Background: Outcome measures that are count variables with excessive zeros are common in health behaviors research. There is a lack of empirical data about the relative performance of prevailing statistical models when outcomes are zero-inflated, particularly compared with recently developed approaches. Methods: The current simulation study examined five commonly used analytical approaches for count outcomes, including two linear models (with outcomes on raw and log-transformed scales, respectively) and three count distribution-based models (i.e., Poisson, negative binomial, and zero-inflated Poisson (ZIP) models). We also considered the marginalized zero-inflated Poisson (MZIP) model, a novel alternative that estimates the effects on overall mean while adjusting for zero-inflation. Extensive simulations were conducted to evaluate their the statistical power and Type I error rate across various data conditions. Results: Under zero-inflation, the Poisson model failed to control the Type I error rate, resulting in higher than expected false positive results. When the intervention effects on the zero (vs. non-zero) and count parts were in the same direction, the MZIP model had the highest statistical power, followed by the linear model with outcomes on raw scale, negative binomial model, and ZIP model. The performance of a linear model with a log-transformed outcome variable was unsatisfactory. When only one of the effects on the zero (vs. non-zero) part and the count part existed, the ZIP model had the highest statistical power. Conclusions: The MZIP model demonstrated better statistical properties in detecting true intervention effects and controlling false positive results for zero-inflated count outcomes. This MZIP model may serve as an appealing analytical approach to evaluating overall intervention effects in studies with count outcomes marked by excessive zeros.
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It is well known that canonical recurrent neural networks (RNNs) face limitations in learning long-term dependencies which have been addressed by memory structures in long short-term memory (LSTM) networks. Neural Turing machines (NTMs) are novel RNNs that implement the notion of programmable computers with neural network controllers that can learn simple algorithmic tasks. Matrix neural networks feature matrix representation which inherently preserves the spatial structure of data when compared to canonical neural networks that use vector-based representation. One may then argue that neural networks with matrix representations may have the potential to provide better memory capacity. In this paper, we define and study a probabilistic notion of memory capacity based on Fisher information for matrix-based RNNs. We find bounds on memory capacity for such networks under various hypotheses and compare them with their vector counterparts. In particular, we show that the memory capacity of such networks is bounded by $N^2$ for $N\times N$ state matrix which generalizes the one known for vector networks. We also show and analyze the increase in memory capacity for such networks which is introduced when one exhibits an external state memory, such as NTMs. Consequently, we construct NTMs with RNN controllers with matrix-based representation of external memory, leading us to introduce Matrix NTMs. We demonstrate the performance of this class of memory networks under certain algorithmic learning tasks such as copying and recall and compare it with Matrix RNNs. We find an improvement in the performance of Matrix NTMs by the addition of external memory, in comparison to Matrix RNNs.
Modern data sets, such as those in healthcare and e-commerce, are often derived from many individuals or systems but have insufficient data from each source alone to separately estimate individual, often high-dimensional, model parameters. If there is shared structure among systems however, it may be possible to leverage data from other systems to help estimate individual parameters, which could otherwise be non-identifiable. In this paper, we assume systems share a latent low-dimensional parameter space and propose a method for recovering $d$-dimensional parameters for $N$ different linear systems, even when there are only $T<d$ observations per system. To do so, we develop a three-step algorithm which estimates the low-dimensional subspace spanned by the systems' parameters and produces refined parameter estimates within the subspace. We provide finite sample subspace estimation error guarantees for our proposed method. Finally, we experimentally validate our method on simulations with i.i.d. regression data and as well as correlated time series data.
