Tools for managing your PhD projects, reading lists, notes, and inspiration.

As a researcher, you have to know everything. But knowledge is useless if it cannot be accessed quickly. An easy-to-use method of archiving information makes taking notes effortless and enjoyable.
As a PhD student in Artificial Intelligence, I use Obsidian (https://obsidian.md) to manage my knowledge.

The article has three parts:

1. What is a note, how to organize notes, tags, folders, and links? This section is tool-agnostic, so you can use most of these ideas with any note-taking app.
2. Instructions for using Obsidian, managing notes, reading lists, and useful plugins. This section demonstrates how I use Obsidian, my preferred knowledge management tool.
3. Workflows: How to use Zotero to take notes from papers, manage multiple projects' notes, create MOCs with Dataview, and more. This section explains how to use Obsidian to solve common scientific problems and manage/maintain your knowledge effectively.

This list is not perfect or complete, but it is my current solution to problems I've encountered during my PhD. Please leave additional comments or contact me if you have any feedback. I'll try to update this article.
Throughout the article, I'll refer to your digital library as your "Obsidian Vault" or "Zettelkasten".
Other useful resources are listed at the end of the article.

1. Philosophy: Taking and organizing notes

Before diving into Obsidian, let's establish a Personal Knowledge Management System and a Zettelkasten. You can skip to Section 2 if you already know these terms.
Niklas Luhmann, a prolific sociologist who wrote 400 papers and 70 books, inspired this section and much of Zettelkasten. Zettelkasten means “slip box” (or library in this article). His Zettlekasten had around 90000 physical notes, which can be found here.
There are now many tools available to help with this process. Obsidian's website has a good introduction section: https://publish.obsidian.md/hub/

Notes

We'll start with "What is a note?" Although it may seem trivial, the answer depends on the topic or your note-taking style. The idea is that a note is as “atomic” (i.e. You should read the note and get the idea right away.
The resolution of your notes depends on their detail. Deep Learning, for example, could be a general description of Neural Networks, with a few notes on the various architectures (eg. Recurrent Neural Networks, Convolutional Neural Networks etc..).
Limiting length and detail is a good rule of thumb. If you need more detail in a specific section of this note, break it up into smaller notes. Deep Learning now has three notes:

• Deep Learning
• Recurrent Neural Networks
  - Convolutional Neural Networks

Repeat this step as needed until you achieve the desired granularity. You might want to put these notes in a “Neural Networks” folder because they are all about the same thing. But there's a better way:

The main issue with folders is that they are not flexible and assume that all notes in the folder belong to a single category. This makes it difficult to make connections between topics.
Deep Learning has been used to predict protein structure (AlphaFold) and classify images (ImageNet). Imagine a folder structure like this:

- /Proteins/ 
     - Protein Folding
- /Deep Learning/
     - /Proteins/ 

Your notes about Protein Folding and Convolutional Neural Networks will be separate, and you won't be able to find them in the same folder.
This can be solved in several ways. The most common one is to use tags rather than folders. A note can be grouped with multiple topics this way. Obsidian tags can also be nested (have subtags).

You can also link two notes together. You can build your “Knowledge Graph” in Obsidian and other note-taking apps like Obsidian.

My Knowledge Graph. Green: Biology, Red: Machine Learning, Yellow: Autoencoders, Blue: Graphs, Brown: Tags.

My Knowledge Graph and the note “Backrpropagation” and its links.

Backpropagation note and all its links

Why use Folders?

Folders help organize your vault as it grows. The main suggestion is to have few folders that "weakly" collect groups of notes or better yet, notes from different sources.
Among my Zettelkasten folders are:

My Zettelkasten's 5 folders

They usually gather data from various sources:

MOC: Map of Contents for the Zettelkasten.
Projects: Contains one note for each side-project of my PhD where I log my progress and ideas. Notes are linked to these.
Bio and ML: These two are the main content of my Zettelkasten and could theoretically be combined.
Papers: All my scientific paper notes go here. A bibliography links the notes. Zotero .bib file
Books: I make a note for each book I read, which I then split into multiple notes.

Keeping images separate from other files can help keep your main folders clean.

