RetroGraph: Retrosynthetic Planning with Graph Search

Retrosynthetic planning, which aims to find a reaction pathway to synthesize a target molecule, plays an important role in chemistry and drug discovery. This task is usually modeled as a search problem. Recently, data-driven methods have attracted many research interests and shown promising results for retrosynthetic planning. We observe that the same intermediate molecules are visited many times in the searching process, and they are usually independently treated in previous tree-based methods (e.g., AND-OR tree search, Monte Carlo tree search). Such redundancies make the search process inefficient. We propose a graph-based search policy that eliminates the redundant explorations of any intermediate molecules. As searching over a graph is more complicated than over a tree, we further adopt a graph neural network to guide the search over graphs. Meanwhile, our method can search a batch of targets together in the graph and remove the inter-target duplication in the tree-based search methods. Experimental results on two datasets demonstrate the effectiveness of our method. Especially on the widely used USPTO benchmark, we improve the search success rate to 99.47%, advancing previous state-of-the-art performance for 2.6 points.

Triformer: Triangular, Variable-Specific Attentions for Long Sequence Multivariate Time Series Forecasting--Full Version

A variety of real-world applications rely on far future information to make decisions, thus calling for efficient and accurate long sequence multivariate time series forecasting. While recent attention-based forecasting models show strong abilities in capturing long-term dependencies, they still suffer from two key limitations. First, canonical self attention has a quadratic complexity w.r.t. the input time series length, thus falling short in efficiency. Second, different variables' time series often have distinct temporal dynamics, which existing studies fail to capture, as they use the same model parameter space, e.g., projection matrices, for all variables' time series, thus falling short in accuracy. To ensure high efficiency and accuracy, we propose Triformer, a triangular, variable-specific attention. (i) Linear complexity: we introduce a novel patch attention with linear complexity. When stacking multiple layers of the patch attentions, a triangular structure is proposed such that the layer sizes shrink exponentially, thus maintaining linear complexity. (ii) Variable-specific parameters: we propose a light-weight method to enable distinct sets of model parameters for different variables' time series to enhance accuracy without compromising efficiency and memory usage. Strong empirical evidence on four datasets from multiple domains justifies our design choices, and it demonstrates that Triformer outperforms state-of-the-art methods w.r.t. both accuracy and efficiency. This is an extended version of "Triformer: Triangular, Variable-Specific Attentions for Long Sequence Multivariate Time Series Forecasting", to appear in IJCAI 2022 [Cirstea et al., 2022a], including additional experimental results.

Weakly-supervised Temporal Path Representation Learning with Contrastive Curriculum Learning -- Extended Version

In step with the digitalization of transportation, we are witnessing a growing range of path-based smart-city applications, e.g., travel-time estimation and travel path ranking. A temporal path(TP) that includes temporal information, e.g., departure time, into the path is fundamental to enable such applications. In this setting, it is essential to learn generic temporal path representations(TPRs) that consider spatial and temporal correlations simultaneously and that can be used in different applications, i.e., downstream tasks. Existing methods fail to achieve the goal since (i) supervised methods require large amounts of task-specific labels when training and thus fail to generalize the obtained TPRs to other tasks; (ii) through unsupervised methods can learn generic representations, they disregard the temporal aspect, leading to sub-optimal results. To contend with the limitations of existing solutions, we propose a Weakly-Supervised Contrastive (WSC) learning model. We first propose a temporal path encoder that encodes both the spatial and temporal information of a temporal path into a TPR. To train the encoder, we introduce weak labels that are easy and inexpensive to obtain and are relevant to different tasks, e.g., temporal labels indicating peak vs. off-peak hours from departure times. Based on the weak labels, we construct meaningful positive and negative temporal path samples by considering both spatial and temporal information, which facilities training the encoder using contrastive learning by pulling closer to the positive samples' representations while pushing away the negative samples' representations. To better guide contrastive learning, we propose a learning strategy based on Curriculum Learning such that the learning performs from easy to hard training instances. Experiments studies verify the effectiveness of the proposed method.

Robust and Explainable Autoencoders for Unsupervised Time Series Outlier Detection---Extended Version

Time series data occurs widely, and outlier detection is a fundamental problem in data mining, which has numerous applications. Existing autoencoder-based approaches deliver state-of-the-art performance on challenging real-world data but are vulnerable to outliers and exhibit low explainability. To address these two limitations, we propose robust and explainable unsupervised autoencoder frameworks that decompose an input time series into a clean time series and an outlier time series using autoencoders. Improved explainability is achieved because clean time series are better explained with easy-to-understand patterns such as trends and periodicities. We provide insight into this by means of a post-hoc explainability analysis and empirical studies. In addition, since outliers are separated from clean time series iteratively, our approach offers improved robustness to outliers, which in turn improves accuracy. We evaluate our approach on five real-world datasets and report improvements over the state-of-the-art approaches in terms of robustness and explainability. This is an extended version of "Robust and Explainable Autoencoders for Unsupervised Time Series Outlier Detection", to appear in IEEE ICDE 2022.

