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The generation of small molecule candidate (ligand) binding poses in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more accurate pose generation using molecular dynamics is hindered by slow protein dynamics. We develop a tiered tensor transform (3T) algorithm to rapidly generate diverse protein-ligand complex conformations for both pose and affinity estimation in drug screening, requiring neither machine learning training nor lengthy dynamics computation, while maintaining both coarse-grain-like coordinated protein dynamics and atomistic-level details of the complex pocket. The 3T conformation structures we generate achieve significantly higher accuracy in active ligand classification than traditional ensemble docking using hundreds of experimental protein conformations. Furthermore, we demonstrate that 3T can be used to explore distant protein-ligand binding poses within the protein pocket. 3T structure transformation is decoupled from the system physics, making future usage in other computational scientific domains possible.

The ability to learn new concepts sequentially is a major weakness for modern neural networks, which hinders their use in non-stationary environments. Their propensity to fit the current data distribution to the detriment of the past acquired knowledge leads to the catastrophic forgetting issue. In this work we tackle the problem of Spoken Language Understanding applied to a continual learning setting. We first define a class-incremental scenario for the SLURP dataset. Then, we propose three knowledge distillation (KD) approaches to mitigate forgetting for a sequence-to-sequence transformer model: the first KD method is applied to the encoder output (audio-KD), and the other two work on the decoder output, either directly on the token-level (tok-KD) or on the sequence-level (seq-KD) distributions. We show that the seq-KD substantially improves all the performance metrics, and its combination with the audio-KD further decreases the average WER and enhances the entity prediction metric.

The practical utility of causality in decision-making is widespread and brought about by the intertwining of causal discovery and causal inference. Nevertheless, a notable gap exists in the evaluation of causal discovery methods, where insufficient emphasis is placed on downstream inference. To address this gap, we evaluate seven established baseline causal discovery methods including a newly proposed method based on GFlowNets, on the downstream task of treatment effect estimation. Through the implementation of a distribution-level evaluation, we offer valuable and unique insights into the efficacy of these causal discovery methods for treatment effect estimation, considering both synthetic and real-world scenarios, as well as low-data scenarios. The results of our study demonstrate that some of the algorithms studied are able to effectively capture a wide range of useful and diverse ATE modes, while some tend to learn many low-probability modes which impacts the (unrelaxed) recall and precision.

The effective control of infectious diseases relies on accurate assessment of the impact of interventions, which is often hindered by the complex dynamics of the spread of disease. We propose a Beta-Dirichlet switching state-space transmission model to track underlying dynamics of disease and evaluate the effectiveness of interventions simultaneously. As time evolves, the switching mechanism introduced in the susceptible-exposed-infected-recovered (SEIR) model is able to capture the timing and magnitude of changes in the transmission rate due to the effectiveness of control measures. The implementation of this model is based on a particle Markov Chain Monte Carlo algorithm, which can estimate the time evolution of SEIR states, switching states, and high-dimensional parameters efficiently. The efficacy of our model and estimation procedure are demonstrated through simulation studies. With a real-world application to British Columbia's COVID-19 outbreak, it indicates approximately a 66.6\% reduction of transmission rate following interventions such as distancing, closures and vaccination. Our proposed model provides a promising tool to inform public health policies aimed at studying the underlying dynamics and evaluating of the effectiveness of interventions during the spread of the disease.

The impact of text length on the estimation of lexical diversity has captured the attention of the scientific community for more than a century. Numerous indices have been proposed, and many studies have been conducted to evaluate them, but the problem remains. This methodological review provides a critical analysis not only of the most commonly used indices in language learning studies, but also of the length problem itself, as well as of the methodology for evaluating the proposed solutions. The analysis of three datasets of English language-learners' texts revealed that indices that reduce all texts to the same length using a probabilistic or an algorithmic approach solve the length dependency problem; however, all these indices failed to address the second problem, which is their sensitivity to the parameter that determines the length to which the texts are reduced. The paper concludes with recommendations for optimizing lexical diversity analysis.