Conversational assistive robots can aid people, especially those with cognitive impairments, to accomplish various tasks such as cooking meals, performing exercises, or operating machines. However, to interact with people effectively, robots must recognize human plans and goals from noisy observations of human actions, even when the user acts sub-optimally. Previous works on Plan and Goal Recognition (PGR) as planning have used hierarchical task networks (HTN) to model the actor/human. However, these techniques are insufficient as they do not have user engagement via natural modes of interaction such as language. Moreover, they have no mechanisms to let users, especially those with cognitive impairments, know of a deviation from their original plan or about any sub-optimal actions taken towards their goal. We propose a novel framework for plan and goal recognition in partially observable domains -- Dialogue for Goal Recognition (D4GR) enabling a robot to rectify its belief in human progress by asking clarification questions about noisy sensor data and sub-optimal human actions. We evaluate the performance of D4GR over two simulated domains -- kitchen and blocks domain. With language feedback and the world state information in a hierarchical task model, we show that D4GR framework for the highest sensor noise performs 1% better than HTN in goal accuracy in both domains. For plan accuracy, D4GR outperforms by 4% in the kitchen domain and 2% in the blocks domain in comparison to HTN. The ALWAYS-ASK oracle outperforms our policy by 3% in goal recognition and 7%in plan recognition. D4GR does so by asking 68% fewer questions than an oracle baseline. We also demonstrate a real-world robot scenario in the kitchen domain, validating the improved plan and goal recognition of D4GR in a realistic setting.
Understanding the intricate operations of Recurrent Neural Networks (RNNs) mechanistically is pivotal for advancing their capabilities and applications. In this pursuit, we propose the Episodic Memory Theory (EMT), illustrating that RNNs can be conceptualized as discrete-time analogs of the recently proposed General Sequential Episodic Memory Model. To substantiate EMT, we introduce a novel set of algorithmic tasks tailored to probe the variable binding behavior in RNNs. Utilizing the EMT, we formulate a mathematically rigorous circuit that facilitates variable binding in these tasks. Our empirical investigations reveal that trained RNNs consistently converge to the variable binding circuit, thus indicating universality in the dynamics of RNNs. Building on these findings, we devise an algorithm to define a privileged basis, which reveals hidden neurons instrumental in the temporal storage and composition of variables, a mechanism vital for the successful generalization in these tasks. We show that the privileged basis enhances the interpretability of the learned parameters and hidden states of RNNs. Our work represents a step toward demystifying the internal mechanisms of RNNs and, for computational neuroscience, serves to bridge the gap between artificial neural networks and neural memory models.
Clinical texts, represented in electronic medical records (EMRs), contain rich medical information and are essential for disease prediction, personalised information recommendation, clinical decision support, and medication pattern mining and measurement. Relation extractions between medication mentions and temporal information can further help clinicians better understand the patients' treatment history. To evaluate the performances of deep learning (DL) and large language models (LLMs) in medication extraction and temporal relations classification, we carry out an empirical investigation of \textbf{MedTem} project using several advanced learning structures including BiLSTM-CRF and CNN-BiLSTM for a clinical domain named entity recognition (NER), and BERT-CNN for temporal relation extraction (RE), in addition to the exploration of different word embedding techniques. Furthermore, we also designed a set of post-processing roles to generate structured output on medications and the temporal relation. Our experiments show that CNN-BiLSTM slightly wins the BiLSTM-CRF model on the i2b2-2009 clinical NER task yielding 75.67, 77.83, and 78.17 for precision, recall, and F1 scores using Macro Average. BERT-CNN model also produced reasonable evaluation scores 64.48, 67.17, and 65.03 for P/R/F1 using Macro Avg on the temporal relation extraction test set from i2b2-2012 challenges. Code and Tools from MedTem will be hosted at \url{//github.com/HECTA-UoM/MedTem}
Graph neural networks (GNNs) have demonstrated a significant boost in prediction performance on graph data. At the same time, the predictions made by these models are often hard to interpret. In that regard, many efforts have been made to explain the prediction mechanisms of these models from perspectives such as GNNExplainer, XGNN and PGExplainer. Although such works present systematic frameworks to interpret GNNs, a holistic review for explainable GNNs is unavailable. In this survey, we present a comprehensive review of explainability techniques developed for GNNs. We focus on explainable graph neural networks and categorize them based on the use of explainable methods. We further provide the common performance metrics for GNNs explanations and point out several future research directions.
