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Search Engine
Homework #5
DATA 1050 Fall 2020
Due 23:59 EST,​ Wednesday, October 28, 2020
Optional: ​Coding Problem 3 Resubmission​ due by 23:59 EST, Monday, ​October 19, 2020
Setup & Submission
1. Use ​this​ GitHub Assignment Invitation ​Link: ​https://classroom.github.com/a/Vbl7I9d9
2. Run pytest pytest-timeout flake8 black nltk in a terminal to install all required
packages.
3. Push to master as much as you want before the homework deadline.
4. If your final push will be late, remember to use the ​Late Day Form *twice*, once before the deadline, and once
again after your final push.
5. When you are ready to submit, visit gradescope and submit your repo. Your report should be included in the repo
as ​report.md
6. Be sure to also Include a copy and paste of the test results and coverage information in coverage.md in each of
your stencil directories. Two students created a helpful ​utility script​ to do this for you.
7. For ​Coding Problem 3 Resubmission​, please ​only include​ the coding problems you want to be
re-graded in a stencil_CodingProblems3 subdirectory of your hw5 repo and submit the entire repo via the corresponding gradescope assignment “Coding Problems3 Resubmission”
Overview
Search engines retrieve a list of documents (typically web pages) that match a given query. Since multiple documents may satisfy the query, most search engines also attempt to list more relevant documents first. In this project, you will use the TF-IDF and PageRank algorithms to create part of a web search engine.
Operationally, each searchable document must be analyzed in advance (in a process called indexing) to gather and integrate statistics about its content. This data is used to form an index (like the one found at the end of a book) that allows user search queries to be performed in real-time without the need to revisit all of the original documents.
Document term count information is enough to perform simple query matching since it allows one to find all documents that contain a particular set of terms. It also allows one rank documents relative to one another based on their term frequencies. ​TF-IDF​, otherwise known as ​term frequency–inverse document frequency​, is one way to do this.
Web search engines use “spiders” to “crawl” to the web in order to automatically visit and index web pages. At each page, a count of the number of times each word (“term”) appears in a document is recorded (i.e, the term histogram is recorded), a list of outbound links (​outlinks​) is collected, and then the spider moves on.
When present, link information defines a document graph, which can be used for document ranking. For example, documents that are referred to many other documents may be more important than ones with very few incoming links (​inlinks​). Today, Google and most other web search engines use ​PageRank on link data to help determine web page performance.
​pip install –user ​
conda install

The PageRank algorithm was created by ​Larry Page and ​Sergey Brin (the founders of Google) while they were still graduate students at Stanford. While Page’s ​original technical report suggested using it to rank web page importance based on link information, it has since been used to analyze many other networks. Identifying social media influencers (based on follower networks), and gauging the importance of scientific papers (via citation networks) are two examples.
A Note on Vocabulary
In this project handout,
● A “​documen​t” refers to a Wikipedia page
● A “​term​” refers to a word (or alphanumeric sequence containing no white space)
Details
We used the Wikipedia ​download interface to download some of its web pages. These documents (web pages) are stored as XML records. In order to create your search engine, you will write code to process these XML files.
In the world of search and natural language processing, a collection of texts is called a ​corpus​. A ​corpus (plural ​corpora​) is a collection of written texts (web pages with links in this case). Thus the corpora you will be working with are subsets of the pages of the English-language Wikipedia.
This project has four main parts, which are described in detail in the sections below:
1. Calculating TF-IDF
2. Calculating PageRanks
3. Processing the XML files
4. Search Engine and user interface
Note: We suggest you implement your solution project in the sequence listed above. TF-IDF and PageRank are both somewhat math-heavy, and it is important you get them working with artificial data for which you are sure of the answers before you start processing real data. Specifically, this data will be used to create ​analytic test cases​, some of which we provide, and some of which you will provide. We encourage you to make git commits once a subcomponent is working. This makes it easier for you to revert to a previous version.
Proceeding in this order will also help the course staff know which parts of the problem you have completed if you have questions.
Stencil files provided:
● TFIDF.py, PageRank.py: ​Task: Implement of TF-IDF/PageRank algorithm.
