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Recent years have seen rapid progress at the intersection between causality and machine learning. Motivated by scientific applications involving high-dimensional data, in particular in biomedicine, we propose a deep neural architecture for learning causal relationships between variables from a combination of empirical data and prior causal knowledge. We combine convolutional and graph neural networks within a causal risk framework to provide a flexible and scalable approach. Empirical results include linear and nonlinear simulations (where the underlying causal structures are known and can be directly compared against), as well as a real biological example where the models are applied to high-dimensional molecular data and their output compared against entirely unseen validation experiments. These results demonstrate the feasibility of using deep learning approaches to learn causal networks in large-scale problems spanning thousands of variables.

Unsupervised discretization is a crucial step in many knowledge discovery tasks. The state-of-the-art method for one-dimensional data infers locally adaptive histograms using the minimum description length (MDL) principle, but the multi-dimensional case is far less studied: current methods consider the dimensions one at a time (if not independently), which result in discretizations based on rectangular cells of adaptive size. Unfortunately, this approach is unable to adequately characterize dependencies among dimensions and/or results in discretizations consisting of more cells (or bins) than is desirable. To address this problem, we propose an expressive model class that allows for far more flexible partitions of two-dimensional data. We extend the state of the art for the one-dimensional case to obtain a model selection problem based on the normalized maximum likelihood, a form of refined MDL. As the flexibility of our model class comes at the cost of a vast search space, we introduce a heuristic algorithm, named PALM, which Partitions each dimension ALternately and then Merges neighboring regions, all using the MDL principle. Experiments on synthetic data show that PALM 1) accurately reveals ground truth partitions that are within the model class (i.e., the search space), given a large enough sample size; 2) approximates well a wide range of partitions outside the model class; 3) converges, in contrast to the state-of-the-art multivariate discretization method IPD. Finally, we apply our algorithm to three spatial datasets, and we demonstrate that, compared to kernel density estimation (KDE), our algorithm not only reveals more detailed density changes, but also fits unseen data better, as measured by the log-likelihood.

We propose a data-driven mean-curvature solver for the level-set method. This work is the natural extension to $\mathbb{R}^3$ of our two-dimensional strategy in [DOI: 10.1007/s10915-022-01952-2][1] and the hybrid inference system of [DOI: 10.1016/j.jcp.2022.111291][2]. However, in contrast to [1,2], which built resolution-dependent neural-network dictionaries, here we develop a pair of models in $\mathbb{R}^3$, regardless of the mesh size. Our feedforward networks ingest transformed level-set, gradient, and curvature data to fix numerical mean-curvature approximations selectively for interface nodes. To reduce the problem's complexity, we have used the Gaussian curvature to classify stencils and fit our models separately to non-saddle and saddle patterns. Non-saddle stencils are easier to handle because they exhibit a curvature error distribution characterized by monotonicity and symmetry. While the latter has allowed us to train only on half the mean-curvature spectrum, the former has helped us blend the data-driven and the baseline estimations seamlessly near flat regions. On the other hand, the saddle-pattern error structure is less clear; thus, we have exploited no latent information beyond what is known. In this regard, we have trained our models on not only spherical but also sinusoidal and hyperbolic paraboloidal patches. Our approach to building their data sets is systematic but gleans samples randomly while ensuring well-balancedness. We have also resorted to standardization and dimensionality reduction and integrated regularization to minimize outliers. In addition, we leverage curvature rotation/reflection invariance to improve precision at inference time. Several experiments confirm that our proposed system can yield more accurate mean-curvature estimations than modern particle-based interface reconstruction and level-set schemes around under-resolved regions.

Graphical models have long been studied in statistics as a tool for inferring conditional independence relationships among a large set of random variables. The most existing works in graphical modeling focus on the cases that the data are Gaussian or mixed and the variables are linearly dependent. In this paper, we propose a double regression method for learning graphical models under the high-dimensional nonlinear and non-Gaussian setting, and prove that the proposed method is consistent under mild conditions. The proposed method works by performing a series of nonparametric conditional independence tests. The conditioning set of each test is reduced via a double regression procedure where a model-free sure independence screening procedure or a sparse deep neural network can be employed. The numerical results indicate that the proposed method works well for high-dimensional nonlinear and non-Gaussian data.

The occurrence of vacuum arcs or radio frequency (rf) breakdowns is one of the most prevalent factors limiting the high-gradient performance of normal conducting rf cavities in particle accelerators. In this paper, we search for the existence of previously unrecognized features related to the incidence of rf breakdowns by applying a machine learning strategy to high-gradient cavity data from CERN's test stand for the Compact Linear Collider (CLIC). By interpreting the parameters of the learned models with explainable artificial intelligence (AI), we reverse-engineer physical properties for deriving fast, reliable, and simple rule-based models. Based on 6 months of historical data and dedicated experiments, our models show fractions of data with a high influence on the occurrence of breakdowns. Specifically, it is shown that the field emitted current following an initial breakdown is closely related to the probability of another breakdown occurring shortly thereafter. Results also indicate that the cavity pressure should be monitored with increased temporal resolution in future experiments, to further explore the vacuum activity associated with breakdowns.