The dominating NLP paradigm of training a strong neural predictor to perform one task on a specific dataset has led to state-of-the-art performance in a variety of applications (eg. sentiment classification, span-prediction based question answering or machine translation). However, it builds upon the assumption that the data distribution is stationary, ie. that the data is sampled from a fixed distribution both at training and test time. This way of training is inconsistent with how we as humans are able to learn from and operate within a constantly changing stream of information. Moreover, it is ill-adapted to real-world use cases where the data distribution is expected to shift over the course of a model's lifetime. The first goal of this thesis is to characterize the different forms this shift can take in the context of natural language processing, and propose benchmarks and evaluation metrics to measure its effect on current deep learning architectures. We then proceed to take steps to mitigate the effect of distributional shift on NLP models. To this end, we develop methods based on parametric reformulations of the distributionally robust optimization framework. Empirically, we demonstrate that these approaches yield more robust models as demonstrated on a selection of realistic problems. In the third and final part of this thesis, we explore ways of efficiently adapting existing models to new domains or tasks. Our contribution to this topic takes inspiration from information geometry to derive a new gradient update rule which alleviate catastrophic forgetting issues during adaptation.
Deep neural networks (DNNs) are successful in many computer vision tasks. However, the most accurate DNNs require millions of parameters and operations, making them energy, computation and memory intensive. This impedes the deployment of large DNNs in low-power devices with limited compute resources. Recent research improves DNN models by reducing the memory requirement, energy consumption, and number of operations without significantly decreasing the accuracy. This paper surveys the progress of low-power deep learning and computer vision, specifically in regards to inference, and discusses the methods for compacting and accelerating DNN models. The techniques can be divided into four major categories: (1) parameter quantization and pruning, (2) compressed convolutional filters and matrix factorization, (3) network architecture search, and (4) knowledge distillation. We analyze the accuracy, advantages, disadvantages, and potential solutions to the problems with the techniques in each category. We also discuss new evaluation metrics as a guideline for future research.
Deep convolutional neural networks (CNNs) have recently achieved great success in many visual recognition tasks. However, existing deep neural network models are computationally expensive and memory intensive, hindering their deployment in devices with low memory resources or in applications with strict latency requirements. Therefore, a natural thought is to perform model compression and acceleration in deep networks without significantly decreasing the model performance. During the past few years, tremendous progress has been made in this area. In this paper, we survey the recent advanced techniques for compacting and accelerating CNNs model developed. These techniques are roughly categorized into four schemes: parameter pruning and sharing, low-rank factorization, transferred/compact convolutional filters, and knowledge distillation. Methods of parameter pruning and sharing will be described at the beginning, after that the other techniques will be introduced. For each scheme, we provide insightful analysis regarding the performance, related applications, advantages, and drawbacks etc. Then we will go through a few very recent additional successful methods, for example, dynamic capacity networks and stochastic depths networks. After that, we survey the evaluation matrix, the main datasets used for evaluating the model performance and recent benchmarking efforts. Finally, we conclude this paper, discuss remaining challenges and possible directions on this topic.
The era of big data provides researchers with convenient access to copious data. However, people often have little knowledge about it. The increasing prevalence of big data is challenging the traditional methods of learning causality because they are developed for the cases with limited amount of data and solid prior causal knowledge. This survey aims to close the gap between big data and learning causality with a comprehensive and structured review of traditional and frontier methods and a discussion about some open problems of learning causality. We begin with preliminaries of learning causality. Then we categorize and revisit methods of learning causality for the typical problems and data types. After that, we discuss the connections between learning causality and machine learning. At the end, some open problems are presented to show the great potential of learning causality with data.
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