The Illustrated AlphaFold
"The Illustrated AlphaFold provides a detailed visual walkthrough of the AlphaFold3 architecture, designed for an ML audience to explain how the model predicts complex protein structures from sequences. The text covers architectural specifics, including new tokenization methods for diverse input types, the use of attention mechanisms, and conditional diffusion for structure prediction. It also highlights the model\'s design components like pair-bias attention, iterative weight recycling, and self-supervised learning nuances."
Optimizing the Lichess Tablebase Server
Lichess\' Syzygy tablebase server was underperforming during RAID integrity checks, prompting a switch to using dm-integrity on LVM, allowing passive block checks and requiring the setup of a second server for migration and benchmarking. Various hardware and software optimizations were implemented to reduce high tail latencies, including switching from mmap to pread for better error handling and performance, analyzing memory access patterns, and optimizing storage usage on limited SSD space. These adjustments led to improved performance, particularly in parallelizing requests and reducing response times in production scenarios.
Disruptor-rs: better latency and throughput than crossbeam
The GitHub repository "disruptor-rs" by nicholassm is a low latency inter-thread communication library in Rust, inspired by the LMAX Disruptor. It supports single and multiple producers and consumers, busy-spin wait strategies, batch publication/consumption of events, and thread affinity settings. The library emphasizes low latency and high throughput, showing significant performance improvements over Crossbeam in benchmark tests.
Summing ASCII encoded integers on Haswell at almost the speed of memcpy
Matt Stuchlik describes a highly optimized method for summing 50 million ASCII-encoded integers, achieving speeds close to the memcpy function. By leveraging SIMD instructions and examining input data in 32-byte chunks instead of parsing each number individually, the solution tracks sums of digits in decimal places, using lookup tables to map bytes efficiently. Although the program is highly specialized and fragile, it operates significantly faster (320x) than a naive C++ implementation on the specified hardware.
STEMFIE, a 3D-printable construction set toy
STEMFIE is a free, open-source, 3D-printable construction set toy designed for educational purposes, which you can download and make at home using a 3D printer. It aims to help children learn STEM concepts through fun and interactive building, and all designs are made with FreeCAD and are upscalable. The toy is not suitable for children under three due to choking hazards, and the project encourages community support to continue expanding.
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