The state-space models (SSMs) are widely utilized in the analysis of time-series data. SSMs rely on an explicit definition of the state and observation processes. Characterizing these processes is not always easy and becomes a modeling challenge when the dimension of observed data grows or the observed data distribution deviates from the normal distribution. Here, we propose a new formulation of SSM for high-dimensional observation processes. We call this solution the deep direct discriminative decoder (D4). The D4 brings deep neural networks' expressiveness and scalability to the SSM formulation letting us build a novel solution that efficiently estimates the underlying state processes through high-dimensional observation signal. We demonstrate the D4 solutions in simulated and real data such as Lorenz attractors, Langevin dynamics, random walk dynamics, and rat hippocampus spiking neural data and show that the D4 performs better than traditional SSMs and RNNs. The D4 can be applied to a broader class of time-series data where the connection between high-dimensional observation and the underlying latent process is hard to characterize.

The ability to design novel proteins with higher fitness on a given task would be revolutionary for many fields of medicine. However, brute-force search through the combinatorially large space of sequences is infeasible. Prior methods constrain search to a small mutational radius from a reference sequence, but such heuristics drastically limit the design space. Our work seeks to remove the restriction on mutational distance while enabling efficient exploration. We propose Gibbs sampling with Graph-based Smoothing (GGS) which iteratively applies Gibbs with gradients to propose advantageous mutations using graph-based smoothing to remove noisy gradients that lead to false positives. Our method is state-of-the-art in discovering high-fitness proteins with up to 8 mutations from the training set. We study the GFP and AAV design problems, ablations, and baselines to elucidate the results.

Recent advances in deep learning have shown that uncertainty estimation is becoming increasingly important in applications such as medical imaging, natural language processing, and autonomous systems. However, accurately quantifying uncertainty remains a challenging problem, especially in regression tasks where the output space is continuous. Deep learning approaches that allow uncertainty estimation for regression problems often converge slowly and yield poorly calibrated uncertainty estimates that can not be effectively used for quantification. Recently proposed post hoc calibration techniques are seldom applicable to regression problems and often add overhead to an already slow model training phase. This work presents a fast calibrated uncertainty estimation method for regression tasks called Likelihood Annealing, that consistently improves the convergence of deep regression models and yields calibrated uncertainty without any post hoc calibration phase. Unlike previous methods for calibrated uncertainty in regression that focus only on low-dimensional regression problems, our method works well on a broad spectrum of regression problems, including high-dimensional regression. Our empirical analysis shows that our approach is generalizable to various network architectures, including multilayer perceptrons, 1D/2D convolutional networks, and graph neural networks, on five vastly diverse tasks, i.e., chaotic particle trajectory denoising, physical property prediction of molecules using 3D atomistic representation, natural image super-resolution, and medical image translation using MRI.

The difficulties of automatic extraction of definitions and methods from scientific documents lie in two aspects: (1) the complexity and diversity of natural language texts, which requests an analysis method to support the discovery of pattern; and, (2) a complete definition or method represented by a scientific paper is usually distributed within text, therefore an effective approach should not only extract single sentence definitions and methods but also integrate the sentences to obtain a complete definition or method. This paper proposes an analysis method for discovering patterns of definition and method and uses the method to discover patterns of definition and method. Completeness of the patterns at the semantic level is guaranteed by a complete set of semantic relations that identify definitions and methods respectively. The completeness of the patterns at the syntactic and lexical levels is guaranteed by syntactic and lexical constraints. Experiments on the self-built dataset and two public definition datasets show that the discovered patterns are effective. The patterns can be used to extract definitions and methods from scientific documents and can be tailored or extended to suit other applications.

In this paper, we introduce a novel causal structure learning algorithm called Endogenous and Exogenous Markov Blankets Intersection (EEMBI), which combines the properties of Bayesian networks and Structural Causal Models (SCM). Exogenous variables are special variables that are applied in SCM. We find that exogenous variables have some special characteristics and these characteristics are still useful under the property of the Bayesian network. EEMBI intersects the Markov blankets of exogenous variables and Markov blankets of endogenous variables, i.e. the original variables, to remove the irrelevant connections and find the true causal structure theoretically. Furthermore, we propose an extended version of EEMBI, namely EEMBI-PC, which integrates the last step of the PC algorithm into EEMBI. This modification enhances the algorithm's performance by leveraging the strengths of both approaches. Plenty of experiments are provided to prove that EEMBI and EEMBI-PC have state-of-the-art performance on both discrete and continuous datasets.

