Bristol
Joined February 2011
1/ You launched a long-running program... And forgot to use screen or tmux. Now you're terrified to close your terminal. I’ve been there. Here’s how to rescue it like a pro.
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Sam Neaves retweeted
Parkinson's disease is the second most common neurodegenerative disease. A recent study investigated whether the GLP-1 receptor agonist, exenatide, could slow the rate of progression of Parkinson's disease: hubs.li/Q037XdV-0
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Sam Neaves retweeted
A Review published in Translational Neurodegeneration explores the connection between Parkinson’s disease and abnormal glucose metabolism, focusing on the underlying pathophysiological mechanisms. translationalneurodegenerati…
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Sam Neaves retweeted
🦋 for Science Starter packs for genomics, bioinformatics, #Rstats, Nextflow. Moderation lists. Feeds. Let's rebuild the old scitwitter community and keep this place nice. blog.stephenturner.us/p/blue… 🧬🖥️🧪
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In one of our first "A path towards AGI" posts we discussed Neuro-symbolic systems. Here's a new example of their implementation👇 Neuro-Symbolic Predicates (NSPs) are smart rules that help robots think by combining visual perception (neural) with logical rules (symbolic). With NSPs robots can easier plan and tackle complex tasks. NSPs use programming basics (conditions, loops) and can connect with VLMs that understand images and text. Here are the details about: - 2 types of NSPs - selecting NSPs - task planning with learning High-Level Actions (HLAs) 🧵
A path towards AGI: Neuro-symbolic systems Sometimes when you can't find the solution it's useful to look back and reflect on past approaches. Since 2015, various neuro-symbolic systems have emerged, including: - IBM's researches - MIT's Neuro-Symbolic Concept Learner (NS-CL) - Logic Tensor Networks (LTN) - Graph Neural Networks - Neural-symbolic visual question answering (NS-VQA) - Neuro-symbolic programming (NSP) and more. DeepMind was also working a lot with similar approaches and developed deep reinforcement learning in 2016, combining reinforcement learning with neural networks. And now, in 2024, we got significant achievement of AlphaProf and AlphaGeometry in the International Math Olympiad. AlphaGeometry notably solved 25/30 geometry problems within competition time limits. And what is also notable - it's a neuro-symbolic system. So how does neuro-symbolic system work? Neuro-symbolic AI systems are hybrid AI architectures that combine neural networks (neuro) with symbolic reasoning methods (symbolic). Neural Networks: - Excel at identifying patterns and relationships in large amount of data - Are strong in perception tasks like image and speech recognition, NLP and others - Are effective for generating predictions and “intuitive” ideas But they are bad at reasoning and explaining their decisions Symbolic Reasoning: - Emphasizes logic, rules, and structured knowledge - For reasoning tasks, it uses human-readable symbols to represent objects, concepts, and relationships in the world - Provide clear and interpretable explanations for their decisions However, they are slow and inflexible and can’t deal well with large amount of data. Advantages of neuro-symbolic hybrid AI: ▪️ Robustness: Combines neural learning with logical reasoning. ▪️ Versatility: Handles a wide range of tasks. ▪️ Interpretability: Enhances trust in model decisions. ▪️ Generalization: Integrates data-driven learning with rule-based reasoning Can this hybrid approach lead to AGI? While it's uncertain, neuro-symbolic systems deserve more exploration as they mimic the human use of both logic and intuition in decision-making. Here's a scheme of neuro-symbolic AI methods from "Neurosymbolic AI - Why, What, and How" paper:
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Sam Neaves retweeted
At the @nextflowio summit @EvanFloden & @SashaDagayev demonstrating @SeqeraLabs AI (seqera.io/ask-ai) for writing Nextflow code that generates DSL2 Nextflow code that actually runs, with a button to run in a sandbox with nf-core test data! Live: youtube.com/watch?v=LkQj1fMZ…
Replying to @SeqeraLabs
GPT-4o and Copilot both _really_ want to write NF code with DSL1, regardless of how aggressively my prompts are.
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scplotter provides a set of functions to visualize single-cell sequencing data in an easy and efficient way. github.com/pwwang/scplotter/…
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🗨️ WANNA TALK TO YOUR CELLS? Try out CellWhisperer – our new multimodal AI that turns single-cell RNA-seq analysis into a conversation. No coding needed, just chat in plain English. Short walkthrough below. Web app & bioRxiv preprint linked in the thread. Let's dive in! (1/9)
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Out now in @AnnualReviews! We share our perspective on using human genetics for drug target identification, with examples from our work of the past 10 years, and our framework for building therapeutic hypotheses #OpenTargetsat10 annualreviews.org/content/jo…
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Data keeps emerging that suggests GLP-1RAs like #Ozempic curb all sorts of appetites... not just appetite for food. Brief thread on some new findings...
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Excited to share our latest paper, where we describe ITSN1 as a novel risk gene for Parkinson's disease! We found that rare loss-of-function variants are associated with a 10-fold increased odds of PD. As far as we know, this is the largest effect size reported for sporadic PD to date medrxiv.org/content/10.1101/…
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GO annotations are associations between gene products and GO terms. These come with evidence codes indicating the basis for the association, such as experimental evidence, computational prediction, or expert curation of scientific literature.
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Datalog/Database/SQL friends, is this like the writer monad for Datalog? cs.jhu.edu/~jason/papers/eis…
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A week ago, I posted that I was cooking a logical reasoning benchmark as a side project. Now it's finally ready! Introducing 🦓 𝙕𝙚𝙗𝙧𝙖𝙇𝙤𝙜𝙞𝙘, designed for evaluating LLMs with Logic Puzzles. ⬇️ Quick summary: - Each example is a Zebra Puzzle (a type of Logic Grid Puzzles), which requires multiple high-order thinking skills (see an example next). - Claude Sonnet 3.5 (@AnthropicAI) is the best, while it can only solve 12% of the Hard puzzles. - 🐳 DeepSeek V2 - 0628 (@deepseek_ai) is the best Open-weight LLM, much better than Llama-3-72b. - GPT-4o-mini (@OpenAI) is particularly strong! - Gemini 1.5 Pro (@GoogleDeepMind) doesn't show expected results. - Smaller LMs under 10B struggle to solve these puzzles; most of them cannot even solve 1% of hard puzzles. More details are in the blog and the below thread: ⬇️ 📰 Blog: hf.co/blog/yuchenlin/zebra-l… 🤗 Leaderboard: hf.co/spaces/allenai/ZebraLo… 🦓 Data: hf.co/datasets/allenai/Zebra… 💻 Code (eval): github.com/yuchenlin/ZeroEva… [1/n]
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