Continuous-time event sequences represent discrete events occurring in continuous time. Such sequences arise frequently in real-life. Usually we expect the sequences to follow some regular pattern over time. However, sometimes these patterns may be interrupted by unexpected absence or occurrences of events. Identification of these unexpected cases can be very important as they may point to abnormal situations that need human attention. In this work, we study and develop methods for detecting outliers in continuous-time event sequences, including unexpected absence and unexpected occurrences of events. Since the patterns that event sequences tend to follow may change in different contexts, we develop outlier detection methods based on point processes that can take context information into account. Our methods are based on Bayesian decision theory and hypothesis testing with theoretical guarantees. To test the performance of the methods, we conduct experiments on both synthetic data and real-world clinical data and show the effectiveness of the proposed methods.
Electronic medical record (EMR) data contains historical sequences of visits of patients, and each visit contains rich information, such as patient demographics, hospital utilisation and medical codes, including diagnosis, procedure and medication codes. Most existing EMR embedding methods capture visit-code associations by constructing input visit representations as binary vectors with a static vocabulary of medical codes. With this limited representation, they fail in encapsulating rich attribute information of visits (demographics and utilisation information) and/or codes (e.g., medical code descriptions). Furthermore, current work considers visits of the same patient as discrete-time events and ignores time gaps between them. However, the time gaps between visits depict dynamics of the patient's medical history inducing varying influences on future visits. To address these limitations, we present $\mathtt{MedGraph}$, a supervised EMR embedding method that captures two types of information: (1) the visit-code associations in an attributed bipartite graph, and (2) the temporal sequencing of visits through a point process. $\mathtt{MedGraph}$ produces Gaussian embeddings for visits and codes to model the uncertainty. We evaluate the performance of $\mathtt{MedGraph}$ through an extensive experimental study and show that $\mathtt{MedGraph}$ outperforms state-of-the-art EMR embedding methods in several medical risk prediction tasks.
In high-stakes machine learning applications, it is crucial to not only perform well on average, but also when restricted to difficult examples. To address this, we consider the problem of training models in a risk-averse manner. We propose an adaptive sampling algorithm for stochastically optimizing the Conditional Value-at-Risk (CVaR) of a loss distribution, which measures its performance on the $\alpha$ fraction of most difficult examples. We use a distributionally robust formulation of the CVaR to phrase the problem as a zero-sum game between two players, and solve it efficiently using regret minimization. Our approach relies on sampling from structured Determinantal Point Processes (DPPs), which enables scaling it to large data sets. Finally, we empirically demonstrate its effectiveness on large-scale convex and non-convex learning tasks.
Temporal point processes are the dominant paradigm for modeling sequences of events happening at irregular intervals. The standard way of learning in such models is by estimating the conditional intensity function. However, parameterizing the intensity function usually incurs several trade-offs. We show how to overcome the limitations of intensity-based approaches by directly modeling the conditional distribution of inter-event times. We draw on the literature on normalizing flows to design models that are flexible and efficient. We additionally propose a simple mixture model that matches the flexibility of flow-based models, but also permits sampling and computing moments in closed form. The proposed models achieve state-of-the-art performance in standard prediction tasks and are suitable for novel applications, such as learning sequence embeddings and imputing missing data.
Various Seq2Seq learning models designed for machine translation were applied for abstractive summarization task recently. Despite these models provide high ROUGE scores, they are limited to generate comprehensive summaries with a high level of abstraction due to its degenerated attention distribution. We introduce Diverse Convolutional Seq2Seq Model(DivCNN Seq2Seq) using Determinantal Point Processes methods(Micro DPPs and Macro DPPs) to produce attention distribution considering both quality and diversity. Without breaking the end to end architecture, DivCNN Seq2Seq achieves a higher level of comprehensiveness compared to vanilla models and strong baselines. All the reproducible codes and datasets are available online.
