Title Here
Papers
- Transformers without Normalization
- Thoughts on how to think (and talk) about RNA structure
- Ribonanza: deep learning of RNA structure through dual crowdsourcing
- trRosettaRNA: automated prediction of RNA 3D structure with transformer network
- FastFold: Reducing AlphaFold Training Time from 11 Days to 67 Hours
- Outsmarting algorithms: A comparative battle between Reinforcement Learning and heuristics in Atari Tetris
Links
- https://medium.com/@kording/hypotheses-no-longer-cut-it-603d4e30a2d0 Hypotheses No Longer Cut It
- https://medium.com/@kording/would-recording-all-neurons-reveal-their-interactions-6288949ba4f5 Would recording all (cortical) neurons reveal their interactions?
- https://cryoetdataportal.czscience.com/competition Competition for Particle Detection in 3D Cryo-Electron Tomography
- https://etheses.whiterose.ac.uk/id/eprint/30377/1/Algul_203058528_Thesis.pdf Understanding RNA
- https://www.kaggle.com/competitions/stanford-ribonanza-rna-folding/discussion/460121 Stanford Ribonanza RNA Folding - [1st place solution] Transformer model with Dynamic positional encoding + CNN for BPPM features
- https://www.kaggle.com/competitions/stanford-ribonanza-rna-folding/discussion/460316 Stanford Ribonanza RNA Folding - 2nd place solution - Squeezeformer + BPP Conv2D Attention
- https://www.kaggle.com/competitions/stanford-ribonanza-rna-folding/discussion/460403 Stanford Ribonanza RNA Folding - [3rd Place Solution] AlphaFold Style Twin Tower Architecture + Squeezeformer
- https://chipsandcheese.com/p/examining-amds-rdna-4-changes-in-llvm Examining AMD’s RDNA 4 Changes in LLVM
- https://josephmate.github.io/2025-02-26-3200p-cpu-util/ 3,200% CPU Utilization
- https://gitingest.com Gitingest - Prompt-friendly codebase
- https://github.com/huggingface/picotron picotron
- https://jepsen.io/analyses/mysql-8.0.34 MySQL 8.0.34
- https://elifesciences.org/articles/105446 Chronic RNA G-quadruplex accumulation in aging and Alzheimer’s disease
- https://biorxiv.org/content/10.1101/2025.02.21.639601v1 A vectorial code for semantics in human hippocampus
- https://definite.app/blog/smallpond Understanding smallpond and 3FS: A Clear Guide
- https://kordinglab.com Kording Lab
- https://biorxiv.org/content/10.1101/2025.02.25.639942v2 EvoFlow-RNA: Generating and Representing non-coding RNA with a Language Model
- https://iliao2345.github.io/blog_posts/arc_agi_without_pretraining/arc_agi_without_pretraining.html ARC-AGI Without Pretraining
- https://arxiv.org/abs/2502.03387 LIMO: Less is More for Reasoning
- https://en.m.wikipedia.org/wiki/LignoSat LignoSat
- https://google-research.github.io/self-organising-systems/difflogic-ca/?hn Differentiable Logic Cellular Automata
- https://reducto.ai/blog/lvm-ocr-accuracy-mistral-gemini Mistral OCR vs. Gemini Flash 2.0: Comparing VLM OCR Accuracy
- https://nature.com/articles/s41586-025-08631-w Brain-wide presynaptic networks of functionally distinct cortical neurons
- https://americanaffairsjournal.org/2021/08/the-value-of-nothing-capital-versus-growth/ The Value of Nothing: Capital versus Growth
- https://en.m.wikipedia.org/wiki/Self-licking_ice_cream_cone Self-licking ice cream cone
- https://glthr.com/discovering-errors-in-donald-knuths-taocp Discovering Errors in Donald Knuth’s TAOCP
- https://jeremybernste.in/writing/deriving-muon Deriving Muon
- https://schaechter.asmblog.org/schaechter/2019/05/the-story-of-free-use-gfp-fugfp.html The Story of Free Use GFP (fuGFP)
- http://rnapdbee.cs.put.poznan.pl RNApdbee, a webserver to annotate secondary structures of knotted and unknotted RNAs.
