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Nature Machine Intelligence, Volume 6
Volume 6, Number 1, 2024
- Is it five already? 1
- Andreas Kleppe
, Ole-Johan Skrede
Guidelines for study protocols describing predefined validations of prediction models in medical deep learning and beyond. 2-3 - Étienne Ollion
The dangers of using proprietary LLMs for research. 4-5 - Noelia Ferruz, Marinka Zitnik, Pierre-Yves Oudeyer, Emmie Hine
Anniversary AI reflections. 6-12 - Séverine Atis, Lionel Agostini
Catching up with missing particles. 13-14 - Milena Pavlovic
Improving generalization of machine learning-identified biomarkers using causal modelling with examples from immune receptor diagnostics. 15-24 - Yutong Sha
Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. 25-39 - Simone Ciceri, Lorenzo Cassani, Matteo Osella
Inversion dynamics of class manifolds in deep learning reveals tradeoffs underlying generalization. 40-47 - Yaning Han
Multi-animal 3D social pose estimation, identification and behaviour embedding with a few-shot learning framework. 48-61 - Wei Feng, Lvwei Wang, Zaiyun Lin, Yanhao Zhu, Han Wang
Generation of 3D molecules in pockets via a language model. 62-73 - Aubin Ramon
Assessing antibody and nanobody nativeness for hit selection and humanization with AbNatiV. 74-91 - Sarmad Ahmad Abbasi
Autonomous 3D positional control of a magnetic microrobot using reinforcement learning. 92-105 - Arvin Tashakori
Capturing complex hand movements and object interactions using machine learning-powered stretchable smart textile gloves. 106-118 - Yutong Sha
Publisher Correction: Reconstructing growth and dynamic trajectories from single-cell transcriptomics data. 119
Volume 6, Number 2, 2024
- AI protein shake-up. 121
- Katja Seeliger, Martin N. Hebart
What comparing deep neural networks can teach us about human vision. 122-123 - Stephan Allenspach
Neural multi-task learning in drug design. 124-137 - Suyue Lyu
Variational autoencoder for design of synthetic viral vector serotypes. 147-160 - Kevin Maik Jablonka, Philippe Schwaller
Leveraging large language models for predictive chemistry. 161-169 - Carlos Outeiral
Codon language embeddings provide strong signals for use in protein engineering. 170-179 - Jens Oppliger
Weak signal extraction enabled by deep neural network denoising of diffraction data. 180-186 - Benjamin Q. Huynh
Mitigating allocative tradeoffs and harms in an environmental justice data tool. 187-194 - Zhuoran Qiao
State-specific protein-ligand complex structure prediction with a multiscale deep generative model. 195-208 - Maxat Kulmanov
Protein function prediction as approximate semantic entailment. 220-228 - Harry Coppock, George Nicholson, Ivan Kiskin, Vasiliki Koutra, Kieran Baker
Audio-based AI classifiers show no evidence of improved COVID-19 screening over simple symptoms checkers. 229-242 - Kenny Schlegel
Lessons from a challenge on forecasting epileptic seizures from non-cerebral signals. 243-244
Volume 6, Number 3, 2024
- The new NeuroAI. 245
- Eva Erman
The democratization of global AI governance and the role of tech companies. 246-248 - Glen M. Hocky
Connecting molecular properties with plain language. 249-250 - Andrea Soltoggio
A collective AI via lifelong learning and sharing at the edge. 251-264 - A. Emin Orhan
Learning high-level visual representations from a child's perspective without strong inductive biases. 271-283 - Yuhe Zhang
Reusability report: Unpaired deep-learning approaches for holographic image reconstruction. 284-290 - Rodrigo Bonazzola
Unsupervised ensemble-based phenotyping enhances discoverability of genes related to left-ventricular morphology. 291-306 - Yingying Cao, Tian-Gen Chang
