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Nature Computational Science
@natcomputsci.nature.com
A @natureportfolio.nature.com journal on mathematical models and computational methods/tools that help advance science in multiple disciplines. https://www.nature.com/natcomputsci
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🚨Our November issue is now live, and it includes a study on how LLMs align with the reading brain, a generative model for structure-based molecular design, and much more! Check it out! www.nature.com/natcomputsci...
🚨Our November issue is now live, and it includes a study on how LLMs align with the reading brain, a generative model for structure-based molecular design, and much more! Check it out! www.nature.com/natcomputsci...
November 21, 2025 at 3:27 PM
📢How should authors go about putting the point-by-point response to reviewers' document together, in order to make the process smoother and more efficient for authors, editors, and reviewers? Check out our latest Editorial! www.nature.com/articles/s43... #SciencePublishing #ResearchPublishing
How to respond to reviewers - Nature Computational Science
We provide recommendations on how to write an effective point-by-point response document.
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November 21, 2025 at 3:14 PM
📢Hao Sun and colleagues introduce Parallel Symbolic Enumeration (PSE) for discovering physical laws from limited data, outperforming state-of-the-art methods by evaluating millions of expressions in parallel and reusing computations. www.nature.com/articles/s43... ⚛️
Discovering physical laws with parallel symbolic enumeration - Nature Computational Science
In this work, the authors introduce parallel symbolic enumeration (PSE), a model that discovers physical laws from data with improved accuracy and speed. By evaluating millions of expressions in paral...
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November 21, 2025 at 2:57 PM
📢Research Highlights out today! We highlight work by @walter4c.bsky.social, @matteocinelli.bsky.social, and colleagues on how LLMs generate judgments about reliability and political bias, and how their procedures compare to human evaluation. www.nature.com/articles/s43... #cssky
How LLMs generate judgments - Nature Computational Science
Nature Computational Science - How LLMs generate judgments
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November 20, 2025 at 6:30 PM
📢Out now: Peng Zhang, Jian Ji and colleagues present PerioGT, a framework for polymer property prediction that enhances generalization under data scarcity. www.nature.com/articles/s43... #chemsky

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Periodicity-aware deep learning for polymers - Nature Computational Science
PerioGT is a self-supervised learning framework for polymer property prediction, integrating periodicity priors and additional conditions to enhance generalization under data scarcity and enable broad...
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November 20, 2025 at 3:58 PM
📢 @samnastase.bsky.social and colleagues show that aligning ECoG data into a shared space improves how well LLMs predict brain activity during language comprehension. www.nature.com/articles/s43... #compneuro #Neuroscience #ArtificialIntelligence

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Aligning brains into a shared space improves their alignment with large language models - Nature Computational Science
Aligning electrocorticography data into a shared space improves how large language models predict brain activity during language comprehension, enhancing encoding accuracy, cross-participant generaliz...
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November 18, 2025 at 3:29 PM
📢 @fionakolbinger.bsky.social and @jnkt.bsky.social characterize the discordance between metrics used to evaluate AI tools and their clinical impact, proposing a framework to reduce this disconnect. www.nature.com/articles/s43... @tudresden.bsky.social @ekfzdigital.bsky.social

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Adaptive validation strategies for real-world clinical artificial intelligence - Nature Computational Science
Technical metrics used to evaluate medical artificial intelligence tools often fail to predict their clinical impact. We characterize this discordance and propose a framework of study designs to guide...
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November 17, 2025 at 3:23 PM
📢Yi Yang and colleagues report two efficient methods to compute topological surface states in photonic and acoustic systems, cutting memory and time use by up to 100-fold. www.nature.com/articles/s43... ⚛️

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Efficient algorithms for the surface density of states in topological photonic and acoustic systems - Nature Computational Science
This study reports two efficient methods—cyclic reduction and transfer matrix—to compute topological surface states in photonic and acoustic systems, cutting memory and time use by up to 100-fold and ...
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November 14, 2025 at 4:54 PM
📢Chang-Yu Hsieh and colleagues introduce SynGFN, a molecular design tool that enables the assembly of molecules from synthesizable building blocks. www.nature.com/articles/s43... #chemsky