Reasoning about graphs evolving over time is a challenging concept in many domains, such as bioinformatics, physics, and social networks. We consider a common case in which edges can be short term interactions (e.g., messaging) or long term structural connections (e.g., friendship). In practice, long term edges are often specified by humans. Human-specified edges can be both expensive to produce and suboptimal for the downstream task. To alleviate these issues, we propose a model based on temporal point processes and variational autoencoders that learns to infer temporal attention between nodes by observing node communication. As temporal attention drives between-node feature propagation, using the dynamics of node interactions to learn this key component provides more flexibility while simultaneously avoiding issues associated with human-specified edges. We also propose a bilinear transformation layer for pairs of node features instead of concatenation, typically used in prior work, and demonstrate its superior performance in all cases. In experiments on two datasets in the dynamic link prediction task, our model often outperforms the baseline model that requires a human-specified graph. Moreover, our learned attention is semantically interpretable and infers connections similar to actual graphs.
Data collection and labeling is one of the main challenges in employing machine learning algorithms in a variety of real-world applications with limited data. While active learning methods attempt to tackle this issue by labeling only the data samples that give high information, they generally suffer from large computational costs and are impractical in settings where data can be collected in parallel. Batch active learning methods attempt to overcome this computational burden by querying batches of samples at a time. To avoid redundancy between samples, previous works rely on some ad hoc combination of sample quality and diversity. In this paper, we present a new principled batch active learning method using Determinantal Point Processes, a repulsive point process that enables generating diverse batches of samples. We develop tractable algorithms to approximate the mode of a DPP distribution, and provide theoretical guarantees on the degree of approximation. We further demonstrate that an iterative greedy method for DPP maximization, which has lower computational costs but worse theoretical guarantees, still gives competitive results for batch active learning. Our experiments show the value of our methods on several datasets against state-of-the-art baselines.
We present a novel Neural Embedding Spatio-Temporal (NEST) point process model for spatio-temporal discrete event data and develop an efficient imitation learning (a type of reinforcement learning) based approach for model fitting. Despite the rapid development of one-dimensional temporal point processes for discrete event data, the study of spatial-temporal aspects of such data is relatively scarce. Our model captures complex spatio-temporal dependence between discrete events by carefully design a mixture of heterogeneous Gaussian diffusion kernels, whose parameters are parameterized by neural networks. This new kernel is the key that our model can capture intricate spatial dependence patterns and yet still lead to interpretable results as we examine maps of Gaussian diffusion kernel parameters. The imitation learning model fitting for the NEST is more robust than the maximum likelihood estimate. It directly measures the divergence between the empirical distributions between the training data and the model-generated data. Moreover, our imitation learning-based approach enjoys computational efficiency due to the explicit characterization of the reward function related to the likelihood function; furthermore, the likelihood function under our model enjoys tractable expression due to Gaussian kernel parameterization. Experiments based on real data show our method's good performance relative to the state-of-the-art and the good interpretability of NEST's result.
The most important obstacles facing multi-document summarization include excessive redundancy in source descriptions and the looming shortage of training data. These obstacles prevent encoder-decoder models from being used directly, but optimization-based methods such as determinantal point processes (DPPs) are known to handle them well. In this paper we seek to strengthen a DPP-based method for extractive multi-document summarization by presenting a novel similarity measure inspired by capsule networks. The approach measures redundancy between a pair of sentences based on surface form and semantic information. We show that our DPP system with improved similarity measure performs competitively, outperforming strong summarization baselines on benchmark datasets. Our findings are particularly meaningful for summarizing documents created by multiple authors containing redundant yet lexically diverse expressions.
Determinantal point processes (DPPs) have attracted substantial attention as an elegant probabilistic model that captures the balance between quality and diversity within sets. DPPs are conventionally parameterized by a positive semi-definite kernel matrix, and this symmetric kernel encodes only repulsive interactions between items. These so-called symmetric DPPs have significant expressive power, and have been successfully applied to a variety of machine learning tasks, including recommendation systems, information retrieval, and automatic summarization, among many others. Efficient algorithms for learning symmetric DPPs and sampling from these models have been reasonably well studied. However, relatively little attention has been given to nonsymmetric DPPs, which relax the symmetric constraint on the kernel. Nonsymmetric DPPs allow for both repulsive and attractive item interactions, which can significantly improve modeling power, resulting in a model that may better fit for some applications. We present a method that enables a tractable algorithm, based on maximum likelihood estimation, for learning nonsymmetric DPPs from data composed of observed subsets. Our method imposes a particular decomposition of the nonsymmetric kernel that enables such tractable learning algorithms, which we analyze both theoretically and experimentally. We evaluate our model on synthetic and real-world datasets, demonstrating improved predictive performance compared to symmetric DPPs, which have previously shown strong performance on modeling tasks associated with these datasets.
