1. AlphaFold 3 predicts the structure and interactions of life’s molecules
Total comment counts : 37
Summary
Google DeepMind and Isomorphic Labs have developed a new AI model called AlphaFold 3 that accurately predicts the structure and interactions of proteins, DNA, RNA, ligands, and other biomolecules. This model aims to revolutionize our understanding of the biological world and drug discovery. AlphaFold 3 improves upon existing prediction methods, showing at least a 50% improvement in protein interaction predictions and a doubling of accuracy in certain categories. The AlphaFold Server allows scientists to access the model’s capabilities for free, and Isomorphic Labs is collaborating with pharmaceutical companies to apply AlphaFold 3 to real-world drug design challenges. AlphaFold 3 builds upon the success of its predecessor, AlphaFold 2, which made breakthroughs in protein structure prediction and has been widely used by researchers. The new model is capable of predicting the structures and interactions of a broader range of biomolecules, potentially leading to advancements in areas like materials development, crop resilience, and genomics research. AlphaFold 3’s predictions surpass the accuracy of existing systems, making it uniquely able to provide comprehensive insights into molecular complexes. It excels in predicting drug-like interactions and binding between proteins, ligands, and antibodies. AlphaFold 3 is the first AI system to outperform physics-based tools for biomolecular structure prediction. Isomorphic Labs is leveraging AlphaFold 3, along with other AI models, to accelerate and improve drug design processes.
Top 1 Comment Summary
The article discusses how a machine learning method is outperforming physically-based methods in accurately predicting the world. It raises questions about what happens when the best methods for scientific processes like computational fluid dynamics, molecular dynamics, and nuclear physics are all uninterpretable machine learning models. This raises concerns about whether this decouples progress from our current understanding of the scientific process and if it is sustainable in the long run.
Top 2 Comment Summary
The article discusses the release of a new model called RosettaFold All Atom by David Baker’s lab, which predicts protein structure along with bound DNA and ligands. This model is open source and can predict a wider range of small molecules compared to AlphaFold 3. The article also mentions that it was David Baker who came up with the idea of extending AlphaFold to predict ligands. One interesting aspect of the RosettaFold model is that it can be used as a denoising model in a diffusion process to design new functional proteins.
2. U.S. Rules Apple Illegally Interrogated Staff and Confiscated Union Flyers
Total comment counts : 16
Summary
The National Labor Relations Board has ruled that Apple illegally questioned employees at its World Trade Center store in New York City regarding their pro-union sympathies. The board upheld a previous ruling that Apple had prohibited workers from placing union flyers in the break room and interrogated them about union matters. Apple has not been punished or ordered to pay damages. This is the first decision against Apple by the board. Other cases against Apple regarding labor violations are still pending. Apple employees in various locations have been attempting to unionize in recent years.
Top 1 Comment Summary
The author questions why US companies continue to resist unionization, despite data showing minimal negative effects on productivity or business survival. They believe this resistance stems from dogmatic ego trips and a demand for blind loyalty, even when it is unnecessary.
Top 2 Comment Summary
The article highlights that the board investigating Apple’s violations cannot impose fines or direct punishments. This raises the question of why they invested two years in the investigation.
3. Decker: A reincarnation of HyperCard with 1-bit graphics
Total comment counts : 17
Summary
Decker is a multimedia platform for creating and sharing interactive documents. It is inspired by HyperCard and the visual aesthetic of classic MacOS. It offers simplicity and ease of learning, as well as quality-of-life improvements like undo history, support for touchscreens, and bulk editing operations. Decker can be used to create E-Zines, organize notes, give presentations, build games, or create pixel art. Finished decks can be saved as standalone .html documents that can be shared anywhere. Decker runs natively on MacOS, Windows, and Linux. It features a scripting language called Lil, which is influenced by Lua and Q. Lil is easy to learn and includes features like implicit scalar-vector arithmetic and an integrated SQL-like query language. Decker provides built-in interactive widgets and allows users to define custom ones. Decks can be stored in a line-oriented text format that is compatible with source control tools like Git. Decker is free and open-source under the MIT license. It has a community forum on Itch.io for discussing and sharing projects.
