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Time is Money, Efficiency is Life
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Time is Money, Efficiency is Life

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OccupyMars2025/README.md

When you read a book, a paper or source code, you are communicating with the brightest minds in human history. This is actually the most "effective" way to communicate. This is also the quickest path to success.

Extroverted and cheerful individuals always adapt to new environments and embrace new challenges more easily than introverted ones.

Since you believe that your introverted personality has caused many setbacks and failures in your life, then actively change your personality!

Since you regard a weak body as an obstacle to your success, be proactive about exercising so you can build a strong, healthy physique.

Root out every bad habit that has turned into a stumbling block on your road to success.

Achieve small victories every hour

The harder the task, the smaller your first step should be.


Go Navy ! Beat Army !

Go Army ! Sink Navy !

Winning matters at West Point !

competitive sport

除了胜利一无所求,为了胜利一无所惜

Just 100 metres from the finishing line he forged ahead.

In order to be able to do 100 consecutive pull-ups, you need to train yourself to hang on the bar for as long as possible.

newest personal records

feat: 2025/6/17, run 5km in 22:50, Average Pace: 4:34/km

2025/6/1 6:09-8:21: run a half marathon in 1:51:53

feat: 2025/6/7, run 5km in 22:59

feat: 2025/6/5, 40 pull-ups in a row

feat: 2025/6/5, 60 Five-Finger Push-Ups in a row(All five fingers of each hand are spread and bear the weight. You perform a push-up with only your fingers touching the ground (instead of your palms))

feat: 2025/6/24, 130 push-ups in a row (using push up bars)


2025/6/17, Tuesday: {"running": 5km}, {"pull ups + Parallel Bar Dips": 200}, {"push ups + Mountain Climbers": 100}
6/17 6:17-6:40:  run 5km in 22:50, Average Pace: 4:34/km
6/17 6:40-9:13: (A.1.1 Preprocessing), (A.1.2 Initial Analysis Plan Generation), ... (A.1.4 Re-evaluating the Analysis Plan)
6/17 9:13-10:58: A.2 CellBench
6/17 16:10-16:50: {"pull ups + Parallel Bar Dips": 200}
6/17 19:10-22:44: study the source code https://github.com/zou-group/CellVoyager, try to figure out how to run it


2025/6/18, Wednesday: {"running": rainy}, {"pull ups + Parallel Bar Dips": 200}, {"push ups + Mountain Climbers": 100}
6/18 7:19-22:20: study the source code https://github.com/zou-group/CellVoyager,

2025/6/19, Thursday: {"running": 5km}, {"pull ups + Parallel Bar Dips": 200}
6/19 6:04-6:30:  run 5km in 25:08, Average Pace: 5:01/km
6/19 7:20-19:20: study "class AnalysisAgent" (https://github.com/zou-group/CellVoyager)

2025/6/20, Friday:  {"running": 5km}, {"pull ups + Parallel Bar Dips": 200}, {"push ups + Mountain Climbers": 200}
6/20 6:19-6:52:  run 5km in 32:24, Average Pace: 6:28/km
6/20 7:58-14:20: study "class AnalysisAgent" (https://github.com/zou-group/CellVoyager)
6/20 14:30-15:40 : Participate in the online public welfare seminar—"Observations and Reflections on the Application of AI in Clinical Drug Development"
6/20 15:40-22:00 :  study "class AnalysisAgent", DeepResearch_Analyses.txt (https://github.com/zou-group/CellVoyager)

2025/6/21, Saturday: {"push ups + Mountain Climbers": 300}
9:46-12:00: study "class AnalysisAgent", DeepResearch_Analyses.txt (https://github.com/zou-group/CellVoyager)

2025/6/22, Sunday: {"running": 5km}, {"pull ups + Parallel Bar Dips": 200}, {"push ups + Mountain Climbers": 300}
6:42-7:10: run 5.25km in 28:39, Average Pace: 5:27/km
8:00-10:45: DeepResearch_Analyses.txt (https://github.com/zou-group/CellVoyager)

2025/6/22: complete the whole paper and part of its source code: [CellVoyager: AI CompBio Agent Generates New Insights by Autonomously Analyzing Biological Data](https://www.biorxiv.org/content/10.1101/2025.06.03.657517v1.full.pdf)  To fully understand the source code, I need to dive deeper into key tools like Scanpy and scVI. For now, I’ve decided to pause my study of this paper (which I’ll consider completed) and return to my work on AlphaFold 3.