Many time series are effectively generated by a combination of deterministic continuous flows along with discrete jumps sparked by stochastic events. However, we usually do not have the equation of motion describing the flows, or how they are affected by jumps. To this end, we introduce Neural Jump Stochastic Differential Equations that provide a data-driven approach to learn continuous and discrete dynamic behavior, i.e., hybrid systems that both flow and jump. Our approach extends the framework of Neural Ordinary Differential Equations with a stochastic process term that models discrete events. We then model temporal point processes with a piecewise-continuous latent trajectory, where the discontinuities are caused by stochastic events whose conditional intensity depends on the latent state. We demonstrate the predictive capabilities of our model on a range of synthetic and real-world marked point process datasets, including classical point processes (such as Hawkes processes), awards on Stack Overflow, medical records, and earthquake monitoring.
Modeling and forecasting forward citations to a patent is a central task for the discovery of emerging technologies and for measuring the pulse of inventive progress. Conventional methods for forecasting these forward citations cast the problem as analysis of temporal point processes which rely on the conditional intensity of previously received citations. Recent approaches model the conditional intensity as a chain of recurrent neural networks to capture memory dependency in hopes of reducing the restrictions of the parametric form of the intensity function. For the problem of patent citations, we observe that forecasting a patent's chain of citations benefits from not only the patent's history itself but also from the historical citations of assignees and inventors associated with that patent. In this paper, we propose a sequence-to-sequence model which employs an attention-of-attention mechanism to capture the dependencies of these multiple time sequences. Furthermore, the proposed model is able to forecast both the timestamp and the category of a patent's next citation. Extensive experiments on a large patent citation dataset collected from USPTO demonstrate that the proposed model outperforms state-of-the-art models at forward citation forecasting.
A temporal point process is a mathematical model for a time series of discrete events, which covers various applications. Recently, recurrent neural network (RNN) based models have been developed for point processes and have been found effective. RNN based models usually assume a specific functional form for the time course of the intensity function of a point process (e.g., exponentially decreasing or increasing with the time since the most recent event). However, such an assumption can restrict the expressive power of the model. We herein propose a novel RNN based model in which the time course of the intensity function is represented in a general manner. In our approach, we first model the integral of the intensity function using a feedforward neural network and then obtain the intensity function as its derivative. This approach enables us to both obtain a flexible model of the intensity function and exactly evaluate the log-likelihood function, which contains the integral of the intensity function, without any numerical approximations. Our model achieves competitive or superior performances compared to the previous state-of-the-art methods for both synthetic and real datasets.
Machine learning models for repeated measurements are limited. Using topological data analysis (TDA), we present a classifier for repeated measurements which samples from the data space and builds a network graph based on the data topology. When applying this to two case studies, accuracy exceeds alternative models with additional benefits such as reporting data subsets with high purity along with feature values. For 300 examples of 3 tree species, the accuracy reached 80% after 30 datapoints, which was improved to 90% after increased sampling to 400 datapoints. Using data from 100 examples of each of 6 point processes, the classifier achieved 96.8% accuracy. In both datasets, the TDA classifier outperformed an alternative model. This algorithm and software can be beneficial for repeated measurement data common in biological sciences, as both an accurate classifier and a feature selection tool.
Gaussian processes are the leading class of distributions on random functions, but they suffer from well known issues including difficulty scaling and inflexibility with respect to certain shape constraints (such as nonnegativity). Here we propose Deep Random Splines, a flexible class of random functions obtained by transforming Gaussian noise through a deep neural network whose output are the parameters of a spline. Unlike Gaussian processes, Deep Random Splines allow us to readily enforce shape constraints while inheriting the richness and tractability of deep generative models. We also present an observational model for point process data which uses Deep Random Splines to model the intensity function of each point process and apply it to neural population data to obtain a low-dimensional representation of spiking activity. Inference is performed via a variational autoencoder that uses a novel recurrent encoder architecture that can handle multiple point processes as input. We use a newly collected dataset where a primate completes a pedaling task, and observe better dimensionality reduction with our model than with competing alternatives.
