How to Effectively Read and Understand Scientific Papers, Study notes of Computer Science

Download How to Effectively Read and Understand Scientific Papers and more Study notes Computer Science in PDF only on Docsity! How to read a scientific paper Mihai Pop Computer Science Center for Bioinformatics and Comptuational Biology Reasons to read a paper ● You were told to ● Describes current research ● Allows you to replicate/extend the results ● Provides you with useful data ● Gives you “pre-digested” thoughts ● To decide whether to publish it ● Teaches you how to write. Types of papers/references ● Primary – actual description of the work/results reported ● Secondary – describe work/results of others – e.g. background section in most papers – survey papers – encyclopedias (e.g. Wikipedia) ● Try to read the primary references (though secondary references are quite useful too)! ● e.g. Mozart and babies Paper organization ● Title & author list ● Abstract ● Introduction ● Materials and Methods ● Results ● Discussion/Conclusion ● Open problems ● Depending on the journal/conference/type of work these can vary in content/order Venue ● First things first: Where was the paper published? ● If the work is similar to what you do, this should give you ideas about which journals/conferences you should target with your own work ● Over time, you'll learn to evaluate journal/conference quality based on the quality of papers you read. Introduction ● Introduces the problem(s) addressed in the paper and prior art ● Questions to ask: – now that the problem is stated in more detail than in the abstract, can you think of a solution (or conclusion)? – is enough/any prior art listed? If not, why? Is the author hiding anything? – can you see why this paper is an advance over what was done in the past? ● Introduction will also give you pointers to other papers you might want to read Materials and Methods ● The “meat” of the paper - how the work was performed. ● Play the guessing game: for every problem or theorem stated, try to think of a solution before reading any further. ● Is sufficient information provided for you to understand how the paper “works”? What's missing? Is the paper correct? ● Note: in conferences papers are often “extended abstracts” - many details are missing. Try to fill them in. Results ● Verbose conclusions of the paper ● Often this section also contains “materials and methods”-type content ● Questions to ask: – what conclusions can you draw from the data presented? (ask before the paper “brainwashes” you) – does the experiment/data support the conclusions described in the paper? – are there alternative conclusions that the authors did not consider? – how would you set up the experiment? ● Make sure figures do not lie Two papers ● Initial sequencing and analysis of the human genome. International Human Genome Sequencing Consortium, Nature 409, 860 (2001). ● http://www.nature.com/nature/journal/v409/n6822/full/409860a0.html ● Microbial Genes in the Human Genome: Lateral Transfer or Gene Loss? Steven L. Salzberg, Owen White, Jeremy Peterson, Jonathan A. Eisen. Science 292:1903-1906 (2001) ● http://www.sciencemag.org/feature/data/scope/keystone1/ Paper 1 ● Conclusion: at least 223 genes were transfered from bacteria to humans ● (note: this event is extremely unlikely - one should be skeptical) ● Method: – find all genes similar between humans and bacteria yet not found in any other “complex” organism ● Logical link: – if an ancestor of both humans and bacteria had any of these genes, it's unlikely they would have been lost in all “complex” organisms but preserved in both human and bacteria. Paper 2 ● Conclusion: Not so fast, batman.... ● Hypothesis: – there are many reasons why one might not find the genes in other “complex” organisms – e.g. we haven't sampled enough of them yet ● Method: – same as in the previous paper ● Results: – many of the “transfered” genes disappeared once more “complex” organisms were found ● New Conclusion: first paper was likely wrong