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
Pinned
🚨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
➡️ nature.com/collections/...
🧵(1/8)
➡️ nature.com/collections/...
🧵(1/8)
📢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...
www.nature.com
November 5, 2025 at 4:43 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... ⚛️
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.
www.nature.com
October 31, 2025 at 6:35 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
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... 🖥️ 🧬
🔓 rdcu.be/eNjse
🔓 rdcu.be/eNjse
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 ...
www.nature.com
October 29, 2025 at 3:36 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... 🖥️ 🧬
🔓 rdcu.be/eNjse
🔓 rdcu.be/eNjse
📢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...
www.nature.com
October 24, 2025 at 4:06 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... ⚛️
📢 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
🔓 rdcu.be/eMoSt
🔓 rdcu.be/eMoSt
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...
www.nature.com
October 23, 2025 at 2:32 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
🔓 rdcu.be/eMoSt
🔓 rdcu.be/eMoSt
📢 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...
www.nature.com
October 22, 2025 at 2:24 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... ⚛️
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...
www.nature.com
October 15, 2025 at 4:03 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 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
🔓 rdcu.be/eLa3Z
🔓 rdcu.be/eLa3Z
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...
www.nature.com
October 15, 2025 at 3:55 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
🔓 rdcu.be/eLa3Z
🔓 rdcu.be/eLa3Z
📢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.
www.nature.com
October 10, 2025 at 7:23 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
🚨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
➡️ nature.com/collections/...
🧵(1/8)
➡️ nature.com/collections/...
🧵(1/8)
October 10, 2025 at 6:57 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
➡️ nature.com/collections/...
🧵(1/8)
➡️ nature.com/collections/...
🧵(1/8)
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...
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
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...
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...
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.”
www.nature.com
October 8, 2025 at 4:11 PM
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 🧪
📢 @shrinivaslab.bsky.social and colleagues introduce a method for designing unstructured proteins with tunable properties. www.nature.com/articles/s43... 🖥️ 🧬
🔓 rdcu.be/eJSuV
🔓 rdcu.be/eJSuV
Generalized design of sequence–ensemble–function relationships for intrinsically disordered proteins - Nature Computational Science
The authors introduce a method that combines physics and machine learning to design dynamic unstructured proteins with tunable ensemble properties like size, shape, sensing and binding.
www.nature.com
October 7, 2025 at 3:03 PM
📢 @shrinivaslab.bsky.social and colleagues introduce a method for designing unstructured proteins with tunable properties. www.nature.com/articles/s43... 🖥️ 🧬
🔓 rdcu.be/eJSuV
🔓 rdcu.be/eJSuV
📢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... 🖥️ 🧬
🔓 rdcu.be/eJlA5
🔓 rdcu.be/eJlA5
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.
www.nature.com
October 3, 2025 at 3:54 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... 🖥️ 🧬
🔓 rdcu.be/eJlA5
🔓 rdcu.be/eJlA5
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...
🔓 rdcu.be/eJlt9
🔓 rdcu.be/eJlt9
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.
www.nature.com
October 3, 2025 at 3:40 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...
🔓 rdcu.be/eJlt9
🔓 rdcu.be/eJlt9
📢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...
🔓 rdcu.be/eI2KP
🔓 rdcu.be/eI2KP
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.
www.nature.com
October 1, 2025 at 1:49 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...
🔓 rdcu.be/eI2KP
🔓 rdcu.be/eI2KP
📢Guan Lin and colleagues present a model for integrating DNA sequence with chromatin accessibility data to predict the regulatory impact of non-coding single nucleotide polymorphisms on gene expression. www.nature.com/articles/s43... 🖥️ 🧬
🔓 rdcu.be/eImpy
🔓 rdcu.be/eImpy
Predicting the regulatory impacts of noncoding variants on gene expression through epigenomic integration across tissues and single-cell landscapes - Nature Computational Science
EMO integrates DNA sequence and chromatin accessibility data to predict how noncoding variants regulate gene expression across tissues and single cells, enabling context-aware personalized insights into genetic effects for precision medicine.
www.nature.com
September 26, 2025 at 3:51 PM
📢Guan Lin and colleagues present a model for integrating DNA sequence with chromatin accessibility data to predict the regulatory impact of non-coding single nucleotide polymorphisms on gene expression. www.nature.com/articles/s43... 🖥️ 🧬
🔓 rdcu.be/eImpy
🔓 rdcu.be/eImpy
📢Out now! Olesia Dogonasheva and colleagues from @neurospeech.bsky.social present a predictive model for speech processing in the auditory cortex. www.nature.com/articles/s43... #compneurosky
🔓 rdcu.be/eImit
🔓 rdcu.be/eImit
Rhythm-based hierarchical predictive computations support acoustic−semantic transformation in speech processing - Nature Computational Science
This study presents a brain rhythm-based inference model (BRyBI) for speech processing in the auditory cortex. BRyBI shows how rhythmic neural activity enables robust speech processing by dynamically predicting context and elucidates mechanistic principles that allow robust speech parsing in the brain.
www.nature.com
September 26, 2025 at 3:46 PM
📢Out now! Olesia Dogonasheva and colleagues from @neurospeech.bsky.social present a predictive model for speech processing in the auditory cortex. www.nature.com/articles/s43... #compneurosky
🔓 rdcu.be/eImit
🔓 rdcu.be/eImit
🚨Our September issue is now live, and it includes a Focus that examines the current state of the art and some of the potential pitfalls and biases of implementing and using LLMs across different domains. #ArtificialIntelligence
➡️ www.nature.com/collections/...