- https://unafold.org/mfold/applications/rna-folding-form.php Mfold web server for nucleic acid folding and hybridization prediction.
- https://biorxiv.org/content/10.1101/2024.09.23.614603v1 Protein Language Models: Is Scaling Necessary?
- https://ashwanirathee.com/blog/2025/sort2/ Sorting Algorithms with CUDA!
- https://openreview.net/forum?id=g3VCIM94ke Multi-domain Distribution Learning for De Novo Drug Design
- https://deepmind.google/discover/blog/gemini-robotics-brings-ai-into-the-physical-world/ Gemini Robotics brings AI into the physical world
- https://nanochess.org/transputer_operating_system.html My teen years: The transputer operating system
- https://sugaku.net/content/understanding-the-cultural-divide-between-mathematics-and-ai/ The Cultural Divide between Mathematics and AI
- https://johndcook.com/blog/distribution_chart/ Diagram of distribution relationships
- https://link.springer.com/article/10.1007/s42087-025-00478-x Oscillations in Natural Neuronal Networks; An Epiphenomenon or a Fundamental Computational Mechanism?
- https://pubmed.ncbi.nlm.nih.gov/32839445/ Grid cells are modulated by local head direction
- https://unqualified-reservations.org/2008/04/open-letter-to-open-minded-progressives/ An Open Letter to Open-Minded Progressives
- https://unqualified-reservations.org/2009/01/gentle-introduction-to-unqualified/ A Gentle Introduction to Unqualified Reservations
- https://tinyhack.com/2025/03/13/decrypting-encrypted-files-from-akira-ransomware-linux-esxi-variant-2024-using-a-bunch-of-gpus/ Decrypting Encrypted files from Akira Ransomware (Linux/ESXI variant 2024) using a bunch of GPUs
- https://jiachenzhu.github.io/DyT/ Transformers without Normalization
- https://evolving-self-organisation-workshop.github.io Evolving Self-organisation
- https://dfarq.homeip.net/when-the-dotcom-bubble-burst/ When the dotcom bubble burst
- https://blog.kevinalbs.com/stupid_smart_pointers Stupid Smart Pointers in C
- https://github.com/formal-land/coq-of-rust?tab=readme-ov-file coq-of-rust
- https://nature.com/articles/s41593-025-01908-3 Constructing future behavior in the hippocampal formation through composition and replay
- https://go-compression.github.io The Hitchhiker’s Guide to Compression
- https://karpathy.bearblog.dev/i-love-calculator/ I love calculator
- https://ranprieur.com/tech.html TechJudge
- https://sohl-dickstein.github.io/2022/11/06/strong-Goodhart.html Too much efficiency makes everything worse: overfitting and the strong version of Goodhart's law
- https://chipsandcheese.com/p/looking-ahead-at-intels-xe3-gpu-architecture Looking Ahead at Intel’s Xe3 GPU Architecture
- https://ezyang.github.io/ai-blindspots/ AI Blindspots
- https://arxiv.org/abs/2503.13522 Advanced Deep Learning Methods for Protein Structure Prediction and Design
- https://vasekrozhon.wordpress.com/2025/03/17/zero-knowledge-proofs/ Zero-knowledge proofs
- https://press.asimov.com/articles/gene-circuit The Making of a Gene Circuit
- https://herman.bearblog.dev/manifesto/ The Bear Manifesto
- https://en.m.wikipedia.org/wiki/Parkinson's_law Parkinson's law
- https://github.com/wells-wood-research/chronowska-stam-wood-2024-protein-design-archive chronowska-stam-wood-2024-protein-design-archive
- https://pragmaticproteindesign.bio.ed.ac.uk/pda/ The Protein Design Archive
