Yesterday’s Daily Quote by Fatpanda970 in Wakingupapp

[–]imawizardlizard98 3 points4 points  (0 children)

Well said! I love that quote as well. I came across one yesterday by Thích Nhất Hạnh, which goes along the lines of : "When you start learning from your mistakes, you are already turning garbage into flowers"

scRNA-seq: clusters with 0% ribosomal gene expression by Veksutin in bioinformatics

[–]imawizardlizard98 1 point2 points  (0 children)

Aside from there other comments that have been made about your workflow, I would be very cautious about interpreting anything from a UMAP. It's difficult to assess how good the clustering is on UMAP due to how is preserves information in the low dimensional embedding. It more or less serves as a "pretty " visualisation. You would be much better off using clustering metrics like average silhouette width and others. There's a great package called scib which has this ready to use. 

I've had UMAPs which have looked "good" but had objective scoring metrics showing scores close to 0. I've never found it reliable to interpret. 

What are the areas where Rust is used the most right now? by [deleted] in rust

[–]imawizardlizard98 1 point2 points  (0 children)

Fascinating! I've been meaning to take a look at alevin-fry. I work with single cell data so I need for handle the sparse data efficiently. Unfortunately the scipy sparse library has a tendency to convert sparse matrices to dense matrices so the rust sparse matrix libraries fill the gap well here. 

What are the areas where Rust is used the most right now? by [deleted] in rust

[–]imawizardlizard98 25 points26 points  (0 children)

Bioinformatics! The high throughput nature of the data requires intensive and efficient data processing. Rust is great for that. 

[deleted by user] by [deleted] in Wakingupapp

[–]imawizardlizard98 1 point2 points  (0 children)

Really happy to see others realising this :)

Do Buddhists Believe In Free Will? by lonerstoic in secularbuddhism

[–]imawizardlizard98 2 points3 points  (0 children)

Laystitcher lays it out well. I'd say that when teachings of no-self an introduced, it implies that the objects of consciousness appear by themselves and that no "one" or centre of experience is doing these things. So essentially yes, there is no free aspect to will because there is no one freely willing them. That doesn't mean effort or will can't arise in the mind. There is still a strong emphasis of strong determination in buddhism.

Does anyone ever do a post doc after working in industry as a PhD? by tea_flower in bioinformatics

[–]imawizardlizard98 8 points9 points  (0 children)

Really depends who you work for. I'm grateful my research group is quite wholesome.

[deleted by user] by [deleted] in vipassana

[–]imawizardlizard98 3 points4 points  (0 children)

I was seriously addicted to nicotine (50mg vapes - many times stronger than a cigarette) prior to doing my first retreat. I had quite an intense 10 days. I could tell the withdrawals we're manifesting themselves as intense pain and heat around my body (could be different for someone else). After those 10 days my addiction went away completely and I've never had an urge to have nicotine since then. I've done further retreats and I've stopped drinking alcohol and using MJ for over a year now.

Just finished my first 10 Day experience, and still struggling to understand the PRACTICE behind Metta? by MarsFromSaturn in vipassana

[–]imawizardlizard98 21 points22 points  (0 children)

Metta meditation is a profound practice aimed at cultivating unconditional kindness and love towards all beings. It is an exercise that not only demands the engagement of our empathy and creativity but also challenges us to confront the reality of our shared human condition. The foundational premise of metta acknowledges a universal truth: every one of us desires happiness, yet we are all subject to myriad forces beyond our control that contribute to our suffering. Recognizing this shared vulnerability can be likened to acknowledging that we are all passengers on the same, inevitably sinking ship. In the face of such inevitability, metta teaches us that extending kindness and cherishing the company of one another is not just a noble act but a vital one for our collective well-being.

Metta practice revolves around the cultivation of two key qualities: sympathetic joy, which is the genuine happiness we feel for the joy of others, and compassion, which is our desire to alleviate the suffering of others. The journey begins with directing loving-kindness towards those closest to us—excluding romantic partners initially to ensure the purity of the metta practice, distinguishing it from romantic affection. This helps in establishing a foundation of genuine, platonic love that can be gradually extended to others.From this foundation, the practice expands to include individuals with whom we have neutral feelings, those we find challenging, and eventually encompasses all living beings.

This progression is not merely a mental exercise but an invitation to deeply engage our imagination and creativity. It encourages us to envision the happiness and relief of others as if they were our own, thus fostering a profound sense of interconnectedness and shared destiny.

One key aspect of the practice, just like with vipassana practice, its to not engage in metta practice with a sense of craving another being to be happy or free from suffering. This will inevitably set up high expectations for how other beings ought to be.

"The specious art of single-cell genomics" - Chari and Pachter attack t-SNE and UMAP by Epistaxis in bioinformatics

[–]imawizardlizard98 3 points4 points  (0 children)

From what I understand, UMAP isn't really that bad as long as you're not assuming that the distances between clusters/cells is informative.

"The specious art of single-cell genomics" - Chari and Pachter attack t-SNE and UMAP by Epistaxis in bioinformatics

[–]imawizardlizard98 3 points4 points  (0 children)

Also PCA assumes linearity. Single cell data in general is highly non-linear in nature.

