CPT S 571 SURVEY PROJECT (Spring 2020)

(applicable only for graduate students - i.e., students registered for CPT S 571 credits)

Important Dates:

May 5, 2021 (Wednesday): Final Survey Report due via Blackboard (by 11:59pm PDT) - hard deadline without any exceptions. If you email me saying you couldn't upload in the last minute, I will *not* accept your submission. No exceptions to this rule. Remember, you always have the option of uploading multiple times a running version instead of waiting until the last minute.

Survey Project Report Details:

For this survey project, you will work individually, pick one published (peer-reviewed) research paper that is representative of a subtopic in the broader area of bioinformatics and computational biology, and conduct a thorough evaluation of the paper.

How to select a paper?

Here are some guidelines to select a paper:

Written Report (PDF only):

The written report should not exceed three pages (using single-space 11-point font). This includes space for the main text alongside figures and tables. For the bibliography (alphabetically listed), you can use up to an extra 2 pages. 

The written report should be entirely in your writing (i.e., no text taken verbatim from the paper you read or any other source), and should primarily contain a critique of the paper you reviewed with the following Section layout addressing the stated points within them:

Section I: Introduction and Problem Statement: What is the problem addressed in this paper? Why is it important (at a high level)? What are the key contributions of the paper (summarize them in your own words)?

Section II: Critique of the paper: In what ways do you think the paper's contributions are important? How did it advance the state of the art at its time of publication? Are the contributions still relevant today (i.e., do you see evidence of the method being still used and/or cited), or have they been superseded by newer/more recent methods? What are the primary computational challenges of the underlying problem? Is the complexity of the proposed method justified given the computational challenge(s) of the problem (or do you think there could be a much simplified solution)? Is the article technically sound (i.e., correct) or do you think there are some errors/flaws? Are there any constraints or assumptions underlying the method that would limit its applicability in practice? If it makes it any easier, you can organize this particular section as one of "Strengths" vs. "Weaknesses". In any case, make sure you touch upon all the above points in the writeup for this section.

Section III: A brief survey of related algorithms: What other algorithms are there on this topic? How are they different from this paper's method - e.g., in scope or effectiveness or performance?

Section IV:Availability of software and tools:  Are there any software or implementation toolkit available for the method proposed in this paper? If so, in what form - i.e., web-based, standalone, languages/platform? Provide a web link here if available.

Section V:Current and future trends: In your assessment of the paper what do you think are still the outstanding set of challenges on this problem? Do you have any ideas to propose potential improvements or developmental pathways for this line of research?

Section VI: References: Compile a comprehensive bibliography (in any standard scientific format of your choice, i.e., IEEE, ACM, Nature, Science, etc.). The list should include *all and only those* papers that you have referred to from the main body of text.  And make sure you refer to those citations from the main body of the text in an appropriate way. For example, if you are using the IEEE format, you will be numbering the references and citing those numbers in the main texts.

GRADING:

Grading will be based on a combination of factors - technical content of your report, presentation, scientific writing practices, readability, etc. In short, your report should be informative as well as readable. You are expected to follow rules of academic integrity consistent with the course policies (syllabus) and also consistent with academic practice. All sources should be appropriately cited; no writing should be taken from any where (including the paper you selected); and all writing should be 100% yours.