● processing.py​: Task: index the Wikipedia corpus
● SearchEngine.py​: Task: Implement an API that takes search queries and returns search results ranked by the
chosen algorithm
● app.py: ​A simple command-line interface (CLI) we supply that will allow you to use your search engine for
interactively
● report.md​: Task: Write your report here
Datasets provided:
(note that all datasets have been zipped together into wiki_data.zip​. You’ll have to extract them into your stencil directory before you can proceed)
● MiniWiki.xml, SmallWiki.xml​: XML files with 2 and 107 Wikipedia articles respectively. As you work on adding functionary to your search engine, we suggest you start by testing with these!

● MedWiki.xml​: An XML containing 871 Wikipedia articles. You can try testing with this file once you get your code working with SmallWiki.
● PageWiki.xml​: An XML file containing 100 documents with titles 1 to 100. Each document contains nothing except for a link to document 100. You can use this file to test your implementation of PageRank. Document 100 should have a much higher PageRank than the other documents.
Using VSCode​
Jupyter notebooks are often used for visualization and analysis, and they work well for one-time coding tasks. In this project and more generally in DATA 1050, we will not be coding in Jupyter notebooks but rather, in Python files. To help with this we recommend you try using the ​Visual Studio Code Interactive Development Environment (IDE) with the Microsoft Python Development extension.
Please read the ​VS Code Instructions​ document to learn how to do the following:
1. How to start The VS Code IDE​ on data.jupyter.brown.edu
2. Install the Python Development Extension
3. Install and configure other helpful packages and extensions
4. Run the debugger
VS Code is an immensely powerful software development tool. Learning how to use its many features takes a long time. However, because it also provides integrated ​terminal window support, you can continue to use all of the command line based python development skills you already have.
Since this is the first time we have run VS Code, we will update the VS Code Instructions as needed. We suggest you add notifications for changes​ to the VS Code Instructions document.
Coding Style Requirements
Using a consistent coding style is a critical part of code quality. For this project, make your style consistent with ​PEP 8​, the style guide for python developers from Guido himself. There are many tools for checking if your code is styled correctly. You can periodically run ​flake8 *.py in a terminal under your code directory. You can also install a flake8 extension to give you PEP-8 style warning as you code. Either way, resolve all style warnings you see to avoid receiving point deductions.
An auto-formatting tool may also come in handy. From the terminal you can run black -l100 ​to automatically reformat your code (e.g., running black -l100 PageRank.py ​will reformat the code in your PageRank.py file.) Various VS Code extensions provide similar functionality and allow you to select regions of text that to reformat.
Part 5.1 TF-IDF
As the name suggests, TF-IDF has two parts: TF (​term frequency​) and IDF (​inverse document frequency)​ . TF-IDF allows us to capture the following two ideas:
● A term that appears many times within a document is likely to be more relevant to that document than a term that appears fewer times (this is captured by TF). we calculate the ​term frequency​ as
T F (term, doc) = # of times term appears in the document = P (term|doc) total # of terms in the document

● A term that occurs in fewer documents in the corpus is likely to be a better signal of relevance compared to a common term like “the”. (this is captured by IDF) A rare term often tells more about the document. The ​inverse document frequency ​of a term is defined as
IDF (term) = log( # of documents in the corpus ) # of documents in which the term appears
Please use ​natural log ​(which is what Python’s ​math.log ​does),
● TFIDF(term, doc) = TF(term, doc)×IDF(term)
Examples
Consider a document containing 100 terms wherein the term ​cat appears 3 times. The term frequency (i.e., tf) for cat is then (3 / 100) = 0.03. Now, assume we have 10 million documents and the term ​cat appears in one thousand of these. Then, the inverse document frequency (i.e., idf) is calculated as ln(10,000,000 / 1,000) = 9.210. Thus, the tf-idf weight for the term ​cat in this document is the product of these quantities: 0.03 * 9.210 = 0.2763.
You may also find a more sophisticated example ​here​. Complete the following tasks in​ TFIDF.py.