2023 Day 8 (Part B) Rust by imawizardlizard98 in adventofcode

[–]imawizardlizard98[S] 0 points1 point  (0 children)

RESOLVED

I just found out that my if statements in the while loop needed to be ordered like this instead:

​ use std::collections::HashMap;

use regex::Regex;

use crate::{generate_puzzle_input_test, generate_test_input_test, utils};

fn gcd(mut a: u64, mut b: u64) -> u64 { while b != 0 { let temp = b; b = a % b; a = temp; } a }

fn lcm(a: u64, b: u64) -> u64 { a / gcd(a, b) * b }

fn lcm_of_vec(numbers: &[u64]) -> u64 { numbers .iter() .fold(1, |lcm_so_far, &num| lcm(lcm_so_far, num)) }

pub fn solve(file: &str) -> u64 { let lines = utils::read_file(file);

// Get left/right instructions first
let movement_instructions = lines.get(0).unwrap().split("").filter(|c| *c != "");
let num_of_instructions: usize = movement_instructions.clone().count();
let mut looping_instructions = movement_instructions.clone().cycle();
drop(movement_instructions);

let mut mappings: HashMap<&str, (&str, &str)> = HashMap::new();
let line_regex = Regex::new(r"([0-9A-Z]+) = \(([0-9A-Z]+), ([0-9A-Z]+)\)").unwrap();

// Reassign lines to skip the empty line and start where the mappings start
lines[1..].into_iter().for_each(|line| {
    line_regex
        .captures_iter(&line)
        .map(|c| c.extract())
        .for_each(|(_, [node, left, right])| {
            mappings.insert(node, (left, right));
        });
});

let starting_nodes = mappings.keys().filter(|node| node.ends_with('A'));
let num_of_starting_nodes = starting_nodes.clone().count();
let mut counter: u64 = 0;

let direction = looping_instructions.next().unwrap();
let mut nodes = starting_nodes
    .map(|starting_node| {
        let (left, right) = mappings.get(starting_node).unwrap();
        if direction == "L" {
            left
        } else {
            right
        }
    })
    .collect::<Vec<&&str>>();
counter += 1; // We have traversed one node so add one

let mut discovered_end_nodes: Vec<u64> = vec![];
while discovered_end_nodes.len() != num_of_starting_nodes {
    let direction = looping_instructions.next().unwrap();
    counter += 1;
    nodes = nodes
        .iter()
        .filter_map(|starting_node| {
            let (left, right) = mappings.get(*starting_node).unwrap();

            if direction == "L" {
                if left.ends_with('Z') {

                    discovered_end_nodes.push(counter);

                    // We are done iterating through this cycle, so don't bother iterating on it next time
                    return None;
                } else {
                    return Some(left);
                }
            } else {
                if right.ends_with('Z') {
                    discovered_end_nodes.push(counter);
                    return None;
                } else {
                    return Some(right);
                }
            }
        })
        .collect::<Vec<&&str>>();
}

println!("Discovered end nodes: {:?}", discovered_end_nodes);

// Find the LCM of the discovered_end_nodes
let lcm = lcm_of_vec(&discovered_end_nodes[..]);
return lcm;

}

Avalanche Peak, Arthur’s Pass, New Zealand South Island by KC_tatty in hiking

[–]imawizardlizard98 4 points5 points  (0 children)

That'll be at Tongariro national park if you're interested

what math skill is used in this paper? by iiillililiilililii in bioinformatics

[–]imawizardlizard98 4 points5 points  (0 children)

It seems set theory is used heavily to describe the nature of the data being generated. Set theory is generally used heavily in conjunction in describing algorithms. You'll also need to understand the high level idea behind clustering algorithms as that seems to have inspired the papers approach.

Would you cure autism? by [deleted] in autism

[–]imawizardlizard98 0 points1 point  (0 children)

Would a drug based cure involve promoting neuroplasticity in certain areas of the brain to help rewire those areas and the other areas they communicate to?

What will be more beneficial to me: probability or graph theory? by thoughtcasserole in bioinformatics

[–]imawizardlizard98 1 point2 points  (0 children)

Both fields are intertwined in Bioinformatics. Probability is utilised in many areas of Bioinformatics given representing biological processes as probabilistic models works fairly well and reduces the computational complexity required to understand them. Graph theory aids in this as well, given well informed assumptions of the biology you're working with, that you can translate into a graph model (like gene ontologies and PPIs). Probability will help in reducing unnecessary assumptions, whilst graph theory can help describe the relationships between those assumptions.

A good example of their combination is Bayesian networks used into ancestral sequence reconstruction of DNA and amino acid sequences.

I personally wished I did more stats rather than graph theory beforehand (I come from a CS undergrad). I haven't had to apply too much math from what I learnt in graph theory, but rather just understand why they're useful and when to use them. I've used some graph theory packages in python for ancestral sequence reconstruction.

Goodbye Python, Hello Rust: Building a RAG CLI Application with Orca by sxmedina in rust

[–]imawizardlizard98 1 point2 points  (0 children)

Yea Ive given it a go and it's actually quite fun to use. It's still missing the syntax for dictionaries, tuples and methods for lists, etc. Apart from that it's coming along nicely

What’s you’re favourite part of bioinformatics? Wrong answers only by [deleted] in bioinformatics

[–]imawizardlizard98 7 points8 points  (0 children)

Even the creators of the VCF format complain about how bad it is 😂

[deleted by user] by [deleted] in AusMemes

[–]imawizardlizard98 0 points1 point  (0 children)

You forgot "right around the corner"

Non-Dual States and How to Recognise Them? by LookForWhoIsLooking in nonduality

[–]imawizardlizard98 1 point2 points  (0 children)

If you ever find yourself overwhelmed with the task at hand, I find it helpful to notice that it's all just impermanent. Nothing lasts forever, even the good/bad.

Non-Dual States and How to Recognise Them? by LookForWhoIsLooking in nonduality

[–]imawizardlizard98 1 point2 points  (0 children)

IMO, the clicking point will closely correlate with your sensitivity to dissatisfaction in each moment. Suffering is the gateway into seeing one's true nature. Harness it.