6/22 12:16-19:30: 3.3 MSA Module (AlphaFold 3, https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-024-07487-w/MediaObjects/41586_2024_7487_MOESM1_ESM.pdf)
6/22 19:30-21:10: study the pytorch implementation of those algorithms in "3.3 MSA Module" (https://github.com/bytedance/Protenix)

2025/6/23, Monday: {"running": 5km}, {"pull ups + Parallel Bar Dips": 200}, {"push ups + Mountain Climbers": 300}, {"Cartwheel Count": 22}
6/23 6:18-6:42: run 5km in 22:55, Average Pace: 4:35/km
6/23 8:02-18:00: study the pytorch implementation of those algorithms in "3.3 MSA Module" (https://github.com/bytedance/Protenix), I am a little confused by the implementation of "trunc_normal_init_"(I get it now, this is actually very simple.)

2025/6/24, Tuesday: {"running": rainy}, {"pull ups + Parallel Bar Dips": 0}, {"push ups + Mountain Climbers": 300}, {"Cartwheel Count": 0}
6/24 6:59-16:00: study the pytorch implementation of those algorithms in "3.3 MSA Module" (https://github.com/bytedance/Protenix), study "LinearNoBias"


2025/6/25, Wednesday: {"running": 2km}, {"pull ups + Parallel Bar Dips": 200}, {"push ups + Mountain Climbers": 200}, {"Cartwheel Count": 0}
6/25 8:00-: study the pytorch implementation of those algorithms in "3.3 MSA Module" (https://github.com/bytedance/Protenix)


TODO: study [Association between resolved hepatitis B virus infection and depression in American adults : a cross-sectional study](https://www.nature.com/articles/s41598-025-99864-2)


6

7, 8

9, 10, 11, 12

2025/6/1 - 2025/9/1(6, 7, 8): Carefully study 45 research papers

2025/6/1 - 2026/1/1(214 days): Carefully study 100 research papers

current progress: 1 paper

2025/6/11 14:20- 6/22 10:45: CellVoyager: AI CompBio Agent Generates New Insights by Autonomously Analyzing Biological Data (Study of the paper's codebase is pending completion. I need to study the new tools Scanpy, scVI, etc)


Goals 2025/6/1 - 2026/1/1 (214 days):

0. Run 10km in 40 minutes, run a half marathon in 1 hour and 25 minutes, do 500 push-ups in a row, do 150 pull-ups in a row

1. Carefully study 100 research papers


Goals 2025/5/30 - 6/20:

0. Run 10km in 50 minutes, run a half marathon in 1 hour and 45 minutes, do 100 push-ups in a row, do 50 pull-ups in a row

1. Complete the study of all papers and source codes related to AlphaFold 2&3


TODO:

https://github.com/ArcInstitute/state (virtual cell model ???)

study the latest work: https://x.com/FutureHouseSF

study UMAP (Uniform Manifold Approximation and Projection)


960px-Time_is_money,_Efficiency_is_life

Eliminate the terminal illness before I get it.

Racing against Death 2025

Eliminate all terminal illnesses 2030

Create a Second Earth 2040

Conquer the Universe 2050

To conquer the universe, we need to attain eternal life.

To conquer the universe, I need a physique as powerful as Goku's, along with his unyielding spirit and relentless determination.

亿万年之后 谁又还记得谁

Billions of years later, who will still remember whom ?