Reusability report: Leveraging supervised learning to uncover phenotype-relevant biology from single-cell RNA sequencing data. 307-314 - Tian Lan, Shuquan Su
Generating mutants of monotone affinity towards stronger protein complexes through adversarial learning. 315-325 - Yuanyuan Jiang, Guo Zhang, Jing You, Hailin Zhang
PocketFlow is a data-and-knowledge-driven structure-based molecular generative model. 326-337 - Kyle Swanson
Generative AI for designing and validating easily synthesizable and structurally novel antibiotics. 338-353 - Jacopo Tagliabue
Author Correction: A challenge for rounded evaluation of recommender systems. 368
Volume 6, Number 4, 2024
- The rewards of reusable machine learning code. 369
- Marieke Ar Bak
Federated learning is not a cure-all for data ethics. 370-372 - Michael Roberts
The curious case of the test set AUROC. 373-376 - Mike H. M. Teodorescu
Dangers of speech technology for workplace diversity. 377-380 - Justin N. Wood
Artificial intelligence tackles the nature-nurture debate. 381-382 - Hannah Rose Kirk
The benefits, risks and bounds of personalizing the alignment of large language models to individuals. 383-392 - Tianyi Li, Luca Biferale
Synthetic Lagrangian turbulence by generative diffusion models. 393-403 - Adamo Young, Hannes L. Röst
Tandem mass spectrum prediction for small molecules using graph transformers. 404-416 - Ilia Igashov
Equivariant 3D-conditional diffusion model for molecular linker design. 417-427 - Taoyong Cui
Geometry-enhanced pretraining on interatomic potentials. 428-436 - Michael A. Skinnider
Invalid SMILES are beneficial rather than detrimental to chemical language models. 437-448 - Yanyi Chu, Dan Yu, Yupeng Li, Kaixuan Huang, Yue Shen, Le Cong
A 5′ UTR language model for decoding untranslated regions of mRNA and function predictions. 449-460 - Tao Xu
Reusability report: Uncovering associations in biomedical bipartite networks via a bilinear attention network with domain adaptation. 461-466 - Xupeng Chen, Ran Wang, Amirhossein Khalilian-Gourtani
A neural speech decoding framework leveraging deep learning and speech synthesis. 467-480 - Johannes Kühn, Tingli Hu, Alexander Toedtheide, Edmundo Pozo Fortunic
The synergy complement control approach for seamless limb-driven prostheses. 481-492 - Dylan S. Shah
Author Correction: A soft robot that adapts to environments through shape change. 493 - Michael Roberts
Publisher Correction: The curious case of the test set AUROC. 494
Volume 6, Number 5, 2024
- Empathic AI can't get under the skin. 495
- Garriy Shteynberg
Does it matter if empathic AI has no empathy? 496-497 - Diego Marcondes
Back to basics to open the black box. 498-501 - Ge Wang
Diving into deep learning. 502-503 - Thomas A. Berrueta
Maximum diffusion reinforcement learning. 504-514 - Florian Fürrutter
Quantum circuit synthesis with diffusion models. 515-524 - Andres M. Bran, Sam Cox, Oliver Schilter
Augmenting large language models with chemistry tools. 525-535 - Milong Ren, Chungong Yu, Dongbo Bu
Accurate and robust protein sequence design with CarbonDesign. 536-547 - Ning Wang
Multi-purpose RNA language modelling with motif-aware pretraining and type-guided fine-tuning. 548-557 - Shuxin Zheng
Predicting equilibrium distributions for molecular systems with deep learning. 558-567 - Abdourahmane Diaw
Efficient learning of accurate surrogates for simulations of complex systems. 568-577
Volume 6, Number 6, 2024
- Will generative AI transform robotics? 579
- Mayank Kejriwal
Challenges, evaluation and opportunities for open-world learning. 580-588 - Yuanqi Du, Arian R. Jamasb
Machine learning-aided generative molecular design. 589-604 - Lidong Yang
Machine learning for micro- and nanorobots. 605-618 - Kevin Max