I will elaborate on these in the Workflow Section.

My general recommendation is to use tags and links instead of folders.

Maps of Content (MOC) 

Making Tables of Contents is a good solution (MOCs).
These are notes that "signposts" your Zettelkasten library, directing you to the right type of notes. It can link to other notes based on common tags. This is usually done with a title, then your notes related to that title. As an example:

An example of a Machine Learning MOC generated with Dataview.

As shown above, my Machine Learning MOC begins with the basics. Then it's on to Variational Auto-Encoders. Not only does this save time, but it also saves scrolling through the tag search section.
So I keep MOCs at the top of my library so I can quickly find information and see my library. These MOCs are generated automatically using an Obsidian Plugin called Dataview (https://github.com/blacksmithgu/obsidian-dataview).
Ideally, MOCs could be expanded to include more information about the notes, their status, and what's left to do. In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.
In the absence of this, Dataview does a fantastic job at creating a good structure for your notes.

2. Tools: Knowing Obsidian

Obsidian is my preferred tool because it is free, all notes are stored in Markdown format, and each panel can be dragged and dropped. You can get it here: https://obsidian.md/

Obsidian interface. 

Obsidian is highly customizable, so here is my preferred interface:

The theme is customized from https://github.com/colineckert/obsidian-things

Alternatively, each panel can be collapsed, moved, or removed as desired. To open a panel later, click on the vertical "..." (bottom left of the note panel).

My interface is organized as follows:

How my Obsidian Interface is organized.

Folders/Search:
This is where I keep all relevant folders. I usually use the MOC note to navigate, but sometimes I use the search button to find a note.

Tags:
I use nested tags and look into each one to find specific notes to link.

cMenu:
Easy-to-use menu plugin cMenu (https://github.com/chetachiezikeuzor/cMenu-Plugin)

Global Graph:
The global graph shows all your notes (linked and unlinked). Linked notes will appear closer together. Zoom in to read each note's title. It's a bit overwhelming at first, but as your library grows, you get used to the positions and start thinking of new connections between notes.

Local Graph:
Your current note will be shown in relation to other linked notes in your library. When needed, you can quickly jump to another link and back to the current note.

Links:
Finally, an outline panel and the plugin Obsidian Power Search (https://github.com/aviral-batra/obsidian-power-search) allow me to search my vault by highlighting text.

Start using the tool and worry about panel positioning later. I encourage you to find the best use-case for your library.

Plugins

An additional benefit of using Obsidian is the large plugin library. I use several (Calendar, Citations, Dataview, Templater, Admonition):
Obsidian Calendar Plugin: https://github.com/liamcain
It organizes your notes on a calendar. This is ideal for meeting notes or keeping a journal.

Calendar addon from hans/obsidian-citation-plugin
Obsidian Citation Plugin: https://github.com/hans/
Allows you to cite papers from a.bib file. You can also customize your notes (eg. Title, Authors, Abstract etc..)

Plugin citation from hans/obsidian-citation-plugin
Obsidian Dataview: https://github.com/blacksmithgu/
A powerful plugin that allows you to query your library as a database and generate content automatically. See the MOC section for an example.
Allows you to create notes with specific templates like dates, tags, and headings.

Templater. Obsidian Admonition: https://github.com/valentine195/obsidian-admonition
Blocks allow you to organize your notes.

Plugin warning. Obsidian Admonition (valentine195)
There are many more, but this list should get you started.

3. Workflows: Cool stuff

Here are a few of my workflows for using obsidian for scientific research. This is a list of resources I've found useful for my use-cases. I'll outline and describe them briefly so you can skim them quickly.
3.1 Using Templates to Structure Notes
3.2 Free Note Syncing (Laptop, Phone, Tablet)
3.3 Zotero/Mendeley/JabRef -> Obsidian — Managing Reading Lists
3.4 Projects and Lab Books
3.5 Private Encrypted Diary

3.1 Using Templates to Structure Notes

Plugins: Templater and Dataview (optional).
To take effective notes, you must first make adding new notes as easy as possible. Templates can save you time and give your notes a consistent structure. As an example:

An example of a note using a template.

