Browse Articles

Single-cell transcriptomics has provided a powerful approach to investigate cellular properties at unprecedented resolution. Sha et al. have developed an optimal transport-based algorithm called TIGON that can connect transcriptomic snapshots from different time points to obtain collective dynamical information, including cell population growth and the underlying gene regulatory network.

A fundamental question in neuroscience is what are the constraints that shape the structural and functional organization of the brain. By bringing biological cost constraints into the optimization process of artificial neural networks, Achterberg, Akarca and colleagues uncover the joint principle underlying a large set of neuroscientific findings.

Further progress in AI may require learning algorithms to generate their own data rather than assimilate static datasets. A Perspective in this issue proposes that they could do so by interacting with other learning agents in a socially structured way.

Advances in machine intelligence often depend on data assimilation, but data generation has been neglected. The authors discuss mechanisms that might achieve continuous novel data generation and the creation of intelligent systems that are capable of human-like innovation, focusing on social aspects of intelligence.

Traditionally, 3D graphics involves numerical methods for physical and virtual simulations of real-world scenes. Spielberg et al. review how deep learning enables differentiable visual computing, which determines how graphics outputs change when the environment changes, with applications in areas such as computer-aided design, manufacturing and robotics.

Deep learning is a powerful method to process large datasets, and shown to be useful in many scientific fields, but models are highly parameterized and there are often challenges in interpretation and generalization. David Gleich and colleagues develop a method rooted in computational topology, starting with a graph-based topological representation of the data, to help assess and diagnose predictions from deep learning and other complex prediction methods.

Continual learning is an innate ability in biological intelligence to accommodate real-world changes, but it remains challenging for artificial intelligence. Wang, Zhang and colleagues model key mechanisms of a biological learning system, in particular active forgetting and parallel modularity, to incorporate neuro-inspired adaptability to improve continual learning in artificial intelligence systems.

scBERT, a pretrained neural network for single-cell sequencing tasks, was published last year in Nature Machine Intelligence. To test the reusability of the method, Khan et al. use the code to assess the generalizablility of transformer architectures on single-cell genomics tasks.

Recommender systems are a predominant feature of online platforms and one of the most widespread applications of artificial intelligence. A new model captures information dynamics driven by algorithmic recommendations and offers ways to ensure that users are exposed to diverse content and information.

Prediction of high-level visual representations in the human brain may benefit from multimodal sources in network training and the incorporation of complex datasets. Wang and colleagues show that language pretraining and a large, diverse dataset together build better models of higher-level visual cortex compared to earlier models.

Graph neural networks have proved useful in modelling proteins and their ligand interactions, but it is not clear whether the patterns they identify have biological relevance or whether interactions are merely memorized. Mastropietro et al. use a Shapley value-based method to identify important edges in protein interaction graphs, enabling explanatory analysis of the model mechanisms.

The rise of artificial intelligence (AI) has relied on an increasing demand for energy, which threatens to outweigh its promised positive effects. To steer AI onto a more sustainable path, quantifying and comparing its energy consumption is key.

Halide perovskites are promising materials for light-emitting devices, given their narrowband emission and solution processability. However, detailed information on device degradation during operation is required to improve their stability, and this is challenging to obtain. Ji et al. propose a self-supervised deep learning method to capture multi-dimensional images of such devices in their operating regime faster than allowed by conventional imaging techniques.

The reconstruction of dynamic, spatial fields from sparse sensor data is an important challenge in various fields of science and technology. Santos et al. introduce the Senseiver, a deep learning framework that reconstructs spatial fields from few observations using attention layers to encode and decode sparse data, enabling efficient inference.

Geometric deep learning has become a powerful tool in virtual drug design, but it is not always obvious when a model makes incorrect predictions. Luo and colleagues improve the accuracy of their deep learning model using uncertainty calibration and Bayesian optimization in an active learning cycle.

Human and animal motion planning works at various timescales to allow the completion of complex tasks. Inspired by this natural strategy, Yuan and colleagues present a hierarchical motion planning approach for robotics, using deep reinforcement learning and predictive proprioception.

Organisms show complex behaviour resulting from a trade-off between obtaining information (explore) and using current information (exploit). Biswas et al. observe a mode-switching strategy modulated by sensory salience in a diverse range of organisms, including electric fish and humans, and argue that the observed heuristic could inform the design of active-sensing behaviours in robotics.

Prime editors are innovative genome-editing tools, but selecting guide RNAs with high efficiency remains challenging and requires costly experimental efforts. Liu and colleagues develop a method to design prime-editing guide RNAs based on transfer learning for in silico prediction of editing efficacy.

Learning causal relationships between variables in large datasets is an outstanding challenge in various scientific applications. Lagemann et al. introduce a deep neural network approach combining convolutional and graph models intended for causal learning in high-dimensional biomedical problems.

Deep learning methods in natural language processing generally become more effective with larger datasets and bigger networks. But it is not evident whether the same is true for more specialized domains such as cheminformatics. Frey and colleagues provide empirical explorations of chemistry models and find that neural-scaling laws hold true even for the largest tested models and datasets.