🧵(1/13)
➡️ www.nature.com/collections/...
🧵(1/13)
September 24, 2025 at 4:51 PM
🚨Our September issue is now live, and it includes a Focus that examines the current state of the art and some of the potential pitfalls and biases of implementing and using LLMs across different domains. #ArtificialIntelligence
➡️ www.nature.com/collections/...
🧵(1/13)
➡️ www.nature.com/collections/...
🧵(1/13)
📢In a recent Comment, @nathanleroux.bsky.social, Jan Finkbeiner, and Emre Neftci argue that neuromorphic engineering may hold the key to more efficient inference with transformer-like models. www.nature.com/articles/s43... #compneuro #ArtificialIntelligence
🔓https://rdcu.be/eGHnc
🔓https://rdcu.be/eGHnc
Neuromorphic principles in self-attention hardware for efficient transformers - Nature Computational Science
Strong barriers remain between neuromorphic engineering and machine learning, especially with regard to recent large language models (LLMs) and transformers. This Comment makes the case that neuromorp...
www.nature.com
September 16, 2025 at 1:53 PM
📢In a recent Comment, @nathanleroux.bsky.social, Jan Finkbeiner, and Emre Neftci argue that neuromorphic engineering may hold the key to more efficient inference with transformer-like models. www.nature.com/articles/s43... #compneuro #ArtificialIntelligence
🔓https://rdcu.be/eGHnc
🔓https://rdcu.be/eGHnc
📢A Perspective from Eva Portelance and Masoud Jasbi discusses the compatibility between generative artificial intelligence and generative linguistics. www.nature.com/articles/s43... #ArtificialIntelligence #linguistics
🔓https://rdcu.be/eGHhA
🔓https://rdcu.be/eGHhA
On the compatibility of generative AI and generative linguistics - Nature Computational Science
This Perspective discusses that generative AI aligns with generative linguistics by showing that neural language models (NLMs) are formal generative models. Furthermore, generative linguistics offers ...
www.nature.com
September 16, 2025 at 1:45 PM
📢A Perspective from Eva Portelance and Masoud Jasbi discusses the compatibility between generative artificial intelligence and generative linguistics. www.nature.com/articles/s43... #ArtificialIntelligence #linguistics
🔓https://rdcu.be/eGHhA
🔓https://rdcu.be/eGHhA
📢Out now! @jixingli.bsky.social, @lamb-cityuhk.bsky.social and colleagues assess whether instruction tuning can enhance LLM's ability to capture linguistic information in the human brain. www.nature.com/articles/s43... #compneuro #ArtificialIntelligence
Increasing alignment of large language models with language processing in the human brain - Nature Computational Science
Larger LLMs’ self-attention more accurately predicts readers’ regressive saccades and fMRI responses in language regions, whereas instruction tuning adds no benefit.
www.nature.com
September 16, 2025 at 1:35 PM
📢Out now! @jixingli.bsky.social, @lamb-cityuhk.bsky.social and colleagues assess whether instruction tuning can enhance LLM's ability to capture linguistic information in the human brain. www.nature.com/articles/s43... #compneuro #ArtificialIntelligence
📢A Perspective from Yong Li, Paolo Santi, Carlo Ratti, Qi R. Wang and colleagues argues that LLMs hold great potential in addressing some of the complexities of urban planning. www.nature.com/articles/s43... #cssky #geosky
🔓https://rdcu.be/eGG26
🔓https://rdcu.be/eGG26
Urban planning in the era of large language models - Nature Computational Science
Large language models remain largely unexplored is the design of cities. In this Perspective, the authors discuss the potential opportunities brought by these models in assisting urban planning.
www.nature.com
September 16, 2025 at 1:26 PM
📢A Perspective from Yong Li, Paolo Santi, Carlo Ratti, Qi R. Wang and colleagues argues that LLMs hold great potential in addressing some of the complexities of urban planning. www.nature.com/articles/s43... #cssky #geosky
🔓https://rdcu.be/eGG26
🔓https://rdcu.be/eGG26
📢Can Li and colleagues report a memristor-based system that analyzes raw analogue signals from genomic sequencer directly in memory. www.nature.com/articles/s43...
🔓https://rdcu.be/eGwVf
🔓https://rdcu.be/eGwVf
Real-time raw signal genomic analysis using fully integrated memristor hardware - Nature Computational Science
The authors report a memristor-based system that analyzes raw analog signals from a genomic sequencer directly in memory. By bypassing slow data conversion, the system achieves substantial improvement...
www.nature.com
September 15, 2025 at 10:01 PM
📢Can Li and colleagues report a memristor-based system that analyzes raw analogue signals from genomic sequencer directly in memory. www.nature.com/articles/s43...
🔓https://rdcu.be/eGwVf
🔓https://rdcu.be/eGwVf
📢A recent Resource proposes a SECRET-GWAS, a rapid, privacy-preserving, population-scale, collaborative GWAS tool. www.nature.com/articles/s43...
🔓https://rdcu.be/eGwUc
🔓https://rdcu.be/eGwUc
Confidential computing for population-scale genome-wide association studies with SECRET-GWAS - Nature Computational Science
Secure collaborative genome-wide association studies (GWAS) with population-scale datasets address gaps in genomic data. This work proposes SECRET-GWAS and system optimizations that overcome resource ...
www.nature.com
September 15, 2025 at 9:57 PM
📢A recent Resource proposes a SECRET-GWAS, a rapid, privacy-preserving, population-scale, collaborative GWAS tool. www.nature.com/articles/s43...
🔓https://rdcu.be/eGwUc
🔓https://rdcu.be/eGwUc