### [[YOUR MOC]]
# Note Title of your note
**Tags**:: 
**Links**::

The top line links to your knowledge base's Map of Content (MOC) (see previous sections). After the title, I add tags (and a link between the note and the tag) and links to related notes.
To quickly identify all notes that need to be expanded, I add the tag “#todo”. In the “TODO:” section, I list the tasks within the note.
The rest are notes on the topic.
Templater can help you create these templates. For new books, I use the following template:

### [[Books MOC]]
# Title
**Author**:: 
**Date::
**Tags:: 
**Links::

A book template example.

Using a simple query, I can hook Dataview to it.

dataview  
table author as Author, date as “Date Finished”, tags as “Tags”, grade as “Grade”  
from “4. Books”  
SORT grade DESCENDING

using Dataview to query templates.

3.2 Free Note Syncing (Laptop, Phone, Tablet)

No plugins used.

One of my favorite features of Obsidian is the library's self-contained and portable format. Your folder contains everything (plugins included).

Ordinary folders and documents are available as well. There is also a “.obsidian” folder. This contains all your plugins and settings, so you can use it on other devices.
So you can use Google Drive, iCloud, or Dropbox for free as long as you sync your folder (note: your folder should be in your Cloud Folder).

For my iOS and macOS work, I prefer iCloud. You can also use the paid service Obsidian Sync.
3.3 Obsidian — Managing Reading Lists and Notes in Zotero/Mendeley/JabRef
Plugins: Quotes (required).

3.3 Zotero/Mendeley/JabRef -> Obsidian — Taking Notes and Managing Reading Lists of Scientific Papers

My preferred reference manager is Zotero, but this workflow should work with any reference manager that produces a .bib file. This file is exported to my cloud folder so I can access it from any platform.

My Zotero library is tagged as follows:

My reference manager's tags

For readings, I usually search for the tags “!!!” and “To-Read” and select a paper. Annotate the paper next (either on PDF using GoodNotes or on physical paper).
Then I make a paper page using a template in the Citations plugin settings:

An example of my citations template.

Create a new note, open the command list with CMD/CTRL + P, and find the Citations “Insert literature note content in the current pane” to see this lovely view.

Citation generated by the article https://doi.org/10.1101/2022.01.24.22269144

You can then convert your notes to digital. I found that transcribing helped me retain information better.

3.4 Projects and Lab Books

Plugins: Tweaker (required).
PhD students offering advice on thesis writing are common (read as regret). I started asking them what they would have done differently or earlier.

Time management requires planning. Keeping track of multiple projects and lab books is difficult during a PhD. How I deal with it:

• One folder for all my projects
• One file for each project
  I use a template to create each project

### [[Projects MOC]]  
# <% tp.file.title %>  
**Tags**::  
**Links**::  
**URL**::  
**Project Description**::## Notes:  
### <% tp.file.last_modified_date(“dddd Do MMMM YYYY”) %>  
#### Done:  
#### TODO:  
#### Notes

You can insert a template into a new note with CMD + P and looking for the Templater option.

I then keep adding new days with another template:

### <% tp.file.last_modified_date("dddd Do MMMM YYYY") %>  
#### Done:  
#### TODO:  
#### Notes:

This way you can keep adding days to your project and update with reasonings and things you still have to do and have done. An example below:

Example of project note with timestamped notes.

3.5 Private Encrypted Diary

This is one of my favorite Obsidian uses.
Mini Diary's interface has long frustrated me. After the author archived the project, I looked for a replacement. I had two demands:

1. It had to be private, and nobody had to be able to read the entries.
2. Cloud syncing was required for editing on multiple devices.

Then I learned about encrypting the Obsidian folder. Then decrypt and open the folder with Obsidian. Sync the folder as usual.
Use CryptoMator (https://cryptomator.org/). Create an encrypted folder in Cryptomator for your Obsidian vault, set a password, and let it do the rest.
If you need a step-by-step video guide, here it is:

Conclusion

So, I hope this was helpful!
In the first section of the article, we discussed notes and note-taking techniques. We discussed when to use tags and links over folders and when to break up larger notes.
Then we learned about Obsidian, its interface, and some useful plugins like Citations for citing papers and Templater for creating note templates.
Finally, we discussed workflows and how to use Zotero to take notes from scientific papers, as well as managing Lab Books and Private Encrypted Diaries.
Thanks for reading and commenting :)

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Senses help us navigate a complicated world. They shape our worldview - how we hear, smell, feel, and taste. People claim a sixth sense, an intuitive capacity that extends perception.