Top 1 Comment Summary
The author is interested in Decker, a software mentioned in a previous discussion about HyperCard replacements. They are particularly curious about how Decker packages its decks. They mention that they like Redbean’s method of packaging everything into one file with Lua and SQLite, which can be easily deployed by compressing it with a zip tool and renaming the file. The author is wondering if Decker is considering a similar deployment method to make it more convenient.
Top 2 Comment Summary
The article suggests that, while the current aesthetic of 1-bit graphics is appealing, using 2-bit graphics could result in more legible photographs. The writer shares a website they love that follows a similar aesthetic, where each image has at most six colors. The website can be found at https://solar.lowtechmagazine.com/.
4. ‘Underwater bicycle’ propels swimmers forward at superhuman speed
Total comment counts : 41
Summary
The article describes a new underwater mobility device called the Seabike. The device consists of a pole that is attached to the waist with a belt, allowing the user to pedal a 15-inch propeller and glide through the water. The Seabike can be used for swimming, gliding, or fully submerging underwater. It is also compatible with a SCUBA setup. The propellers can be flipped and the device can be used with arms instead of legs. The Seabike is buoyant and can be easily charged by eating a hot dog. The device is available for purchase starting at EU€290 (US$310) and is considered a simple and fun gadget.
Top 1 Comment Summary
The article is about a company called Seabike, which is a French company with a showroom in Cannes but is headquartered in Italy. The article points out that the French version of their website has many errors, which raises doubts about the credibility of the company.
Top 2 Comment Summary
The article discusses two obscure contraptions from the past. The first contraption, which was trialled by the seals and CIA in the 1950s, is not well-known. The second contraption is a pedal-powered smuggling submarine from the 1940s.
5. XLSTM: Extended Long Short-Term Memory
Total comment counts : 10
Summary
The article introduces arXivLabs, a framework that enables collaborators to create and share new features on the arXiv website. Individuals and organizations who work with arXivLabs must uphold values such as openness, community, excellence, and user data privacy. arXiv is devoted to these principles and only collaborates with partners who share them. The article concludes by mentioning that users can receive notifications about the operational status of arXiv via email or slack.
Top 1 Comment Summary
The article discusses Sepp Hochreiter’s model, which has been discussed since October 2023. The author questions the validity of comparing the number of parameters between Llama, Mamba, RWKV, and xLSTM, and suggests that compute time is a more relevant metric. The author also notes that the sLSTM still has recurrence, which limits parallelization, and suggests that scaling up the Transformer model may appear more efficient when considering compute time. The article mentions that neither the code nor the model parameters have been released, and questions if they will be made available in the future.
Top 2 Comment Summary
This article mentions that Sepp Hochreiter, the senior author of a paper, was the first author of the original paper that introduced Long Short-Term Memory (LSTM) in 1997, along with Schmidhuber.
6. Arena-based parsers
Total comment counts : 10
Summary
The article discusses parsers, memory allocations, and arenas. The author provides a code that is available in the arena-fixes branch and recommends enabling the –features=development if running it from a Git repo. However, they mention that they are not planning to release it. Instead, they suggest trying the prism Ruby parser, which has Rust bindings available on crates.io. Overall, the article is an experiment to determine the value of this kind of work.
Top 1 Comment Summary
The author discusses their love for parsing and their preference for hand-rolling custom parsers. Their main motivation is speed, and they have crafted custom JSON and SQL parsers. They explain their general approach, which involves using a tokenizer to generate tokens represented by integers. They discuss the benefits of this approach, such as eliminating bottlenecks in data processing and the ability to store tokens in an array for multiple passes. They also mention using a writeable arena for future steps like reordering and transforming the Abstract Syntax Tree (AST). Overall, the author is interested in knowing how mainstream this approach is.
Top 2 Comment Summary
The article discusses the use of an arena allocator called “hammer” in the C combinator parser. The article mentions that hammer has bindings for multiple languages, including Python and Java. It also talks about the performance of hammer’s arena allocator compared to other allocators. The author mentions a prototype arena allocator they wrote, which performs better than glibc’s malloc. The article also references another article by Chris Wellons about his approach to arena allocation in C. Finally, the article mentions the use of garbage collectors in languages like JavaScript, C#, OCaml, and Java, which often use an arena allocator for new allocations. The article concludes by mentioning the availability of arena allocators in libraries like the Apache Portable Runtime (APR) and the GCC obstacks.