In recurrent neural networks, learning long-term dependency is the main difficulty due to the vanishing and exploding gradient problem. Many researchers are dedicated to solving this issue and they proposed many algorithms. Although these algorithms have achieved great success, understanding how the information decays remains an open problem. In this paper, we study the dynamics of the hidden state in recurrent neural networks. We propose a new perspective to analyze the hidden state space based on an eigen decomposition of the weight matrix. We start the analysis by linear state space model and explain the function of preserving information in activation functions. We provide an explanation for long-term dependency based on the eigen analysis. We also point out the different behavior of eigenvalues for regression tasks and classification tasks. From the observations on well-trained recurrent neural networks, we proposed a new initialization method for recurrent neural networks, which improves consistently performance. It can be applied to vanilla-RNN, LSTM, and GRU. We test on many datasets, such as Tomita Grammars, pixel-by-pixel MNIST datasets, and machine translation datasets (Multi30k). It outperforms the Xavier initializer and kaiming initializer as well as other RNN-only initializers like IRNN and sp-RNN in several tasks.

Accurate load forecasting plays a vital role in numerous sectors, but accurately capturing the complex dynamics of dynamic power systems remains a challenge for traditional statistical models. For these reasons, time-series models (ARIMA) and deep-learning models (ANN, LSTM, GRU, etc.) are commonly deployed and often experience higher success. In this paper, we analyze the efficacy of the recently developed Transformer-based Neural Network model in Load forecasting. Transformer models have the potential to improve Load forecasting because of their ability to learn long-range dependencies derived from their Attention Mechanism. We apply several metaheuristics namely Differential Evolution to find the optimal hyperparameters of the Transformer-based Neural Network to produce accurate forecasts. Differential Evolution provides scalable, robust, global solutions to non-differentiable, multi-objective, or constrained optimization problems. Our work compares the proposed Transformer based Neural Network model integrated with different metaheuristic algorithms by their performance in Load forecasting based on numerical metrics such as Mean Squared Error (MSE) and Mean Absolute Percentage Error (MAPE). Our findings demonstrate the potential of metaheuristic-enhanced Transformer-based Neural Network models in Load forecasting accuracy and provide optimal hyperparameters for each model.

Finding abnormal lymph nodes in radiological images is highly important for various medical tasks such as cancer metastasis staging and radiotherapy planning. Lymph nodes (LNs) are small glands scattered throughout the body. They are grouped or defined to various LN stations according to their anatomical locations. The CT imaging appearance and context of LNs in different stations vary significantly, posing challenges for automated detection, especially for pathological LNs. Motivated by this observation, we propose a novel end-to-end framework to improve LN detection performance by leveraging their station information. We design a multi-head detector and make each head focus on differentiating the LN and non-LN structures of certain stations. Pseudo station labels are generated by an LN station classifier as a form of multi-task learning during training, so we do not need another explicit LN station prediction model during inference. Our algorithm is evaluated on 82 patients with lung cancer and 91 patients with esophageal cancer. The proposed implicit station stratification method improves the detection sensitivity of thoracic lymph nodes from 65.1% to 71.4% and from 80.3% to 85.5% at 2 false positives per patient on the two datasets, respectively, which significantly outperforms various existing state-of-the-art baseline techniques such as nnUNet, nnDetection and LENS.

Video-assisted transoral tracheal intubation (TI) necessitates using an endoscope that helps the physician insert a tracheal tube into the glottis instead of the esophagus. The growing trend of robotic-assisted TI would require a medical robot to distinguish anatomical features like an experienced physician which can be imitated by utilizing supervised deep-learning techniques. However, the real datasets of oropharyngeal organs are often inaccessible due to limited open-source data and patient privacy. In this work, we propose a domain adaptive Sim-to-Real framework called IoU-Ranking Blend-ArtFlow (IRB-AF) for image segmentation of oropharyngeal organs. The framework includes an image blending strategy called IoU-Ranking Blend (IRB) and style-transfer method ArtFlow. Here, IRB alleviates the problem of poor segmentation performance caused by significant datasets domain differences; while ArtFlow is introduced to reduce the discrepancies between datasets further. A virtual oropharynx image dataset generated by the SOFA framework is used as the learning subject for semantic segmentation to deal with the limited availability of actual endoscopic images. We adapted IRB-AF with the state-of-the-art domain adaptive segmentation models. The results demonstrate the superior performance of our approach in further improving the segmentation accuracy and training stability.

We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.