This paper proposes a novel approach to explain the predictions made by data-driven methods. Since such predictions rely heavily on the data used for training, explanations that convey information about how the training data affects the predictions are useful. The paper proposes a novel approach to quantify how different data-clusters of the training data affect a prediction. The quantification is based on Shapley values, a concept which originates from coalitional game theory, developed to fairly distribute the payout among a set of cooperating players. A player's Shapley value is a measure of that player's contribution. Shapley values are often used to quantify feature importance, ie. how features affect a prediction. This paper extends this to cluster importance, letting clusters of the training data act as players in a game where the predictions are the payouts. The novel methodology proposed in this paper lets us explore and investigate how different clusters of the training data affect the predictions made by any black-box model, allowing new aspects of the reasoning and inner workings of a prediction model to be conveyed to the users. The methodology is fundamentally different from existing explanation methods, providing insight which would not be available otherwise, and should complement existing explanation methods, including explanations based on feature importance.

Agent-based model (ABM) has been widely used to study infectious disease transmission by simulating behaviors and interactions of autonomous individuals called agents. In the ABM, agent states, for example infected or susceptible, are assigned according to a set of simple rules, and a complex dynamics of disease transmission is described by the collective states of agents over time. Despite the flexibility in real-world modeling, ABMs have received less attention by statisticians because of the intractable likelihood functions which lead to difficulty in estimating parameters and quantifying uncertainty around model outputs. To overcome this limitation, we propose to treat the entire system as a Hidden Markov Model and develop the ABM for infectious disease transmission within the Bayesian framework. The hidden states in the model are represented by individual agent's states over time. We estimate the hidden states and the parameters associated with the model by applying particle Markov Chain Monte Carlo algorithm. Performance of the approach for parameter recovery and prediction along with sensitivity to prior assumptions are evaluated under various simulation conditions. Finally, we apply the proposed approach to the study of COVID-19 outbreak on Diamond Princess cruise ship and examine the differences in transmission by key demographic characteristics, while considering different network structures and the limitations of COVID-19 testing in the cruise.

We consider semi-supervised binary classification for applications in which data points are naturally grouped (e.g., survey responses grouped by state) and the labeled data is biased (e.g., survey respondents are not representative of the population). The groups overlap in the feature space and consequently the input-output patterns are related across the groups. To model the inherent structure in such data, we assume the partition-projected class-conditional invariance across groups, defined in terms of the group-agnostic feature space. We demonstrate that under this assumption, the group carries additional information about the class, over the group-agnostic features, with provably improved area under the ROC curve. Further assuming invariance of partition-projected class-conditional distributions across both labeled and unlabeled data, we derive a semi-supervised algorithm that explicitly leverages the structure to learn an optimal, group-aware, probability-calibrated classifier, despite the bias in the labeled data. Experiments on synthetic and real data demonstrate the efficacy of our algorithm over suitable baselines and ablative models, spanning standard supervised and semi-supervised learning approaches, with and without incorporating the group directly as a feature.

Deep semantic matching aims to discriminate the relationship between documents based on deep neural networks. In recent years, it becomes increasingly popular to organize documents with a graph structure, then leverage both the intrinsic document features and the extrinsic neighbor features to derive discrimination. Most of the existing works mainly care about how to utilize the presented neighbors, whereas limited effort is made to filter appropriate neighbors. We argue that the neighbor features could be highly noisy and partially useful. Thus, a lack of effective neighbor selection will not only incur a great deal of unnecessary computation cost, but also restrict the matching accuracy severely. In this work, we propose a novel framework, Cascaded Deep Semantic Matching (CDSM), for accurate and efficient semantic matching on textual graphs. CDSM is highlighted for its two-stage workflow. In the first stage, a lightweight CNN-based ad-hod neighbor selector is deployed to filter useful neighbors for the matching task with a small computation cost. We design both one-step and multi-step selection methods. In the second stage, a high-capacity graph-based matching network is employed to compute fine-grained relevance scores based on the well-selected neighbors. It is worth noting that CDSM is a generic framework which accommodates most of the mainstream graph-based semantic matching networks. The major challenge is how the selector can learn to discriminate the neighbors usefulness which has no explicit labels. To cope with this problem, we design a weak-supervision strategy for optimization, where we train the graph-based matching network at first and then the ad-hoc neighbor selector is learned on top of the annotations from the matching network.

While reinforcement learning (RL) has become a more popular approach for robotics, designing sufficiently informative reward functions for complex tasks has proven to be extremely difficult due their inability to capture human intent and policy exploitation. Preference based RL algorithms seek to overcome these challenges by directly learning reward functions from human feedback. Unfortunately, prior work either requires an unreasonable number of queries implausible for any human to answer or overly restricts the class of reward functions to guarantee the elicitation of the most informative queries, resulting in models that are insufficiently expressive for realistic robotics tasks. Contrary to most works that focus on query selection to \emph{minimize} the amount of data required for learning reward functions, we take an opposite approach: \emph{expanding} the pool of available data by viewing human-in-the-loop RL through the more flexible lens of multi-task learning. Motivated by the success of meta-learning, we pre-train preference models on prior task data and quickly adapt them for new tasks using only a handful of queries. Empirically, we reduce the amount of online feedback needed to train manipulation policies in Meta-World by 20$\times$, and demonstrate the effectiveness of our method on a real Franka Panda Robot. Moreover, this reduction in query-complexity allows us to train robot policies from actual human users. Videos of our results and code can be found at //sites.google.com/view/few-shot-preference-rl/home.