- https://llm.hunyuan.tencent.com/#/blog/hy-t1?lang=en Reasoning Efficiency Redefined! Meet Tencent’s 'Hunyuan-T1'—The First Mamba-Powered Ultra-Large Model
- https://blog.ezyang.com/2019/05/pytorch-internals/ PyTorch internals
- https://ethanzuckerman.com/2011/04/06/those-white-plastic-chairs-the-monobloc-and-the-context-free-object/ Those White Plastic Chairs – The Monobloc and the Context-Free Object
- https://www.rdkit.org/docs/RDKit_Book.html The RDKit Book
- https://eugeneyan.com/writing/recsys-llm/ Improving Recommendation Systems & Search in the Age of LLMs
- https://goyalpramod.github.io/blogs/Transformers_laid_out/#coding-the-transformer Transformers Laid Out
- https://en.m.wikipedia.org/wiki/Socratic_questioning Socratic questioning
- https://transformer-circuits.pub/2025/attribution-graphs/biology.html On the Biology of a Large Language Model
- https://seb-v.github.io/optimization/update/2025/01/20/Fast-GPU-Matrix-multiplication.html Deep Dive into Matrix Optimization on AMD GPUs
- https://www.anthropic.com/research/tracing-thoughts-language-model Tracing the thoughts of a large language model
- https://rfam.org/ The Rfam database is a collection of RNA families
- https://archive.ph/2025.03.27-055757/https://www.wired.com/story/openworm-worm-simulator-biology-code/ The Worm That No Computer Scientist Can Crack
- https://mitp-content-server.mit.edu/books/content/sectbyfn/books_pres_0/6515/sicp.zip/full-text/book/book-Z-H-4.html Structure and Interpretation of Computer Programs
- https://jenevoldsen.com/posts/excitable-cells/ Excitable cells
- https://www.rcsb.org/ RCSB Protein Data Bank (RCSB PDB)
- https://pmc.ncbi.nlm.nih.gov/articles/PMC1370104/pdf/11345429.pdf Geometric nomenclature and classification of RNA base pairs
- https://www.genome.gov/about-genomics/fact-sheets/Sequencing-Human-Genome-cost The Cost of Sequencing a Human Genome
- https://elanapearl.github.io/blog/2024/the-illustrated-alphafold/ The Illustrated AlphaFold
- https://github.com/leeyang/DRfold2 DRfold2: Ab initio RNA structure prediction with composite language model and denoised end-to-end learning
- https://michaelhla.com/blog/pro1.html Pro-1
- https://github.com/bytedance/Protenix Protenix: Protein + X
- https://www.sciencedirect.com/science/article/pii/S0959440X25000090 Deep learning for RNA structure prediction
- https://predictioncenter.org/casp16/index.cgi CASP16
- https://www.rnapuzzles.org/ RNA-Puzzles
- https://vfold.missouri.edu/research.html RNA 2D structure folding
- https://www.nature.com/articles/s41592-024-02543-9 RNA-Puzzles Round V: blind predictions of 23 RNA structures
- https://github.com/ml4bio/RhoFold RhoFold+: Accurate RNA 3D structure prediction using a language model-based deep learning approach
- https://github.com/jwohlwend/boltz Boltz-1: Democratizing Biomolecular Interaction Modeling
- https://github.com/chaidiscovery/chai-lab Chai-1
- https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html Introduction to Protein Data Bank Format
- https://www.nature.com/articles/d41586-025-00920-8 RNA function follows form – why is it so hard to predict?
- https://www.biorxiv.org/content/10.1101/2023.12.13.571579v1 ATOM-1: A Foundation Model for RNA Structure and Function Built on Chemical Mapping Data
- https://rnacentral.org/ RNAcentral: The non-coding RNA sequence database
- http://rna.tbi.univie.ac.at/forna/ RNA Secondary Structure Visualization Using a Force Directed Graph Layout