Medical systematic reviews typically require assessing all the documents retrieved by a search. The reason is two-fold: the task aims for ``total recall''; and documents retrieved using Boolean search are an unordered set, and thus it is unclear how an assessor could examine only a subset. Screening prioritisation is the process of ranking the (unordered) set of retrieved documents, allowing assessors to begin the downstream processes of the systematic review creation earlier, leading to earlier completion of the review, or even avoiding screening documents ranked least relevant. Screening prioritisation requires highly effective ranking methods. Pre-trained language models are state-of-the-art on many IR tasks but have yet to be applied to systematic review screening prioritisation. In this paper, we apply several pre-trained language models to the systematic review document ranking task, both directly and fine-tuned. An empirical analysis compares how effective neural methods compare to traditional methods for this task. We also investigate different types of document representations for neural methods and their impact on ranking performance. Our results show that BERT-based rankers outperform the current state-of-the-art screening prioritisation methods. However, BERT rankers and existing methods can actually be complementary, and thus, further improvements may be achieved if used in conjunction.

高质量的医学系统评价需要全面的文献搜索，以确保建议和结果足够可靠。确实，寻找相关的医学文献是构建系统评价的关键阶段，并且通常涉及域（医学研究人员）和搜索（信息专家）专家，以开发搜索查询。基于布尔逻辑，在这种情况下的查询非常复杂，包括标准化术语（例如，医学主题标题（网格）词库）的自由文本项和索引项，并且难以构建。特别是显示网格术语的使用可以提高搜索结果的质量。但是，确定正确的网格术语以在查询中包含很难：信息专家通常不熟悉网格数据库，并且不确定查询网格条款的适当性。自然地，网格术语的全部价值通常不会完全利用。本文研究了基于仅包含自由文本项的初始布尔查询提出网格术语的方法。在这种情况下，我们设计了基于语言模型的词汇和预训练的方法。这些方法有望自动识别高效的网格术语，以包含在系统的审查查询中。我们的研究对几种网格术语建议方法进行了经验评估。我们进一步对每种方法的网格项建议进行了广泛的分析，以及这些建议如何影响布尔查询的有效性。

当查询使用不同的词汇表时，在大型临床本体中寻找概念可能是挑战。一种克服这个问题的搜索算法在概念归一化和本体匹配之类的应用中有用，其中概念可以以不同的方式引用，使用不同的同义词。在本文中，我们提出了一种基于深度学习的方法来构建大型临床本体的语义搜索系统。我们提出了一种三重型BERT模型和一种直接从本体产生培训数据的方法。该模型使用五个真实的基准数据集进行评估，结果表明，我们的方法在自由文本上实现了高结果，以概念和概念到概念搜索任务，并且优越所有基线方法。

Given the increasingly intricate forms of partial differential equations (PDEs) in physics and related fields, computationally solving PDEs without analytic solutions inevitably suffers from the trade-off between accuracy and efficiency. Recent advances in neural operators, a kind of mesh-independent neural-network-based PDE solvers, have suggested the dawn of overcoming this challenge. In this emerging direction, Koopman neural operator (KNO) is a representative demonstration and outperforms other state-of-the-art alternatives in terms of accuracy and efficiency. Here we present KoopmanLab, a self-contained and user-friendly PyTorch module of the Koopman neural operator family for solving partial differential equations. Beyond the original version of KNO, we develop multiple new variants of KNO based on different neural network architectures to improve the general applicability of our module. These variants are validated by mesh-independent and long-term prediction experiments implemented on representative PDEs (e.g., the Navier-Stokes equation and the Bateman-Burgers equation) and ERA5 (i.e., one of the largest high-resolution data sets of global-scale climate fields). These demonstrations suggest the potential of KoopmanLab to be considered in diverse applications of partial differential equations.

Regularising the parameter matrices of neural networks is ubiquitous in training deep models. Typical regularisation approaches suggest initialising weights using small random values, and to penalise weights to promote sparsity. However, these widely used techniques may be less effective in certain scenarios. Here, we study the Koopman autoencoder model which includes an encoder, a Koopman operator layer, and a decoder. These models have been designed and dedicated to tackle physics-related problems with interpretable dynamics and an ability to incorporate physics-related constraints. However, the majority of existing work employs standard regularisation practices. In our work, we take a step toward augmenting Koopman autoencoders with initialisation and penalty schemes tailored for physics-related settings. Specifically, we propose the "eigeninit" initialisation scheme that samples initial Koopman operators from specific eigenvalue distributions. In addition, we suggest the "eigenloss" penalty scheme that penalises the eigenvalues of the Koopman operator during training. We demonstrate the utility of these schemes on two synthetic data sets: a driven pendulum and flow past a cylinder; and two real-world problems: ocean surface temperatures and cyclone wind fields. We find on these datasets that eigenloss and eigeninit improves the convergence rate by up to a factor of 5, and that they reduce the cumulative long-term prediction error by up to a factor of 3. Such a finding points to the utility of incorporating similar schemes as an inductive bias in other physics-related deep learning approaches.