Task 5.1
● calc_term_frequency​: For each document and each term, calculate term frequency. Store the results in a dictionary that maps from each ​term to a secondary dict. The secondary dict maps document title ​doc to TF(term, doc)​. Indexing looks like this: [term][document that contains the term][frequency of that term in each document that contains it] Pay close attention to the docstring. ​See the provided function test_tfidf_basic for example inputs and outputs.
● calc_tf_idf: Iterate through the dictionary created for TF and multiply each term frequency by the term’s inverse document frequency. Note that the returned dictionary can also serve as a “reverse index,” (i.e., given a term, you can use a single dictionary lookup to get the documents that contain this term)
● search: Given a list of keywords, return a list of matching documents paired with their tf-idf scores. Each returned document should contain at least 1 of the keywords. The returned list should be sorted by document score. When a limit is specified, only return that many ​(doc, tf-idf-score) pairs (e.g., if limit = 10, you would only return the top 10 matches). Compute tf-idf score by summing the tf-idf values of each query word found in the document.
score(doc,keywords)= ∑ TFIDF(term, doc) term∈keywords
● Include your pytest compatible tests in ​TFIDF.py​.

Notes
● Read carefully through the docstring (prose, parameter description). The docstrings most precisely specify the behavior of each method.
● Use​ test_tfidf_basic​ as a starting point to help you understand the expected input and output.
● Some methods are labeled as @staticmethod​. This means they do not depend on instance or class data, notice they do not include a self variable. @staticmethods can be invoked without a class instance as illustrated in ​test_tfidf_basic​. Their output does not depend on instance or class variables (i.e. they are regular stateless functions). This is sometimes helpful because each method can be tested separately. (For interested readers, see ​here for a discussion on the difference between @classmethods (which can depend on class
variables) and @staticmethods.)
Report Q&A: Ordering and Logs
Hw5.1 ​Your boss has been reviewing your code and wants you to do the following:
“store word frequencies the way you compute”, i.e. s/he wants you to use a dict of dicts which is indexed via
{document:{word:word frequency}}
Think carefully about this suggestion and give an appropriate response.
Part 5.2 PageRank
So far we have scored documents based on their relevance to a given query only. This is how early search engines like AltaVista worked. But then, in the late 90s, the founders of Google came up with an idea for ranking documents based on their position in the web itself. Their PageRank algorithm gives an overall importance score and it pays no attention whatsoever to the documents’ content. Rather, the rankings it computes are based entirely on the link structure between documents: i.e., which documents link to one another and which documents link to it. Documents with high scores (i.e., high PageRanks) have links from other documents that also have high ranks (which are linked to other documents with high ranks). This is a kind of crazy circular idea, but when converted into the appropriate mathematics the algorithm works quite well.
There are many variants of the PageRank algorithm. In this project, we will implement one of the most basic. Key principles underlying the design of PageRank:
1. The more documents that link to a page, the more authoritative it should be.
○ For example, if my personal blog post on “Providence Internet Outages” is linked to by 5 different web
pages (5 different incoming links, aka 5 inlinks), and the Wikipedia document on “Providence, Rhode Island” is linked to by 1000s of web pages (1000s of inlinks), then it makes sense to consider the Wikipedia document more authoritative.
○ Many early search engines use incoming page counts, and at first, this worked well, but over time people realized they could promote a page by making many fake pages that pointed to it.
○ The PageRank innovation was to also consider the authority score of incoming pages. Authoritative pages should also be linked to by other authoritative pages.,
2. The ability of an authoritative page to promote other pages should be constrained by the total number of outgoing links it has, fewer links provide better references.
○ Assume “Research at Brown” is linked to by an ​NYTimes document which links to only 10 other pages, and my blog “About Me” page is linked to by “Rhode Island Technology Bloggers”, which links to 2000 other pages. Because the “NYTimes” page has only a few links, and “Rhode Island Blogger” has many links, a link from the “NYTimes” page lends a larger fraction of its importance than a link from the “Rhode

Island Technology Bloggers”, leading us to attribute more authority to “Research at Brown” than “About Me”
Let u be a document, Bu be the set of documents that have a link to u , L(u) be the number of outgoing edges from u . The ​PageRank​ score for document u is defined as
P ageRank(v) L(v)
The trouble with this equation is that it is circular; in order to calculate the weight of document u , we have to know the weights of all document linking to u . How do we begin calculating the document weights? In practice, we use an ​iterative approach and stop once the document weights have converged. Here is a suggested approach to implementing PageRank:
● Create a dict ​weights​. Initialize weights for all documents to 1/N​, where ​N is the number of documents in the corpus
● While maximum # of iterations not reached
P ageRank(u) = ∑ v∈B
u
Note​:
○
○
○ ○ ○
Create a dict ​new_weights ​with weights for all documents set to 0 Iterate through each document ​x​.