Our brain is a half-pool of grey and white matter that stores data from our senses. Brains provide us context, so zombies' obsession makes sense.

Bionic reading uses the brain's visual information and context to simplify text comprehension.

Stay with me.

What is Bionic Reading?

Bionic reading is a software application established by Swiss typographic designer Renato Casutt. The term honors the brain (bio) and technology's collaboration to better text comprehension.

The image above shows two similar paragraphs with bionic reading.

Notice anything yet?

This Twitter user did.

I did too...

Image text describes bionic reading-

How is Bionic Reading possible?

Do you remember seeing social media posts asking you to stare at a black dot for 30 seconds (or more)? You blink and see an after-image on your wall.

Our brains are skilled at identifying patterns and'seeing' familiar objects, therefore optical illusions are conceivable.

Brain and sight collaborate well. Text comprehension proves it.

Considering evolutionary patterns, humans' understanding skills may be cosmic luck.
Scientists don't know why people can read and write, but they do know what reading does to the brain.

One portion of your brain recognizes words, while another analyzes their meaning. Fixation, saccade, and linguistic transparency/opacity aid.

Let's explain some terms.

• Fixation is how the eyes move when reading. It's where you look. If the eyes fixate less, a reader can read quicker. [Eye fixation is a physiological process](Eye fixation is a naturally occurring physiological process) impacted by the reader's vocabulary, vision span, and text familiarity.

• Saccade - Pause and look around. That's a saccade. Rapid eye movements that alter the place of fixation, as reading text or looking around a room. They can happen willingly (when you choose) or instinctively, even when your eyes are fixed.

• Linguistic transparency and opacity analyze how well a composite word or phrase may be deduced from its constituents.

The Bionic reading website compares these tools.

Text highlights lead the eye. Fixation, saccade, and opacity can transfer visual stimuli to text, changing typeface.

## Final Thoughts on Bionic Reading

I'm excited about how this could influence my long-term assimilation and productivity.

This technology is still in development, with prototypes working on only a few apps. Like any new tech, it will be criticized.

I'll be watching Bionic Reading closely. Comment on it!

What is Bitcoin?

The blockchain is a shared, immutable ledger that helps businesses record transactions and track assets. The blockchain can track tangible assets like cars, houses, and land. Tangible assets like intellectual property can also be tracked on the blockchain.

Imagine a blockchain as a distributed database split among computer nodes. A blockchain stores data in blocks. When a block is full, it is closed and linked to the next. As a result, all subsequent information is compiled into a new block that will be added to the chain once it is filled.

The blockchain is designed so that adding a transaction requires consensus. That means a majority of network nodes must approve a transaction. No single authority can control transactions on the blockchain. The network nodes use cryptographic keys and passwords to validate each other's transactions.

Blockchain History

The blockchain was not as popular in 1991 when Stuart Haber and W. Scott Stornetta worked on it. The blocks were designed to prevent tampering with document timestamps. Stuart Haber and W. Scott Stornetta improved their work in 1992 by using Merkle trees to increase efficiency and collect more documents on a single block.

In 2004, he developed Reusable Proof of Work. This system allows users to verify token transfers in real time. Satoshi Nakamoto invented distributed blockchains in 2008. He improved the blockchain design so that new blocks could be added to the chain without being signed by trusted parties.

Satoshi Nakomoto mined the first Bitcoin block in 2009, earning 50 Bitcoins. Then, in 2013, Vitalik Buterin stated that Bitcoin needed a scripting language for building decentralized applications. He then created Ethereum, a new blockchain-based platform for decentralized apps. Since the Ethereum launch in 2015, different blockchain platforms have been launched: from Hyperledger by Linux Foundation, EOS.IO by block.one, IOTA, NEO and Monero dash blockchain. The block chain industry is still growing, and so are the businesses built on them.