This work builds on the models and concepts presented in part 1 to learn approximate dictionary representations of Koopman operators from data. Part I of this paper presented a methodology for arguing the subspace invariance of a Koopman dictionary. This methodology was demonstrated on the state-inclusive logistic lifting (SILL) basis. This is an affine basis augmented with conjunctive logistic functions. The SILL dictionary's nonlinear functions are homogeneous, a norm in data-driven dictionary learning of Koopman operators. In this paper, we discover that structured mixing of heterogeneous dictionary functions drawn from different classes of nonlinear functions achieve the same accuracy and dimensional scaling as the deep-learning-based deepDMD algorithm. We specifically show this by building a heterogeneous dictionary comprised of SILL functions and conjunctive radial basis functions (RBFs). This mixed dictionary achieves the same accuracy and dimensional scaling as deepDMD with an order of magnitude reduction in parameters, while maintaining geometric interpretability. These results strengthen the viability of dictionary-based Koopman models to solving high-dimensional nonlinear learning problems.

Koopman operators model nonlinear dynamics as a linear dynamic system acting on a nonlinear function as the state. This nonstandard state is often called a Koopman observable and is usually approximated numerically by a superposition of functions drawn from a dictionary. In a widely used algorithm, Extended Dynamic Mode Decomposition, the dictionary functions are drawn from a fixed class of functions. Recently, deep learning combined with EDMD has been used to learn novel dictionary functions in an algorithm called deep dynamic mode decomposition (deepDMD). The learned representation both (1) accurately models and (2) scales well with the dimension of the original nonlinear system. In this paper we analyze the learned dictionaries from deepDMD and explore the theoretical basis for their strong performance. We explore State-Inclusive Logistic Lifting (SILL) dictionary functions to approximate Koopman observables. Error analysis of these dictionary functions show they satisfy a property of subspace approximation, which we define as uniform finite approximate closure. Our results provide a hypothesis to explain the success of deep neural networks in learning numerical approximations to Koopman operators. Part 2 of this paper will extend this explanation by demonstrating the subspace invariant of heterogeneous dictionaries and presenting a head-to-head numerical comparison of deepDMD and low-parameter heterogeneous dictionary learning.

Transfer operators offer linear representations and global, physically meaningful features of nonlinear dynamical systems. Discovering transfer operators, such as the Koopman operator, require careful crafted dictionaries of observables, acting on states of the dynamical system. This is ad hoc and requires the full dataset for evaluation. In this paper, we offer an optimization scheme to allow joint learning of the observables and Koopman operator with online data. Our results show we are able to reconstruct the evolution and represent the global features of complex dynamical systems.

Credit assignment problem of neural networks refers to evaluating the credit of each network component to the final outputs. For an untrained neural network, approaches to tackling it have made great contributions to parameter update and model revolution during the training phase. This problem on trained neural networks receives rare attention, nevertheless, it plays an increasingly important role in neural network patch, specification and verification. Based on Koopman operator theory, this paper presents an alternative perspective of linear dynamics on dealing with the credit assignment problem for trained neural networks. Regarding a neural network as the composition of sub-dynamics series, we utilize step-delay embedding to capture snapshots of each component, characterizing the established mapping as exactly as possible. To circumvent the dimension-difference problem encountered during the embedding, a composition and decomposition of an auxiliary linear layer, termed minimal linear dimension alignment, is carefully designed with rigorous formal guarantee. Afterwards, each component is approximated by a Koopman operator and we derive the Jacobian matrix and its corresponding determinant, similar to backward propagation. Then, we can define a metric with algebraic interpretability for the credit assignment of each network component. Moreover, experiments conducted on typical neural networks demonstrate the effectiveness of the proposed method.

基于近似基础的Koopman操作员或发电机的数据驱动的非线性动力系统模型已被证明是预测，功能学习，状态估计和控制的成功工具。众所周知，用于控制膜系统的Koopman发电机还对输入具有仿射依赖性，从而导致动力学的方便有限维双线性近似。然而，仍然存在两个主要障碍，限制了当前方法的范围，以逼近系统的koopman发电机。首先，现有方法的性能在很大程度上取决于要近似Koopman Generator的基础函数的选择；目前，目前尚无通用方法来为无法衡量保存的系统选择它们。其次，如果我们不观察到完整的状态，我们可能无法访问足够丰富的此类功能来描述动态。这是因为在有驱动时，通常使用时间延迟的可观察物的方法失败。为了解决这些问题，我们将Koopman Generator控制的可观察到的动力学写为双线性隐藏Markov模型，并使用预期最大化（EM）算法确定模型参数。 E-Step涉及标准的Kalman滤波器和更光滑，而M-Step类似于发电机的控制效果模式分解。我们在三个示例上证明了该方法的性能，包括恢复有限的Koopman-Invariant子空间，用于具有缓慢歧管的驱动系统；估计非强制性行驶方程的Koopman本征函数；仅基于提升和阻力的嘈杂观察，对流体弹球系统的模型预测控制。