Towards Spatio-Temporal Aware Traffic Time Series Forecasting--Full Version

Traffic time series forecasting is challenging due to complex spatio-temporal dynamics time series from different locations often have distinct patterns; and for the same time series, patterns may vary across time, where, for example, there exist certain periods across a day showing stronger temporal correlations. Although recent forecasting models, in particular deep learning based models, show promising results, they suffer from being spatio-temporal agnostic. Such spatio-temporal agnostic models employ a shared parameter space irrespective of the time series locations and the time periods and they assume that the temporal patterns are similar across locations and do not evolve across time, which may not always hold, thus leading to sub-optimal results. In this work, we propose a framework that aims at turning spatio-temporal agnostic models to spatio-temporal aware models. To do so, we encode time series from different locations into stochastic variables, from which we generate location-specific and time-varying model parameters to better capture the spatio-temporal dynamics. We show how to integrate the framework with canonical attentions to enable spatio-temporal aware attentions. Next, to compensate for the additional overhead introduced by the spatio-temporal aware model parameter generation process, we propose a novel window attention scheme, which helps reduce the complexity from quadratic to linear, making spatio-temporal aware attentions also have competitive efficiency. We show strong empirical evidence on four traffic time series datasets, where the proposed spatio-temporal aware attentions outperform state-of-the-art methods in term of accuracy and efficiency. This is an extended version of "Towards Spatio-Temporal Aware Traffic Time Series Forecasting", to appear in ICDE 2022 [1], including additional experimental results.

AutoCTS: Automated Correlated Time Series Forecasting -- Extended Version

Correlated time series (CTS) forecasting plays an essential role in many cyber-physical systems, where multiple sensors emit time series that capture interconnected processes. Solutions based on deep learning that deliver state-of-the-art CTS forecasting performance employ a variety of spatio-temporal (ST) blocks that are able to model temporal dependencies and spatial correlations among time series. However, two challenges remain. First, ST-blocks are designed manually, which is time consuming and costly. Second, existing forecasting models simply stack the same ST-blocks multiple times, which limits the model potential. To address these challenges, we propose AutoCTS that is able to automatically identify highly competitive ST-blocks as well as forecasting models with heterogeneous ST-blocks connected using diverse topologies, as opposed to the same ST-blocks connected using simple stacking. Specifically, we design both a micro and a macro search space to model possible architectures of ST-blocks and the connections among heterogeneous ST-blocks, and we provide a search strategy that is able to jointly explore the search spaces to identify optimal forecasting models. Extensive experiments on eight commonly used CTS forecasting benchmark datasets justify our design choices and demonstrate that AutoCTS is capable of automatically discovering forecasting models that outperform state-of-the-art human-designed models. This is an extended version of ``AutoCTS: Automated Correlated Time Series Forecasting'', to appear in PVLDB 2022.

Unsupervised Time Series Outlier Detection with Diversity-Driven Convolutional Ensembles -- Extended Version

With the sweeping digitalization of societal, medical, industrial, and scientific processes, sensing technologies are being deployed that produce increasing volumes of time series data, thus fueling a plethora of new or improved applications. In this setting, outlier detection is frequently important, and while solutions based on neural networks exist, they leave room for improvement in terms of both accuracy and efficiency. With the objective of achieving such improvements, we propose a diversity-driven, convolutional ensemble. To improve accuracy, the ensemble employs multiple basic outlier detection models built on convolutional sequence-to-sequence autoencoders that can capture temporal dependencies in time series. Further, a novel diversity-driven training method maintains diversity among the basic models, with the aim of improving the ensemble's accuracy. To improve efficiency, the approach enables a high degree of parallelism during training. In addition, it is able to transfer some model parameters from one basic model to another, which reduces training time. We report on extensive experiments using real-world multivariate time series that offer insight into the design choices underlying the new approach and offer evidence that it is capable of improved accuracy and efficiency. This is an extended version of "Unsupervised Time Series Outlier Detection with Diversity-Driven Convolutional Ensembles", to appear in PVLDB 2022.

Unsupervised Path Representation Learning with Curriculum Negative Sampling

Path representations are critical in a variety of transportation applications, such as estimating path ranking in path recommendation systems and estimating path travel time in navigation systems. Existing studies often learn task-specific path representations in a supervised manner, which require a large amount of labeled training data and generalize poorly to other tasks. We propose an unsupervised learning framework Path InfoMax (PIM) to learn generic path representations that work for different downstream tasks. We first propose a curriculum negative sampling method, for each input path, to generate a small amount of negative paths, by following the principles of curriculum learning. Next, \emph{PIM} employs mutual information maximization to learn path representations from both a global and a local view. In the global view, PIM distinguishes the representations of the input paths from those of the negative paths. In the local view, \emph{PIM} distinguishes the input path representations from the representations of the nodes that appear only in the negative paths. This enables the learned path representations to encode both global and local information at different scales. Extensive experiments on two downstream tasks, ranking score estimation and travel time estimation, using two road network datasets suggest that PIM significantly outperforms other unsupervised methods and is also able to be used as a pre-training method to enhance supervised path representation learning.

Graph Attention Recurrent Neural Networks for Correlated Time Series Forecasting -- Full version

We consider a setting where multiple entities inter-act with each other over time and the time-varying statuses of the entities are represented as multiple correlated time series. For example, speed sensors are deployed in different locations in a road network, where the speed of a specific location across time is captured by the corresponding sensor as a time series, resulting in multiple speed time series from different locations, which are often correlated. To enable accurate forecasting on correlated time series, we proposes graph attention recurrent neural networks.First, we build a graph among different entities by taking into account spatial proximity and employ a multi-head attention mechanism to derive adaptive weight matrices for the graph to capture the correlations among vertices (e.g., speeds at different locations) at different timestamps. Second, we employ recurrent neural networks to take into account temporal dependency while taking into account the adaptive weight matrices learned from the first step to consider the correlations among time series.Experiments on a large real-world speed time series data set suggest that the proposed method is effective and outperforms the state-of-the-art in most settings. This manuscript provides a full version of a workshop paper [1].