PoPPy is a Point Process toolbox based on PyTorch, which achieves flexible designing and efficient learning of point process models. It can be used for interpretable sequential data modeling and analysis, e.g., Granger causality analysis of multi-variate point processes, point process-based simulation and prediction of event sequences. In practice, the key points of point process-based sequential data modeling include: 1) How to design intensity functions to describe the mechanism behind observed data? 2) How to learn the proposed intensity functions from observed data? The goal of PoPPy is providing a user-friendly solution to the key points above and achieving large-scale point process-based sequential data analysis, simulation and prediction.
Determinantal point processes (DPPs) are specific probability distributions over clouds of points that are used as models and computational tools across physics, probability, statistics, and more recently machine learning. Sampling from DPPs is a challenge and therefore we present DPPy, a Python toolbox that gathers known exact and approximate sampling algorithms for both finite and continuous DPPs. The project is hosted on GitHub and equipped with an extensive documentation.
We here focus on the task of learning Granger causality matrices for multivariate point processes. In order to accomplish this task, our work is the first to explore the use of Wold processes. By doing so, we are able to develop asymptotically fast MCMC learning algorithms. With $N$ being the total number of events and $K$ the number of processes, our learning algorithm has a $O(N(\,\log(N)\,+\,\log(K)))$ cost per iteration. This is much faster than the $O(N^3\,K^2)$ or $O(K^3)$ for the state of the art. Our approach, called GrangerBusca, is validated on nine datasets. This is an advance in relation to most prior efforts which focus mostly on subsets of the Memetracker data. Regarding accuracy, GrangerBusca is three times more accurate (in Precision@10) than the state of the art for the commonly explored subsets Memetracker. Due to GrangerBusca's much lower training complexity, our approach is the only one able to train models for larger, full, sets of data.
Studying neural connectivity is considered one of the most promising and challenging areas of modern neuroscience. The underpinnings of cognition are hidden in the way neurons interact with each other. However, our experimental methods of studying real neural connections at a microscopic level are still arduous and costly. An efficient alternative is to infer connectivity based on the neuronal activations using computational methods. A reliable method for network inference, would not only facilitate research of neural circuits without the need of laborious experiments but also reveal insights on the underlying mechanisms of the brain. In this work, we perform a review of methods for neural circuit inference given the activation time series of the neural population. Approaching it from machine learning perspective, we divide the methodologies into unsupervised and supervised learning. The methods are based on correlation metrics, probabilistic point processes, and neural networks. Furthermore, we add a data mining methodology inspired by influence estimation in social networks as a new supervised learning approach. For comparison, we use the small version of the Chalearn Connectomics competition, that is accompanied with ground truth connections between neurons. The experiments indicate that unsupervised learning methods perform better, however, supervised methods could surpass them given enough data and resources.
When governed by underlying low-dimensional dynamics, the interdependence of simultaneously recorded population of neurons can be explained by a small number of shared factors, or a low-dimensional trajectory. Recovering these latent trajectories, particularly from single-trial population recordings, may help us understand the dynamics that drive neural computation. However, due to the biophysical constraints and noise in the spike trains, inferring trajectories from data is a challenging statistical problem in general. Here, we propose a practical and efficient inference method, called the variational latent Gaussian process (vLGP). The vLGP combines a generative model with a history-dependent point process observation together with a smoothness prior on the latent trajectories. The vLGP improves upon earlier methods for recovering latent trajectories, which assume either observation models inappropriate for point processes or linear dynamics. We compare and validate vLGP on both simulated datasets and population recordings from the primary visual cortex. In the V1 dataset, we find that vLGP achieves substantially higher performance than previous methods for predicting omitted spike trains, as well as capturing both the toroidal topology of visual stimuli space, and the noise-correlation. These results show that vLGP is a robust method with a potential to reveal hidden neural dynamics from large-scale neural recordings.