Cardiac digital twins are computational tools capturing key functional and anatomical characteristics of patient hearts for investigating disease phenotypes and predicting responses to therapy. When paired with large-scale computational resources and large clinical datasets, digital twin technology can enable virtual clinical trials on virtual cohorts to fast-track therapy development. Here, we present an automated pipeline for personalising ventricular anatomy and electrophysiological function based on routinely acquired cardiac magnetic resonance (CMR) imaging data and the standard 12-lead electrocardiogram (ECG). Using CMR-based anatomical models, a sequential Monte-Carlo approximate Bayesian computational inference method is extended to infer electrical activation and repolarisation characteristics from the ECG. Fast simulations are conducted with a reaction-Eikonal model, including the Purkinje network and biophysically-detailed subcellular ionic current dynamics for repolarisation. For each patient, parameter uncertainty is represented by inferring a population of ventricular models rather than a single one, which means that parameter uncertainty can be propagated to therapy evaluation. Furthermore, we have developed techniques for translating from reaction-Eikonal to monodomain simulations, which allows more realistic simulations of cardiac electrophysiology. The pipeline is demonstrated in a healthy female subject, where our inferred reaction-Eikonal models reproduced the patient's ECG with a Pearson's correlation coefficient of 0.93, and the translated monodomain simulations have a correlation coefficient of 0.89. We then apply the effect of Dofetilide to the monodomain population of models for this subject and show dose-dependent QT and T-peak to T-end prolongations that are in keeping with large population drug response data.
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The application of eigenvalue theory to dual quaternion Hermitian matrices holds significance in the realm of multi-agent formation control. In this paper, we study the Rayleigh quotient iteration (RQI) for solving the right eigenpairs of dual quaternion Hermitian matrices. Combined with dual representation, the RQI algorithm can effectively compute the extreme eigenvalue along with the associated eigenvector of the large dual quaternion Hermitian matrices. Furthermore, a convergence analysis of the Rayleigh quotient iteration is derived, demonstrating a local convergence rate of at least cubic, which is faster than the linear convergence rate of the power method. Numerical examples are provided to illustrate the high accuracy and low CPU time cost of the proposed Rayleigh quotient iteration compared with the power method for solving the dual quaternion Hermitian eigenvalue problem.
This paper presents the results of finetuning large language models (LLMs) for the task of detecting vulnerabilities in source code. We leverage WizardCoder, a recent improvement of the state-of-the-art LLM StarCoder, and adapt it for vulnerability detection through further finetuning. To accelerate training, we modify WizardCoder's training procedure, also we investigate optimal training regimes. For the imbalanced dataset with many more negative examples than positive, we also explore different techniques to improve classification performance. The finetuned WizardCoder model achieves improvement in ROC AUC and F1 measures on balanced and imbalanced vulnerability datasets over CodeBERT-like model, demonstrating the effectiveness of adapting pretrained LLMs for vulnerability detection in source code. The key contributions are finetuning the state-of-the-art code LLM, WizardCoder, increasing its training speed without the performance harm, optimizing the training procedure and regimes, handling class imbalance, and improving performance on difficult vulnerability detection datasets. This demonstrates the potential for transfer learning by finetuning large pretrained language models for specialized source code analysis tasks.
In contact-rich tasks, like dexterous manipulation, the hybrid nature of making and breaking contact creates challenges for model representation and control. For example, choosing and sequencing contact locations for in-hand manipulation, where there are thousands of potential hybrid modes, is not generally tractable. In this paper, we are inspired by the observation that far fewer modes are actually necessary to accomplish many tasks. Building on our prior work learning hybrid models, represented as linear complementarity systems, we find a reduced-order hybrid model requiring only a limited number of task-relevant modes. This simplified representation, in combination with model predictive control, enables real-time control yet is sufficient for achieving high performance. We demonstrate the proposed method first on synthetic hybrid systems, reducing the mode count by multiple orders of magnitude while achieving task performance loss of less than 5%. We also apply the proposed method to a three-fingered robotic hand manipulating a previously unknown object. With no prior knowledge, we achieve state-of-the-art closed-loop performance within a few minutes of online learning, by collecting only a few thousand environment samples.
Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future.
This paper tackles the challenge of teaching code semantics to Large Language Models (LLMs) for program analysis by incorporating code symmetries into the model architecture. We introduce a group-theoretic framework that defines code symmetries as semantics-preserving transformations, where forming a code symmetry group enables precise and efficient reasoning of code semantics. Our solution, SymC, develops a novel variant of self-attention that is provably equivariant to code symmetries from the permutation group defined over the program dependence graph. SymC obtains superior performance on five program analysis tasks, outperforming state-of-the-art code models, including GPT-4, without any pre-training. Our results suggest that code LLMs that encode the code structural prior via the code symmetry group generalize better and faster.
With the rapid development of deep learning, training Big Models (BMs) for multiple downstream tasks becomes a popular paradigm. Researchers have achieved various outcomes in the construction of BMs and the BM application in many fields. At present, there is a lack of research work that sorts out the overall progress of BMs and guides the follow-up research. In this paper, we cover not only the BM technologies themselves but also the prerequisites for BM training and applications with BMs, dividing the BM review into four parts: Resource, Models, Key Technologies and Application. We introduce 16 specific BM-related topics in those four parts, they are Data, Knowledge, Computing System, Parallel Training System, Language Model, Vision Model, Multi-modal Model, Theory&Interpretability, Commonsense Reasoning, Reliability&Security, Governance, Evaluation, Machine Translation, Text Generation, Dialogue and Protein Research. In each topic, we summarize clearly the current studies and propose some future research directions. At the end of this paper, we conclude the further development of BMs in a more general view.
Geometric deep learning (GDL), which is based on neural network architectures that incorporate and process symmetry information, has emerged as a recent paradigm in artificial intelligence. GDL bears particular promise in molecular modeling applications, in which various molecular representations with different symmetry properties and levels of abstraction exist. This review provides a structured and harmonized overview of molecular GDL, highlighting its applications in drug discovery, chemical synthesis prediction, and quantum chemistry. Emphasis is placed on the relevance of the learned molecular features and their complementarity to well-established molecular descriptors. This review provides an overview of current challenges and opportunities, and presents a forecast of the future of GDL for molecular sciences.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
Recent advancements in deep neural networks for graph-structured data have led to state-of-the-art performance on recommender system benchmarks. However, making these methods practical and scalable to web-scale recommendation tasks with billions of items and hundreds of millions of users remains a challenge. Here we describe a large-scale deep recommendation engine that we developed and deployed at Pinterest. We develop a data-efficient Graph Convolutional Network (GCN) algorithm PinSage, which combines efficient random walks and graph convolutions to generate embeddings of nodes (i.e., items) that incorporate both graph structure as well as node feature information. Compared to prior GCN approaches, we develop a novel method based on highly efficient random walks to structure the convolutions and design a novel training strategy that relies on harder-and-harder training examples to improve robustness and convergence of the model. We also develop an efficient MapReduce model inference algorithm to generate embeddings using a trained model. We deploy PinSage at Pinterest and train it on 7.5 billion examples on a graph with 3 billion nodes representing pins and boards, and 18 billion edges. According to offline metrics, user studies and A/B tests, PinSage generates higher-quality recommendations than comparable deep learning and graph-based alternatives. To our knowledge, this is the largest application of deep graph embeddings to date and paves the way for a new generation of web-scale recommender systems based on graph convolutional architectures.
We investigate a lattice-structured LSTM model for Chinese NER, which encodes a sequence of input characters as well as all potential words that match a lexicon. Compared with character-based methods, our model explicitly leverages word and word sequence information. Compared with word-based methods, lattice LSTM does not suffer from segmentation errors. Gated recurrent cells allow our model to choose the most relevant characters and words from a sentence for better NER results. Experiments on various datasets show that lattice LSTM outperforms both word-based and character-based LSTM baselines, achieving the best results.
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