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SynGFN: learning across chemical space with generative flow-based molecular discovery - Nature Computational Science
A persistent gap from theoretical molecules to experimentally viable compounds has hindered the practical adoption of generative algorithms. This study proposes SynGFN as a bridge linking molecular de...
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November 13, 2025 at 4:20 PM
📢Yiqing Zhou, Eun-Ah Kim and colleagues report an ML decoder that efficiently corrects errors in quantum logical circuits with entangling gates, with the decoder achieving competitive accuracy while running much faster than conventional methods. www.nature.com/articles/s43... ⚛️
Learning to decode logical circuits - Nature Computational Science
This study reports a machine learning decoder that efficiently corrects errors in quantum logical circuits with entangling gates. The Multi-Core Circuit Decoder achieves competitive accuracy while run...
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November 5, 2025 at 4:43 PM
Sandro Lera and colleagues introduce a data-driven method for ranking law firms based on litigation outcomes, revealing that traditional reputation-based rankings do not reflect legal performance accurately. www.nature.com/articles/s43... #cssky #MLSky
Data-driven law firm rankings to reduce information asymmetry in legal disputes - Nature Computational Science
This study introduces a data-driven method for ranking law firms based on litigation outcomes, revealing that traditional reputation-based rankings do not reflect legal performance accurately.
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October 31, 2025 at 6:35 PM
Guang Chen and colleagues present a deep learning model that integrates unpaired spatial multi-omics data and enables unsupervised cross-modal prediction, aiding spatial domain identification and downstream biological analysis. www.nature.com/articles/s43... 🖥️ 🧬

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Integrative deep learning of spatial multi-omics with SWITCH - Nature Computational Science
In this study the authors present SWITCH, a deep learning model that integrates unpaired spatial multi-omics data and enables unsupervised cross-modal prediction, aiding spatial domain identification ...
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October 29, 2025 at 3:36 PM
📢Stefan Woerner and colleagues investigate using quantum computing to tackle multi-objective optimization, showing promising results on IBM Quantum computer when compared to classical methods. www.nature.com/articles/s43... ⚛️
Quantum approximate multi-objective optimization - Nature Computational Science
This study explores the use of quantum computing to address multi-objective optimization challenges. By using a low-depth quantum approximate optimization algorithm to approximate the optimal Pareto f...
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October 24, 2025 at 4:06 PM
📢 Yong Li and colleagues report a neural symbolic regression method that uncovers network dynamics from data, refining biological and ecological models and revealing new insights into disease transmission. www.nature.com/articles/s43... #complexity #NetSci

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Discover network dynamics with neural symbolic regression - Nature Computational Science
This study presents a neural symbolic regression approach that autonomously uncovers network dynamics from data. It was demonstrated to refine existing models of gene regulation and ecology, and ident...
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October 23, 2025 at 2:32 PM
📢 Philipp Grohs and colleagues present an approach that reduces the computational cost to model and compute crystalline materials, such as graphene or lithium hydride, by a factor of 50 compared with previous work. www.nature.com/articles/s43... ⚛️
Transferable neural wavefunctions for solids - Nature Computational Science
Investigating crystalline materials often requires calculations for many variations of a system, substantially increasing the computational burden. By training a transferable neural wavefunction acros...
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October 22, 2025 at 2:24 PM
Out now! Djordje Miladinovic, Patrick Schwab and colleagues present the Large Perturbation Model, a tool for predicting biological responses to chemical and genetic perturbations. www.nature.com/articles/s43... #chemsky
In silico biological discovery with large perturbation models - Nature Computational Science
A large perturbation model that integrates diverse laboratory experiments is presented to predict biological responses to chemical or genetic perturbations and support various biological discovery tas...
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October 15, 2025 at 4:03 PM
In a recent Article, Tingjun Hou and colleagues develop ECloudGen, a method for generating electron clouds from protein pockets and decoding them into molecules. www.nature.com/articles/s43... #chemsky