Blockchain Components

The Blockchain is made up of many parts:

1. Node: The node is split into two parts: full and partial. The full node has the authority to validate, accept, or reject any transaction. Partial nodes or lightweight nodes only keep the transaction's hash value. It doesn't keep a full copy of the blockchain, so it has limited storage and processing power.

2. Ledger: A public database of information. A ledger can be public, decentralized, or distributed. Anyone on the blockchain can access the public ledger and add data to it. It allows each node to participate in every transaction. The distributed ledger copies the database to all nodes. A group of nodes can verify transactions or add data blocks to the blockchain.

3. Wallet: A blockchain wallet allows users to send, receive, store, and exchange digital assets, as well as monitor and manage their value. Wallets come in two flavors: hardware and software. Online or offline wallets exist. Online or hot wallets are used when online. Without an internet connection, offline wallets like paper and hardware wallets can store private keys and sign transactions. Wallets generally secure transactions with a private key and wallet address.

4. Nonce: A nonce is a short term for a "number used once''. It describes a unique random number. Nonces are frequently generated to modify cryptographic results. A nonce is a number that changes over time and is used to prevent value reuse. To prevent document reproduction, it can be a timestamp. A cryptographic hash function can also use it to vary input. Nonces can be used for authentication, hashing, or even electronic signatures.

5. Hash: A hash is a mathematical function that converts inputs of arbitrary length to outputs of fixed length. That is, regardless of file size, the hash will remain unique. A hash cannot generate input from hashed output, but it can identify a file. Hashes can be used to verify message integrity and authenticate data. Cryptographic hash functions add security to standard hash functions, making it difficult to decipher message contents or track senders.

Blockchain: Pros and Cons

The blockchain provides a trustworthy, secure, and trackable platform for business transactions quickly and affordably. The blockchain reduces paperwork, documentation errors, and the need for third parties to verify transactions.

Blockchain security relies on a system of unaltered transaction records with end-to-end encryption, reducing fraud and unauthorized activity. The blockchain also helps verify the authenticity of items like farm food, medicines, and even employee certification. The ability to control data gives users a level of privacy that no other platform can match.

In the case of Bitcoin, the blockchain can only handle seven transactions per second. Unlike Hyperledger and Visa, which can handle ten thousand transactions per second. Also, each participant node must verify and approve transactions, slowing down exchanges and limiting scalability.

The blockchain requires a lot of energy to run. In addition, the blockchain is not a hugely distributable system and it is destructible. The security of the block chain can be compromised by hackers; it is not completely foolproof. Also, since blockchain entries are immutable, data cannot be removed. The blockchain's high energy consumption and limited scalability reduce its efficiency.

Why Is Blockchain So Popular?
The blockchain is a technology giant. In 2018, 90% of US and European banks began exploring blockchain's potential. In 2021, 24% of companies are expected to invest $5 million to $10 million in blockchain. By the end of 2024, it is expected that corporations will spend $20 billion annually on blockchain technical services.

Blockchain is used in cryptocurrency, medical records storage, identity verification, election voting, security, agriculture, business, and many other fields. The blockchain offers a more secure, decentralized, and less corrupt system of making global payments, which cryptocurrency enthusiasts love. Users who want to save time and energy prefer it because it is faster and less bureaucratic than banking and healthcare systems.

Most organizations have jumped on the blockchain bandwagon, and for good reason: the blockchain industry has never had more potential. The launch of IBM's Blockchain Wire, Paystack, Aza Finance and Bloom are visible proof of the wonders that the blockchain has done. The blockchain's cryptocurrency segment may not be as popular in the future as the blockchain's other segments, as evidenced by the various industries where it is used. The blockchain is here to stay, and it will be discussed for a long time, not just in tech, but in many industries.

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If tasked with the problem of coming up with a zk-SNARK protocol, many people would make their way to this point and then get stuck and give up. How can a verifier possibly check every single piece of the computation, without looking at each piece of the computation individually? But it turns out that there is a clever solution.

