Research articles

AlphaFold2 has revolutionized bioinformatics, but its ability to predict protein structures with high accuracy comes at the price of a costly database search for multiple sequence alignments. Fang and colleagues pre-train a large-scale protein language model and use it in conjunction with AlphaFold2 as a fully trainable and efficient model for structure prediction.

It is widely known that AI-based recommendation systems on social media and news websites can isolate humans from diverse information, eventually trapping them in so-called information cocoons, where they are exposed to a narrow range of viewpoints. Li et al. introduce an adaptive information dynamics model to uncover the origin of information cocoons in complex human–AI interaction systems, and test their findings on two large real-world datasets.

Deep learning can help develop non-invasive technology for decoding speech from brain activity, which could improve the lives of patients with brain injuries. Défossez et al. report a contrastive-learning approach to decode speech listening from human participants, using public databases of recordings based on non-invasive magnetic and electrical measurements.

Online matching platforms are increasingly used for applications with positive social impact such as matching blood donors with recipients, where matching algorithms need to balance fairness with an efficiency objective. The authors demonstrate, both in computational simulations and using real data from the Facebook Blood Donations tool, that introducing a simple online matching policy can substantially increase the likelihood of donor action.

Fine motor skill recovery in hand rehabilitation is a challenge due to limited finger movement sensing and closed-loop control algorithms in existing rehabilitation gloves. Sui et al. develop a soft-packaged rehabilitation glove, integrating sensing, actuation, a human–machine interface, power, electronics and a closed-loop algorithm. The glove aids patients after a stroke to recover fine motor skills of the fingers in a portable manner.

Identifying interventions that can induce a desired effect is challenging owing to the combinatorial number of possible choices in design space. Zhang and colleagues propose an active learning approach with theoretical guarantees to discover optimal interventions in causal models, and demonstrate the framework in the context of genetic perturbation design using single-cell transcriptomic data.

State-of-the-art image reconstruction for multispectral optoacoustic tomography is currently too slow for clinical applications. Dehner, Zahnd et al. propose a deep learning framework to reconstruct optoacoustic images in real-time while maintaining similar quality.

The recent accessibility of large language models brought them into contact with a large number of users and, due to the social nature of language, it is hard to avoid prescribing human characteristics such as intentions to a chatbot. Pataranutaporn and colleagues investigated how framing a bot as helpful or manipulative can influence this perception and the behaviour of the humans that interact with it.

Despite their efficiency advantages, the performance of photonic neural networks is hampered by the accumulation of inherent systematic errors. Zheng et al. propose a dual backpropagation training approach, which allows the network to adapt to systematic errors, thus outperforming state-of-the-art in situ training approaches.

Local methods of explainable artificial intelligence identify where important features or inputs occur, while global methods try to understand what features or concepts have been learned by a model. The authors propose a concept-level explanation method that bridges the local and global perspectives, enabling more comprehensive and human-understandable explanations.

With the advances in neural language models, the question arises if some models align better with human processing than others. Golan et al. identify sentences that language models disagree about and use them to compare the shortcomings of different language models.

An outstanding challenge in materials science is doing large-scale simulations with complex electron interactions. Deng and colleagues introduce a universal graph neural network-based interatomic potential integrating atomic magnetic moments as charge constraints, which allows for capturing subtle chemical properties in several lithium-based solid-state materials

Generating novel molecules that bind to specific protein targets is a challenging but important task in computational drug design. Zhang and colleagues present a molecular generation method based on hierarchical auto-regression.

For virtual protein docking, an accurate scoring function is necessary that evaluates how likely a protein conformation is. Stebliankin and colleagues present a method based on vision transformers that provides a more accurate score by evaluating individual binding interfaces as multi-channel images.

Achieving sequential robotic actions involving different manipulation skills is an open challenge that is critical to enable robots to interact meaningfully with their physical environment. Triantafyllidis and colleagues present a hierarchical learning framework based on an ensemble of specialized neural networks to solve complex long-horizon manipulation tasks.

Traditional feedback-state selection in robot learning is empirical and requires substantial engineering efforts. Yu et al. develop a quantitative and systematic state-importance analysis, revealing crucial feedback signals for learning locomotion skills.

Tandem mass spectroscopy is a useful tool to identify metabolites but is limited by the capability of computational methods to annotate peaks with chemical structures when spectra are dissimilar to previously observed spectra. Goldman and colleagues use a transformer-based method to annotate chemical structure fragments, thereby incorporating domain insights into its architecture, and to simultaneously predict the structure of the metabolite and its fragments from the spectrum.

The heterogeneous and compartmentalized environments within living cells make it difficult to deploy theranostic agents with precise spatiotemporal accuracy. Zhao et al. demonstrate a DNA framework state machine that can switch among multiple structural states according to the temporal sequence of molecular cues, enabling temporally controlled CRISPR–Cas9 targeting in living mammalian cells.