Diffusion on graphs is ubiquitous with numerous high-impact applications. In these applications, complete diffusion histories play an essential role in terms of identifying dynamical patterns, reflecting on precaution actions, and forecasting intervention effects. Despite their importance, complete diffusion histories are rarely available and are highly challenging to reconstruct due to ill-posedness, explosive search space, and scarcity of training data. To date, few methods exist for diffusion history reconstruction. They are exclusively based on the maximum likelihood estimation (MLE) formulation and require to know true diffusion parameters. In this paper, we study an even harder problem, namely reconstructing Diffusion history from A single SnapsHot} (DASH), where we seek to reconstruct the history from only the final snapshot without knowing true diffusion parameters. We start with theoretical analyses that reveal a fundamental limitation of the MLE formulation. We prove: (a) estimation error of diffusion parameters is unavoidable due to NP-hardness of diffusion parameter estimation, and (b) the MLE formulation is sensitive to estimation error of diffusion parameters. To overcome the inherent limitation of the MLE formulation, we propose a novel barycenter formulation: finding the barycenter of the posterior distribution of histories, which is provably stable against the estimation error of diffusion parameters. We further develop an effective solver named DIffusion hiTting Times with Optimal proposal (DITTO) by reducing the problem to estimating posterior expected hitting times via the Metropolis--Hastings Markov chain Monte Carlo method (M--H MCMC) and employing an unsupervised graph neural network to learn an optimal proposal to accelerate the convergence of M--H MCMC. We conduct extensive experiments to demonstrate the efficacy of the proposed method.

Annotation quality and quantity positively affect the learning performance of sequence labeling, a vital task in Natural Language Processing. Hiring domain experts to annotate a corpus is very costly in terms of money and time. Crowdsourcing platforms, such as Amazon Mechanical Turk (AMT), have been deployed to assist in this purpose. However, the annotations collected this way are prone to human errors due to the lack of expertise of the crowd workers. Existing literature in annotation aggregation assumes that annotations are independent and thus faces challenges when handling the sequential label aggregation tasks with complex dependencies. To conquer the challenges, we propose an optimization-based method that infers the ground truth labels using annotations provided by workers for sequential labeling tasks. The proposed Aggregation method for Sequential Labels from Crowds ($AggSLC$) jointly considers the characteristics of sequential labeling tasks, workers' reliabilities, and advanced machine learning techniques. Theoretical analysis on the algorithm's convergence further demonstrates that the proposed $AggSLC$ halts after a finite number of iterations. We evaluate $AggSLC$ on different crowdsourced datasets for Named Entity Recognition (NER) tasks and Information Extraction tasks in biomedical (PICO), as well as a simulated dataset. Our results show that the proposed method outperforms the state-of-the-art aggregation methods. To achieve insights into the framework, we study the effectiveness of $AggSLC$'s components through ablation studies.

Climate change is the defining issue of our time, and we are at a defining moment. Various interest groups, social movement organizations, and individuals engage in collective action on this issue on social media. In addition, issue advocacy campaigns on social media often arise in response to ongoing societal concerns, especially those faced by energy industries. Our goal in this paper is to analyze how those industries, their advocacy group, and climate advocacy group use social media to influence the narrative on climate change. In this work, we propose a minimally supervised model soup [57] approach combined with messaging themes to identify the stances of climate ads on Facebook. Finally, we release our stance dataset, model, and set of themes related to climate campaigns for future work on opinion mining and the automatic detection of climate change stances.

To comprehend complex systems with multiple states, it is imperative to reveal the identity of these states by system outputs. Nevertheless, the mathematical models describing these systems often exhibit nonlinearity so that render the resolution of the parameter inverse problem from the observed spatiotemporal data a challenging endeavor. Starting from the observed data obtained from such systems, we propose a novel framework that facilitates the investigation of parameter identification for multi-state systems governed by spatiotemporal varying parametric partial differential equations. Our framework consists of two integral components: a constrained self-adaptive physics-informed neural network, encompassing a sub-network, as our methodology for parameter identification, and a finite mixture model approach to detect regions of probable parameter variations. Through our scheme, we can precisely ascertain the unknown varying parameters of the complex multi-state system, thereby accomplishing the inversion of the varying parameters. Furthermore, we have showcased the efficacy of our framework on two numerical cases: the 1D Burgers' equation with time-varying parameters and the 2D wave equation with a space-varying parameter.

Statistical relational AI and probabilistic logic programming have so far mostly focused on discrete probabilistic models. The reasons for this is that one needs to provide constructs to succinctly model the independencies in such models, and also provide efficient inference. Three types of independencies are important to represent and exploit for scalable inference in hybrid models: conditional independencies elegantly modeled in Bayesian networks, context-specific independencies naturally represented by logical rules, and independencies amongst attributes of related objects in relational models succinctly expressed by combining rules. This paper introduces a hybrid probabilistic logic programming language, DC#, which integrates distributional clauses' syntax and semantics principles of Bayesian logic programs. It represents the three types of independencies qualitatively. More importantly, we also introduce the scalable inference algorithm FO-CS-LW for DC#. FO-CS-LW is a first-order extension of the context-specific likelihood weighting algorithm (CS-LW), a novel sampling method that exploits conditional independencies and context-specific independencies in ground models. The FO-CS-LW algorithm upgrades CS-LW with unification and combining rules to the first-order case.