7. Needle: A DFA Based Regex Library That Compiles to JVM ByteCode
Total comment counts : 6
Summary
The article discusses the release of a new library called “needle” that compiles regular expressions to JVM bytecode. The library converts each regular expression into a Deterministic Finite Automaton (DFA) and then compiles it into a Java class. The DFA is analyzed to improve matching efficiency by identifying required prefixes, suffixes, and infixes that can be found using String.indexOf. The library also optimizes the matching process by determining the minimum and maximum length of a match and aborting early if a match is not possible. The author compares the performance of the needle library with the Java standard library and another library called brics automaton. The results show that needle performs better in most cases, except when there are no substrings to search for, in which case brics automaton is faster. The author plans to further optimize the needle library to match or exceed the performance of brics automaton and welcomes suggestions for improvement.
Top 1 Comment Summary
The article mentions a project that compiles regular expressions into bytecode. There are benchmarks that show impressive performance. The project can be found on GitHub at [1] and more information about its performance can be found at [2].
Top 2 Comment Summary
The article mentions a related project called “one-more-re-nightmare” and provides a link to its Github page. It also references a blog post about the project, giving a link to the post as well.
8. Ointers: A library for representing pointers where bits have been stolen (2021)
Total comment counts : 11
Summary
The article discusses a library called “Ointers” that allows programmers to represent pointers with stolen high bits. The library provides a small amount of free storage by stealing bits from the pointer’s alignment. It also takes advantage of the organization of virtual memory space in operating systems to steal an extra bit. The number of bits that can be safely stolen depends on the microarchitecture and page table depth. The article mentions the test suite for the library and notes that contributions are welcome. The article concludes with copyright and licensing information.
Top 1 Comment Summary
The article discusses different strategies for increasing memory efficiency in programming. Instead of reducing the size of pointers by stealing bits, the article suggests using indices or relative pointers. For example, in a linked list, instead of storing 64-bit prev and next pointers, storing two 16-bit offsets can be more memory efficient. Additionally, the article mentions that encoding values in the base address of pointers using virtual memory allocation can provide further memory optimization, such as conveying information about alignment and thread sharing without modifying the pointer itself.
Top 2 Comment Summary
This article explains that the “ointer” is a type of pointer that is specifically designed for PowerPC and SPARC processors. However, it is also applicable and compatible with other types of processors.
9. Common Google XSS
Total comment counts : 5
Summary
The article discusses a vulnerability called SSRF in the Google website https://toolbox.googleapps.com. The author explains how they discovered and exploited the vulnerability, allowing them to execute JavaScript code on the site. They reported the issue to Google and received a reward for their findings. The article also briefly mentions other topics such as hidden browsers and building an online converter using WebAssembly.
Top 1 Comment Summary
The article provides a comprehensive guide on conducting research and finding the target website *.googleapps.com. It highlights the importance of thorough initial research and covers all the necessary steps involved in the process.
Top 2 Comment Summary
The person hopes to receive a Google bug bounty in the future.
10. Why use ECC? (2015)
Total comment counts : 25
Summary
The article discusses Jeff Atwood’s argument against using ECC memory. Atwood points out that Google’s experiment with non-ECC machines was deemed unsuccessful and resulted in various issues such as fires, regrowth problems, and messy cabling. He emphasizes that copying Google’s failed experiments is not a good strategy. Atwood also highlights the importance of error correction in preventing memory corruption and total data corruption. The article concludes by cautioning against blindly imitating everything Google does, despite their reputable infrastructure.
Top 1 Comment Summary
The author, a developer working on GPU drivers, expresses frustration with reported issues that cannot be explained or reproduced. They believe that there is an antagonistic relationship between performance and reliability, and that the enthusiast forums tend to prioritize performance over reliability. While the author acknowledges that some issues may be due to hardware or game code, they feel that even straightforward code paths can lead to “impossible” states. The author wishes there were more gamers using error-correcting code (ECC) memory to determine if it makes a difference in resolving these issues.
Top 2 Comment Summary
This article claims that not having Error Correcting Code (ECC) in computing is a big scam. It mentions “bitrot” as memory errors saved to disk, resulting in data loss for millions of people and artificially inflating server prices. Intel is held responsible for this, and the author expresses satisfaction with seeing them lose the market lead.