Learning efficient backprojections across cortical hierarchies in real time. 619-630 - Qianying Cao, Somdatta Goswami
Laplace neural operator for solving differential equations. 631-640 - Alpha Renner
Neuromorphic visual scene understanding with resonator networks. 641-652 - Alpha Renner
Visual odometry with neuromorphic resonator networks. 653-663 - Nasimeh Heydaribeni
Distributed constrained combinatorial optimization leveraging hypergraph neural networks. 664-672 - Huan Yee Koh
Physicochemical graph neural network for learning protein-ligand interaction fingerprints from sequence data. 673-687 - Duanhua Cao, Geng Chen, Jiaxin Jiang, Jie Yu
Generic protein-ligand interaction scoring by integrating physical prior knowledge and data augmentation modelling. 688-700 - Evan Seitz
Interpreting cis-regulatory mechanisms from genomic deep neural networks using surrogate models. 701-713 - Iksung Kang
Coordinate-based neural representations for computational adaptive optics in widefield microscopy. 714-725 - Chenguang Li
Discovering neural policies to drive behaviour by integrating deep reinforcement learning agents with biological neural networks. 726-738
Volume 6, Number 7, 2024
- A question of trust for AI research in medicine. 739
- Robert L. Baines
The need for reproducible research in soft robotics. 740-741 - Gaoyang Liu, Chen Wang
Shielding sensitive medical imaging data. 742-743 - Weixin Liang
Systematic analysis of 32,111 AI model cards characterizes documentation practice in AI. 744-753 - Maria Boulougouri
Molecular set representation learning. 754-763 - Alexander Ziller
Reconciling privacy and accuracy in AI for medical imaging. 764-774 - Osama Abdin
Direct conformational sampling from peptide energy landscapes through hypernetwork-conditioned diffusion. 775-786 - Lei Han
Lifelike agility and play in quadrupedal robots using reinforcement learning and generative pre-trained models. 787-798 - Dong Chen
Multiscale topology-enabled structure-to-sequence transformer for protein-ligand interaction predictions. 799-810 - Petru-Daniel Tudosiu
Realistic morphology-preserving generative modelling of the brain. 811-819 - James Gornet, Matt Thomson
Automated construction of cognitive maps with visual predictive coding. 820-833 - Yoo-Geun Ham
Partial-convolution-implemented generative adversarial network for global oceanic data assimilation. 834-843
Volume 6, Number 8, 2024
- What is in your LLM-based framework? 845
- Silvia Milano
Advanced AI assistants that act on our behalf may not be ethically or legally feasible. 846-847 - Nicholas Vincent:
A step forward in tracing and documenting dataset provenance. 848-849 - Margaret C. von Ebers, Xue-Xin Wei:
Cognitive maps from predictive vision. 850-851 - Isabelle Augenstein
Factuality challenges in the era of large language models and opportunities for fact-checking. 852-863 - Shuangxia Ren, Gregory F. Cooper, Lujia Chen
An interpretable deep learning framework for genome-informed precision oncology. 864-875 - Rui Jiang
A transformer-based weakly supervised computational pathology method for clinical-grade diagnosis and molecular marker discovery of gliomas. 876-891 - Yue Huang
High-resolution real-space reconstruction of cryo-EM structures using a neural field network. 892-903 - Yang Long
Unsupervised learning of topological non-Abelian braiding in non-Hermitian bands. 904-910 - Melissa Sanabria
DNA language model GROVER learns sequence context in the human genome. 911-923 - Shihao Feng, Zhenyu Chen, Chengwei Zhang, Yuhao Xie, Sergey Ovchinnikov
Integrated structure prediction of protein-protein docking with experimental restraints using ColabDock. 924-935 - Surbhi Mittal, Kartik Thakral
