov. 4 | Graphs and Breadth-first Search | Ch. 9, sec. 1,3 | Huffman Coding due Nov. 6 | Depth-first Search | Ch. 9 sec. 6 Nov. 8 | | | Lab: Connected Components (Quiz in Lab) Nov. 11 | Shortest Paths | Ch. 9 sec. 3 | Connected Components due Nov. 13 | Union Find | Ch. 8 Nov. 15 | | | Project: Routing Wires Nov. 18 | Minimum Spanning Tree | Ch. 9 sec. 5 Nov. 20 | Dynamic Programming | Ch. 10, sec. 3 Nov. 22 | | | Project: Routing Wires, cont'd (Quiz in Lab) Nov. 24 - Dec. 1 | Thanksgiving Break Dec. 2 | DNA Alignment | | Routing Wires due Dec. 4 | More Dynamic Programming Dec. 6 | | | Lab: DNA Sequence Alignment | code, test Dec. 9 | Code Review (Routing Wires) | | DNA Sequence Alignment due Dec. 11 | Review for Final Exam Dec. 13 | | | Optional lab for exam review Dec. 18 | Final Exam 8-10am

Resources

Grade Weighting

  • Assignments (35%)
  • Quizzes (5%)
  • Midterm Exam (25%)
  • Final Exam (35%)

Late Policy

This policy applies to labs, projects, textbook exercises, and quizzes. For quizzes, you can do a make-up quiz during office hours. This policy does not apply to the midterm and final exam. When you complete something late, there is a 10% deduction to its grade.

100% | before 1st deadline 90% | before 2nd deadline (one week after 1st) 0% | after 2nd deadline

Bias-Based Incident Reporting.

Bias-based incident reports can be made by students, faculty and staff. Any act of discrimination or harassment based on race, ethnicity, religious affiliation, gender, gender identity, sexual orientation or disability can be reported through any of the options:

  1. email biasincident@indiana.edu or incident@indiana.edu;

  2. call the Dean of Students Office at (812) 855-8188 or

  3. use the IU mobile App (m.iu.edu). Reports can be made anonymously.

Counseling and Psychological Services.

CAPS has expanded their services. For information about the variety of services offered to students by CAPS visit: https://healthcenter.indiana.edu/counseling/index.html

Disability Services for Students (DSS).

The process to establish accommodations for a student with a disability is a responsibility shared by the student and the DSS Office. Only DSS approved accommodations should be utilized in the classroom. After the student has met with DSS, it is the student’s responsibility to share their accommodations with the faculty member. For information about support services or accommodations available to students with disabilities and for the procedures to be followed by students and instructors, please visit: https://studentaffairs.indiana.edu/disability-services-students/.

Students needing additional financial or other assistance.

The Student Advocates Office (SAO) can help students work through personal and academic problems as well as financial difficulties and concerns. SAO also assists students working through grade appeals and withdrawals from all classes. SAO also has emergency funds for IU students experiencing emergency financial crisis https://studentaffairs.indiana.edu/student-advocates/.

Academic Misconduct.

If you suspect that a student has cheated, plagiarized or otherwise committed academic misconduct, refer to the Code of Student Rights, Responsibilities and Conduct: http://studentcode.iu.edu/.

Sexual Misconduct.

As your instructor, one of my responsibilities is to create a positive learning environment for all students. Title IX and IU’s Sexual Misconduct Policy prohibit sexual misconduct in any form, including sexual harassment, sexual assault, stalking, and dating and domestic violence. If you have experienced sexual misconduct, or know someone who has, the University can help.

If you are seeking help and would like to speak to someone confidentially, you can make an appointment with:

  • The Sexual Assault Crisis Services (SACS) at (812) 855-8900 (counseling services)

  • Confidential Victim Advocates (CVA) at (812) 856-2469 (advocacy and advice services)

  • IU Health Center at (812) 855-4011 (health and medical services)

It is also important that you know that Title IX and University policy require me to share any information brought to my attention about potential sexual misconduct, with the campus Deputy Title IX Coordinator or IU’s Title IX Coordinator. In that event, those individuals will work to ensure that appropriate measures are taken and resources are made available. Protecting student privacy is of utmost concern, and information will only be shared with those that need to know to ensure the University can respond and assist. I encourage you to visit stopsexualviolence.iu.edu to learn more.