DR-BERT: A protein language model to annotate disordered regions
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Structured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB). GARNET links RNA sequences to experimental and predicted optimal growth temperatures of GTDB reference organisms. Using GARNET, we develop sequence- and structure-aware RNA generative models, with overlapping triplet tokenization providing optimal encoding for a GPT-like model. Leveraging hyperthermophilic RNAs in GARNET and these RNA generative models, we identify mutations in ribosomal RNA that confer increased thermostability to the Escherichia coli ribosome. The GTDB-derived data and deep learning models presented here provide a foundation for understanding the connections between RNA sequence, structure, and function.
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The capabilities of modern artificial intelligence (AI) as a “scientific collaborator” are explored by engaging it with three nuanced problems in quantum optics: state populations in optical pumping, resonant transitions between decaying states (the Burshtein effect), and degenerate mirrorless lasing. Through iterative dialogue, the authors observe that AI models–when prompted and corrected–can reason through complex scenarios, refine their answers, and provide expert-level guidance, closely resembling the interaction with an adept colleague. The findings highlight that AI can democratize access to sophisticated modeling and analysis, shifting the focus in scientific practice from technical mastery to the generation and testing of ideas, and reducing the time for completing research tasks from days to minutes.
ProtAgents is a de novo protein design platform based on multimodal LLMs, where distinct AI agents with expertise in knowledge retrieval, protein structure analysis, physics-based simulations, and results analysis tackle tasks in a dynamic setting.
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Production LLM serving must simultaneously deliver high throughput, low latency, and sufficient context capacity under non-stationary traffic and mixed request requirements. Data parallelism (DP) maximizes throughput by running independent replicas, while tensor parallelism (TP) reduces per-request latency and pools memory for long-context inference. However, existing serving stacks typically commit to a static parallelism configuration at deployment; adapting to bursts, priorities, or long-context requests is often disruptive and slow. We present Flying Serving, a vLLM-based system that enables online DP-TP switching without restarting engine workers. Flying Serving makes reconfiguration practical by virtualizing the state that would otherwise force data movement: (i) a zero-copy Model Weights Manager that exposes TP shard views on demand, (ii) a KV Cache Adaptor that preserves request KV state across DP/TP layouts, (iii) an eagerly initialized Communicator Pool to amortize collective setup, and (iv) a deadlock-free scheduler that coordinates safe transitions under execution skew. Across three popular LLMs and realistic serving scenarios, Flying Serving improves performance by up to 4.79 × under high load and 3.47 × under low load while supporting latency- and memory-driven requests.
Generative AI models garnered a large amount of public attention and speculation with the release of OpenAI’s chatbot, ChatGPT in November of 2022. At least two opinion camps exist – one that is excited about the possibilities these models offer for fundamental changes to human tasks, and another that is highly concerned about the power these models seem to have – especially since the release of GPT-4, which was trained on multimodal data and has ~1.7 trillion (T) parameters. We evaluated some concerns regarding these models’ power by assessing GPT-3.5 using standard, normed, and validated cognitive and personality measures. These measures come from the tradition of psychometrics in experimental psychology and have a long history of providing valuable insights and predictive distinctions in humans. For this seedling project, we developed a battery of tests that allowed us to estimate the boundaries of some of these models’ capabilities, how stable those capabilities are over a short period of time, and how they compare to humans.
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