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ECloudGen: leveraging electron clouds as a latent variable to scale up structure-based molecular design - Nature Computational Science
This study presents ECloudGen, which uses latent diffusion to generate electron clouds from protein pockets and decodes them into molecules. The adopted two-stage training expands the chemical space a...
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October 15, 2025 at 3:55 PM
📢Out now! @jianxuchen.bsky.social and colleagues from @isas-leibniz.bsky.social present a flexible AI-based method for compressing microscopy images, achieving high compression while preserving details that are critical for downstream analysis. www.nature.com/articles/s43... #Bioimaging #microscopy
Implicit neural image field for biological microscopy image compression - Nature Computational Science
This study presents a flexible AI-based method for compressing microscopy images, achieving high compression while preserving details critical for analysis, with support for task-specific optimization and arbitrary-resolution decompression.
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October 10, 2025 at 7:23 PM
🚨To celebrate #WorldMentalHealthDay, our October issue includes a Focus that examines the advances in computational psychiatry and the challenges of developing computational models to address mental health disorders. #mentalhealthresearch #Psychiatry

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October 10, 2025 at 6:57 PM
Reposted by Nature Computational Science
Happy to share our latest in @natcomputsci.nature.com
led by (amazing) Ryan Krueger + colab w M. Brenner!

We introduce a framework to directly design intrinsically disordered proteins (IDPs) from physics-based simulations.
🧬 doi.org/10.1038/s435...
📰 www.mccormick.northwestern.edu/news/article...
October 10, 2025 at 6:16 PM
Reposted by Nature Computational Science
The @natureportfolio.nature.com Collection celebrating the award of the 2025 #chemnobel to Susumu Kitagawa, Richard Robson and Omar Yaghi for the development of metal–organic frameworks is now live! #chemsky 🧪
Nobel Prize in Chemistry 2025
The 2025 Nobel Prize in Chemistry has been awarded to Susumu Kitagawa, Richard Robson and Omar M. Yaghi “for the development of metal–organic frameworks.”
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October 8, 2025 at 4:11 PM
📢Ming Li, Lusheng Wang and colleagues present a search algorithm for proteoform identification that computes the largest-size error-correction alignments between a protein mass graph and a spectrum mass graph. www.nature.com/articles/s43... 🖥️ 🧬

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Proteoform search from protein database with top-down mass spectra - Nature Computational Science
An algorithm for proteoform identification with top-down mass spectra is proposed, and a pipeline is developed for generating simulated top-down spectra on the basis of input protein sequences with modifications.
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October 3, 2025 at 3:54 PM
Out now! Yu Li and colleagues develop CRISP, a foundation-model-based framework for predicting drug responses at single-cell resolution. www.nature.com/articles/s43...

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Predicting drug responses of unseen cell types through transfer learning with foundation models - Nature Computational Science
This work develops CRISP, a framework using foundation models to predict drug responses in previously unseen cell types at single-cell resolution, advancing drug repurposing and drug screening capabilities.
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October 3, 2025 at 3:40 PM
📢In a recent Comment, Evan Collins, Robert Langer and Daniel G. Anderson discuss strategies and ongoing challenges for assessing the suitability of self-driving labs for biochemical design problems. www.nature.com/articles/s43...

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Self-driving labs for biotechnology - Nature Computational Science
Self-driving laboratories that integrate robotic production with artificial intelligence have the potential to accelerate innovation in biotechnology. Because self-driving labs can be complex and not universally applicable, it is useful to consider their suitable use cases for successful integration into discovery workflows. Here, we review strategies for assessing the suitability of self-driving labs for biochemical design problems.
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October 1, 2025 at 1:49 PM