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Great advances in protein structure prediction have been made with recent deep learning-based methods, but proteins interact with their environment and can change shape drastically when binding to ligand molecules. To predict the 3D structure of these combined protein–ligand complexes, Qiao et al. developed a generative diffusion model with biophysical constraints and geometric deep learning.

AI-enabled diagnostic applications in healthcare can be powerful, but study design is very important to avoid subtle issues of bias in the dataset and evaluation. Coppock et al. demonstrate how an AI-based classifier for diagnosing SARS-Cov-2 infection from audio recordings can seem to make predictions with high accuracy but shows much lower performance after taking into account confounders, providing insights in study design and replicability in AI-based audio analysis.

Recent work has demonstrated important parallels between human visual representations and those found in deep neural networks. A new study comparing functional MRI data to deep neural network models highlights factors that may determine this similarity.

Machine learning techniques are widely employed in chemical science, but are application specific and their development requires dedicated expertise. Jablonka and colleagues fine-tune the GPT-3 model and show that it can provide surprisingly accurate answers to a wide range of chemical questions.

We reflect on five years of Nature Machine Intelligence and on providing a venue for discussions in AI.

Machine learning is increasingly applied for disease diagnostics due to its ability to discover differentiating features in data. However, the clinical applicability of these models remains a challenge. Pavlović et al. provide an overview of the challenges in using machine learning for biomarker discovery and suggest a causal perspective as a solution.

For our fifth anniversary, we reconnected with authors of recent Comments and Perspectives in Nature Machine Intelligence and asked them how the topic they wrote about developed. We also wanted to know what other topics in AI they found exciting, surprising or worrying, and what their hopes and expectations are for AI in 2024—and the next five years. A recurring theme is the ongoing developments in large language models and generative AI, their transformative effect on the scientific process and concerns about ethical implications.

Recent years have seen many advances in deep learning models for protein design, usually involving a large amount of training data. Focusing on potential clinical impact, Garton et al. develop a variational autoencoder approach trained on sparse data of natural sequences of adenoviruses to generate large proteins that can be used as viral vectors in gene therapy.

Designing antibodies and assessing their biophysical properties for potential therapeutic development is challenging with current computational methods. Ramon et al. have developed a deep learning approach called AbNatiV, based on a vector-quantized variational encoder that accurately assesses the nativeness of antibodies and nanobodies, which are small single-domain antibodies that have recently attracted considerable interest.

Drug design has recently seen immense improvements in computational methods, but models can still struggle generalizing across binding pockets. Feng and colleagues combine a language model with geometric deep learning to provide efficient generation of potential new drugs.

Accurate real-time tracking of dexterous hand movements and interactions has applications in human–computer interaction, the metaverse, robotics and tele-health. Capturing realistic hand movements is challenging due to the large number of articulations and degrees of freedom. Tashakori and colleagues report accurate and dynamic tracking of articulated hand and finger movements using machine-learning powered stretchable, washable smart gloves.

Magnetic microrobots are of considerable interest for non-invasive biomedical applications but it is challenging to develop a general strategy for controlling microrobot positions, for varying configurations and environments. Choi et al. develop a reinforcement learning control method, training the model in a simulation environment for initial exploration after which the learning process is transferred to a physical electromagnetic actuation system.

Multi-animal behaviour quantification is pivotal for deciphering animal social behaviours and has broad applications in neuroscience and ecology. Han and colleagues develop a few-shot learning framework for multi-animal 3D pose estimation, identity recognition and social behaviour classification.

Feed-forward neural networks have become powerful tools in machine learning, but their behaviour during optimization is still not well understood. Ciceri and colleagues find that during optimization, class representations first separate and then rejoin, prompted by specific elements of the training set.

The implementation of particle-tracking techniques with deep neural networks is a promising way to determine particle motion within complex flow structures. A graph neural network-enhanced method enables accurate particle tracking by significantly reducing the number of lost trajectories.

Looking back at a year of escalating, divisive debates in AI safety and who determines the agenda.

New research reveals a duality between neural network weights and neuron activities that enables a geometric decomposition of the generalization gap. The framework provides a way to interpret the effects of regularization schemes such as stochastic gradient descent and dropout on generalization — and to improve upon these methods.