Josh Abramson

Abstract The introduction of AlphaFold 2 1 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design 2–6 . Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein–ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein–nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody–antigen prediction accuracy compared with AlphaFold-Multimer v.2.3 7,8 . Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.

In our original article, we provided an extensive

The area of automatic speaker recognition has been dominated by systems using only short-term, low-level acoustic information, such as cepstral features. While these systems have indeed produced very low error rates, they ignore other levels of information beyond low-level acoustics that convey speaker information. Recently published work has shown examples that such high-level information can be used successfully in automatic speaker recognition systems and has the potential to improve accuracy and add robustness. For the 2002 JHU CLSP summer workshop, the SuperSID project (http://www.clsp.jhu.edu/ws2002/groups/supersid/) was undertaken to exploit these high-level information sources and dramatically increase speaker recognition accuracy on a defined NIST evaluation corpus and task. The paper provides an overview of the structure, data, task, tools, and accomplishments of this project. Wide ranging approaches using pronunciation models, prosodic dynamics, pitch and duration features, phone streams, and conversational interactions were explored and developed. We show how these novel features and classifiers indeed provide complementary information and can be fused together to drive down the equal error rate on the 2001 NIST extended data task to 0.2% - a 71% relative reduction in error over the previous state of the art.

Animals execute goal-directed behaviours despite the limited range and scope of their sensors. To cope, they explore environments and store memories maintaining estimates of important information that is not presently available. Recently, progress has been made with artificial intelligence (AI) agents that learn to perform tasks from sensory input, even at a human level, by merging reinforcement learning (RL) algorithms with deep neural networks, and the excitement surrounding these results has led to the pursuit of related ideas as explanations of non-human animal learning. However, we demonstrate that contemporary RL algorithms struggle to solve simple tasks when enough information is concealed from the sensors of the agent, a property called "partial observability". An obvious requirement for handling partially observed tasks is access to extensive memory, but we show memory is not enough; it is critical that the right information be stored in the right format. We develop a model, the Memory, RL, and Inference Network (MERLIN), in which memory formation is guided by a process of predictive modeling. MERLIN facilitates the solution of tasks in 3D virtual reality environments for which partial observability is severe and memories must be maintained over long durations. Our model demonstrates a single learning agent architecture that can solve canonical behavioural tasks in psychology and neurobiology without strong simplifying assumptions about the dimensionality of sensory input or the duration of experiences.

While there has been a long tradition of research seeking to use prosodic features, especially pitch, in speaker recognition systems, results have generally been disappointing when such features are used in isolation and only modest improvements have been seen when used in conjunction with traditional cepstral GMM systems. In contrast, we report here on work from the JHU 2002 Summer Workshop exploring a range of prosodic features, using as testbed the 2001 NIST Extended Data task. We examined a variety of modeling techniques, such as n-gram models of turn-level prosodic features and simple vectors of summary statistics per conversation side scored by k/sup th/ nearest-neighbor classifiers. We found that purely prosodic models were able to achieve equal error rates of under 10%, and yielded significant gains when combined with more traditional systems. We also report on exploratory work on "conversational" features, capturing properties of the interaction across conversation sides, such as turn-taking patterns.