人生如同白驹过隙,转瞬即逝,你所取得的一切成就荣耀,你所经历的一切失败,痛苦,磨难, 在你死后都将随风消散.在宇宙面前,你又算是什么? 亿万年之后, 谁又还记得谁 ? 既然如此,何不痛痛快快活一场, 轰轰烈烈干一番事业, 不枉此生, 也就足够了

Life is as fleeting as a white steed’s shadow—gone in the blink of an eye. All the achievements and honors you’ve earned, all the failures, pain, and hardships you’ve endured, will vanish like dust in the wind after your death. In the face of the universe, what are you? Billions of years later, who will still remember whom? Since that’s the case, why not live boldly, pursue great endeavors passionately, and make this life truly worthwhile? That alone is enough.

You only live once, but if you do it right, once is enough.

We're here to put a dent in the universe. Otherwise why else even be here?

Make Humanity Great Again

The World Needs Heroes

开疆拓土, 天纵风华

Become the first human to set foot on Mars and immortalize your name among the greatest explorers of all time.

石达开在被洪秀全“访请出山”时只有16岁,金田起义时19岁,在湖口、九江大捷中令曾国藩兵败投水时是23岁,在成都英勇就义时年仅32岁

坚忍不拔酬壮志,药济天下慨而慷

记住,一所大学的名气和学术水平,很大程度上也是学生们拼出来,打出来的 !

Remember, a university's prestige and academic excellence are largely built and proven by the hard work and accomplishments of its students.

求实求真,大气大为

立大志 明大德 成大才 担大任

Set lofty aspirations, uphold great virtue, cultivate great talent, shoulder great responsibilities.

"Duty, Honor, Country": Those three hallowed words reverently dictate what you ought to be, what you can be, what you will be. They are your rallying points: to build courage when courage seems to fail; to regain faith when there seems to be little cause for faith; to create hope when hope becomes forlorn.

"Ask not what your country can do for you—ask what you can do for your country."

赢就要赢得光明磊落, 输更要输得光芒万丈 !

干大事而惜身,见小利而忘命

像卡卡罗特一样, 吃得香, 睡得死

欲文明其精神,先自野蛮其体魄

Swimming across the Pacific Ocean

Swimming across the Arctic Ocean

兄弟登山, 各自努力, 让我们在顶峰相聚

Done is better than perfect.

Keep it up, boys ! Fight ! Fight to the finish !

Remember: You survive in this world by relying on your own genuine abilities—not by anyone’s charity!

The teams performed exceptionally by quickly pivoting to meet the increased demand from our customers.

The harder the task, the smaller the first step should be.

suffer the pain of discipline or suffer the pain of regret

Pain is inevitable. You either suffer the pain of discipline or the pain of regret. The difference is the pain of discipline is temporary while that of regret is permanent.

A wild boar barged into the vegetable garden, eager to take a bite out of everything it saw.

The messier your exploration, the richer the feast of knowledge you’ll uncover.

Richard Feynmann — 'Study hard what interests you the most in the most undisciplined, irreverent and original manner possible.'

大考大玩、小考小玩、不考不玩


Current progress:

2025/5/30 7:00 - : study the paper of AlphaFold 3: Accurate structure prediction of biomolecular interactions with AlphaFold 3

The central purpose of CellVoyager is to find a single-cell analysis distinct from the ones conducted in the paper but still biologically interesting and in line with the research goals of the paper

Pinned Loading

  1. ColabFold ColabFold Public

    Forked from sokrypton/ColabFold

    Making Protein folding accessible to all!

    Jupyter Notebook

  2. alphafold3-pytorch alphafold3-pytorch Public

    Forked from lucidrains/alphafold3-pytorch

    Implementation of Alphafold 3 from Google Deepmind in Pytorch

    Python

  3. openfold openfold Public

    Forked from aqlaboratory/openfold

    Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

    Python

  4. google-deepmind-alphafold3 google-deepmind-alphafold3 Public

    Forked from google-deepmind/alphafold3

    AlphaFold 3 inference pipeline.

    Python

  5. evo2 evo2 Public

    Forked from ArcInstitute/evo2

    Genome modeling and design across all domains of life

    Jupyter Notebook

  6. Protenix Protenix Public

    Forked from bytedance/Protenix

    A trainable PyTorch reproduction of AlphaFold 3.

    Python