Polynomials

Polynomials are a special class of algebraic expressions of the form:

• x+5
• x^4
• x^3+3x^2+3x+1
• 628x^{271}+318x^{270}+530x^{269}+…+69x+381

i.e. they are a sum of any (finite!) number of terms of the form cx^k

There are many things that are fascinating about polynomials. But here we are going to zoom in on a particular one: polynomials are a single mathematical object that can contain an unbounded amount of information (think of them as a list of integers and this is obvious). The fourth example above contained 816 digits of tau, and one can easily imagine a polynomial that contains far more.

Furthermore, a single equation between polynomials can represent an unbounded number of equations between numbers. For example, consider the equation A(x)+ B(x) = C(x). If this equation is true, then it's also true that:

• A(0)+B(0)=C(0)
• A(1)+B(1)=C(1)
• A(2)+B(2)=C(2)
• A(3)+B(3)=C(3)

And so on for every possible coordinate. You can even construct polynomials to deliberately represent sets of numbers so you can check many equations all at once. For example, suppose that you wanted to check:

• 12+1=13
• 10+8=18
• 15+8=23
• 15+13=28

You can use a procedure called Lagrange interpolation to construct polynomials A(x) that give (12,10,15,15) as outputs at some specific set of coordinates (eg. (0,1,2,3)), B(x) the outputs (1,8,8,13) on thos same coordinates, and so forth. In fact, here are the polynomials:

• A(x)=-2x^3+\frac{19}{2}x^2-\frac{19}{2}x+12
• B(x)=2x^3-\frac{19}{2}x^2+\frac{29}{2}x+1
• C(x)=5x+13

Checking the equation A(x)+B(x)=C(x) with these polynomials checks all four above equations at the same time.

Comparing a polynomial to itself

You can even check relationships between a large number of adjacent evaluations of the same polynomial using a simple polynomial equation. This is slightly more advanced. Suppose that you want to check that, for a given polynomial F, F(x+2)=F(x)+F(x+1) with the integer range {0,1…89} (so if you also check F(0)=F(1)=1, then F(100) would be the 100th Fibonacci number)

As polynomials, F(x+2)-F(x+1)-F(x) would not be exactly zero, as it could give arbitrary answers outside the range x={0,1…98}. But we can do something clever. In general, there is a rule that if a polynomial P is zero across some set S=\{x_1,x_2…x_n\} then it can be expressed as P(x)=Z(x)*H(x), where Z(x)=(x-x_1)*(x-x_2)*…*(x-x_n) and H(x) is also a polynomial. In other words, any polynomial that equals zero across some set is a (polynomial) multiple of the simplest (lowest-degree) polynomial that equals zero across that same set.

Why is this the case? It is a nice corollary of polynomial long division: the factor theorem. We know that, when dividing P(x) by Z(x), we will get a quotient Q(x) and a remainder R(x) is strictly less than that of Z(x). Since we know that P is zero on all of S, it means that R has to be zero on all of S as well. So we can simply compute R(x) via polynomial interpolation, since it's a polynomial of degree at most n-1 and we know n values (the zeros at S). Interpolating a polynomial with all zeroes gives the zero polynomial, thus R(x)=0 and H(x)=Q(x).

Going back to our example, if we have a polynomial F that encodes Fibonacci numbers (so F(x+2)=F(x)+F(x+1) across x=\{0,1…98\}), then I can convince you that F actually satisfies this condition by proving that the polynomial P(x)=F(x+2)-F(x+1)-F(x) is zero over that range, by giving you the quotient:
H(x)=\frac{F(x+2)-F(x+1)-F(x)}{Z(x)}
Where Z(x) = (x-0)*(x-1)*…*(x-98).
You can calculate Z(x) yourself (ideally you would have it precomputed), check the equation, and if the check passes then F(x) satisfies the condition!

Now, step back and notice what we did here. We converted a 100-step-long computation into a single equation with polynomials. Of course, proving the N'th Fibonacci number is not an especially useful task, especially since Fibonacci numbers have a closed form. But you can use exactly the same basic technique, just with some extra polynomials and some more complicated equations, to encode arbitrary computations with an arbitrarily large number of steps.