For each document ​y​ that document ​x​ links to, update
​new_weights[y] += weights[x] / (# of documents x links to)
Calculate L2-distance between ​weights ​and n​ ew_weights​. Break out of the loop if​ distance < eps * N Set​ weights = new_weights ● L2-distance is ​Euclidean distance ● If you sum up the PageRank value for each document in a corpus, you should get ​1. ● Links from a document to itself are ignored. ​Links to documents outside the corpus are ignored. You may need to filter such links. ● Documents that link to nothing (i.e. sinks, like B below) are considered linked (once) to all documents ​including itself. Therefore, each document receives​ (weight of this sink) / N​. ● Multiple links from one document to another are treated as a single link. Examples Let’s say that we have the corpus shown above, which consists of the documents (a.k.a. pages), A, B, ​and C. A links to ​B ​and ​C​, and ​C ​links to A. ​The table below shows the results of running the PageRank algorithm on this corpus in order to determine the weight (a.k.a. rank) of each document. Remember that since ​B does not link to anything, we treat it as if it links to every document ​including​ itself. Iteration Weight of A Weight of B Weight of C Formula B/3+C/1 A/2+B/3 A/2+B/3 Initial 1/3 = .333 1/3 = .333 1/3 = .333 1 .333 / 3 + .333 / 1= .444 .333 / 2 + .333 / 3 = .277 .333 / 2 + .333 / 3= .277 2 .277 / 3 + .277 / 1 = .370 .444 / 2 + .277 / 3 = .314 .444 / 2 + .277 / 3 = .314 3 .314 / 3 + .314 / 1 = .419 .370 / 2 + .314 / 3 = .290 .370 / 2 + .314 / 3 = .290 4 .290 / 3 + .290 / 1 = .386 .419 / 2 + .290 / 3 = .306 .419 / 2 + .209 / 3 = .306 Task 5.2 ● calc_page_rank​: Given links between the documents, calculate the PageRank values for each page as specified above. ● search​: Searches for documents containing at least one of the query words, sorted by PageRank values and return up to `​limit​` of them. ● Write unit tests for​ PageRank.py​. ● Use​ test_page_rank_basic​ as a starting point to h​ elp you understand the expected input and output​. ● Add file docstring and class ​docstring​ in​ PageRank.py​ and remove all TODOs. Report Q&A: Page Rank Understanding Hw5.2 ​There is a Markov Chain interpretation of the PageRank algorithm that PageRank value represents the frequency that web surfers arrive at a specific web page following hyperlinks found on other pages. Included in the model is the idea that a user can also visit a page without clicking a link (e.g., they can visit via bookmark or a typed url). This random jumping process around process can be included in an iterative solution via a damping factor d​. Explainthefollowingequationintermsofprobabilitynotationif​PR(X)istheprobabilityofarrivingatnode​X​,and​L(X) is the number of outbound links from ​X​. (i.e., What does ​d represent, what does ​(1 - d)/N represent, and what does the sum represent.) If 32% of traffic to a webpage comes from non-inlink sources what should the value of d be? See ​https://en.wikipedia.org/wiki/PageRank​ if you are stuck. Part 5.3 Processing the XML file Tf-idf computes word counts. In order to do this, irrelevant data (like punctuation and word spelling variations) must be removed. Tf-idf calculation is then done with respect to this simplified corpus. PageRank requires all the links in the corpus. It is now time to process the Wikipedia dump XML to extract each type of data. Introduction to XML files The Wikipedia corpora used for this project are stored as ​XML files​. ​XML stands for eXtensible Markup Language. It is similar to HTML in that elements are surrounded by matching opening and closing tags. An opening tag looks like