On responsible machine learning datasets emphasizing fairness, privacy and regulatory norms with examples in biometrics and healthcare. 936-949 - Yu Zong, Yuxin Wang, Xipeng Qiu
Deep learning prediction of glycopeptide tandem mass spectra powers glycoproteomics. 950-961 - Bin Feng, Zequn Liu, Nanlan Huang
A bioactivity foundation model using pairwise meta-learning. 962-974 - Shayne Longpre, Robert Mahari
A large-scale audit of dataset licensing and attribution in AI. 975-987 - Yanyi Chu, Dan Yu, Yupeng Li, Kaixuan Huang, Yue Shen, Le Cong, Jason Zhang, Mengdi Wang
Author Correction: A 5′ UTR language model for decoding untranslated regions of mRNA and function predictions. 988
Volume 6, Number 9, 2024
- Taewi Kim
Wing-strain-based flight control of flapping-wing drones through reinforcement learning. 992-1005 - Davide Carnevali
A deep learning method that identifies cellular heterogeneity using nanoscale nuclear features. 1021-1033 - Mark Endo, Favour Nerrise, Qingyu Zhao, Edith V. Sullivan, Li Fei-Fei, Victor W. Henderson, Kilian M. Pohl, Kathleen L. Poston, Ehsan Adeli
Data-driven discovery of movement-linked heterogeneity in neurodegenerative diseases. 1034-1045 - Emanuele Zappala
Learning integral operators via neural integral equations. 1046-1062 - Shawn Reeves
Zero-shot transfer of protein sequence likelihood models to thermostability prediction. 1063-1076 - Pushpak Pati, Sofia Karkampouna, Francesco Bonollo
Accelerating histopathology workflows with generative AI-based virtually multiplexed tumour profiling. 1077-1093 - Yi Zhong
Learning motif-based graphs for drug-drug interaction prediction via local-global self-attention. 1094-1105
Volume 6, Number 10, 2024
- Pick your AI poison. 1119
- Cas Wognum, Jeremy R. Ash, Matteo Aldeghi, Raquel Rodríguez-Pérez, Cheng Fang
A call for an industry-led initiative to critically assess machine learning for real-world drug discovery. 1120-1121 - Alexander Rodríguez
Machine learning for data-centric epidemic forecasting. 1122-1131 - Sully F. Chen
Sparse learned kernels for interpretable and efficient medical time series processing. 1132-1144 - Enrica Tricomi
Soft robotic shorts improve outdoor walking efficiency in older adults. 1145-1155 - Junwei Yang
Poisoning medical knowledge using large language models. 1156-1168 - Yuyan Ni
Pre-training with fractional denoising to enhance molecular property prediction. 1169-1178 - Guruprasad Raghavan, Bahey Tharwat, Surya Narayanan Hari, Dhruvil Satani
Engineering flexible machine learning systems by traversing functionally invariant paths. 1179-1196 - Anthony Bilodeau, Albert Michaud-Gagnon, Julia Chabbert, Benoît Turcotte, Jörn Heine, Audrey Durand, Flavie Lavoie-Cardinal
Development of AI-assisted microscopy frameworks through realistic simulation with pySTED. 1197-1215 - Ziyan Feng, Jingyang Chen, Youlong Hai
Sliding-attention transformer neural architecture for predicting T cell receptor-antigen-human leucocyte antigen binding. 1216-1230 - Liangying Yin, Yaning Feng, Yujia Shi, Alexandria Lau, Jinghong Qiu, Pak Chung Sham
Estimation of causal effects of genes on complex traits using a Bayesian-network-based framework applied to GWAS data. 1231-1244 - Bohao Zou, Jingjing Wang, Yi Ding, Zhenmiao Zhang
A multi-modal deep language model for contaminant removal from metagenome-assembled genomes. 1245-1255 - Nick McGreivy
Weak baselines and reporting biases lead to overoptimism in machine learning for fluid-related partial differential equations. 1256-1269 - Shihao Feng, Zhenyu Chen, Chengwei Zhang, Yuhao Xie, Sergey Ovchinnikov
Author Correction: Integrated structure prediction of protein-protein docking with experimental restraints using ColabDock. 1270
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