The objective of this paper is to provide an introduction to the principles of Bayesian joint modeling of longitudinal measurements and time-to-event outcomes, as well as model implementation using the BUGS language syntax. This syntax can be executed directly using OpenBUGS or by utilizing convenient functions to invoke OpenBUGS and JAGS from R software. In this paper, all details of joint models are provided, ranging from simple to more advanced models. The presentation started with the joint modeling of a Gaussian longitudinal marker and time-to-event outcome. The implementation of the Bayesian paradigm of the model is reviewed. The strategies for simulating data from the JM are also discussed. A proportional hazard model with various forms of baseline hazards, along with the discussion of all possible association structures between the two sub-models are taken into consideration. The paper covers joint models with multivariate longitudinal measurements, zero-inflated longitudinal measurements, competing risks, and time-to-event with cure fraction. The models are illustrated by the analyses of several real data sets. All simulated and real data and code are available at \url{//github.com/tbaghfalaki/JM-with-BUGS-and-JAGS}.
This paper constructs an algorithmic framework for adaptively achieving the mechanism design objective, finding a mechanism inducing socially optimal Nash equilibria, without knowledge of the utility functions of the agents. We consider a probing scheme where the designer can iteratively enact mechanisms and observe Nash equilibria responses. We first derive necessary and sufficient conditions, taking the form of linear program feasibility, for the existence of utility functions under which the empirical Nash equilibria responses are socially optimal. Then, we utilize this to construct a loss function with respect to the mechanism, and show that its global minimization occurs at mechanisms under which Nash equilibria system responses are also socially optimal. We develop a simulated annealing-based gradient algorithm, and prove that it converges in probability to this set of global minima, thus achieving adaptive mechanism design.
Randomization tests rely on simple data transformations and possess an appealing robustness property. In addition to being finite-sample valid if the data distribution is invariant under the transformation, these tests can be asymptotically valid under a suitable studentization of the test statistic, even if the invariance does not hold. However, practical implementation often encounters noisy data, resulting in approximate randomization tests that may not be as robust. In this paper, our key theoretical contribution is a non-asymptotic bound on the discrepancy between the size of an approximate randomization test and the size of the original randomization test using noiseless data. This allows us to derive novel conditions for the validity of approximate randomization tests under data invariances, while being able to leverage existing results based on studentization if the invariance does not hold. We illustrate our theory through several examples, including tests of significance in linear regression. Our theory can explain certain aspects of how randomization tests perform in small samples, addressing limitations of prior theoretical results.
We propose a method to couple local and nonlocal diffusion models. By inheriting desirable properties such as patch tests, asymptotic compatibility and unintrusiveness from related splice and optimization-based coupling schemes, it enables the use of weak (or variational) formulations, is computationally efficient and straightforward to implement. We prove well-posedness of the coupling scheme and demonstrate its properties and effectiveness in a variety of numerical examples.
This paper presents a new boundary-value problem formulation for quantifying uncertainty induced by the presence of small Brownian noise near transversally stable periodic orbits (limit cycles) and quasiperiodic invariant tori of the deterministic dynamical systems obtained in the absence of noise. The formulation uses adjoints to construct a continuous family of transversal hyperplanes that are invariant under the linearized deterministic flow near the limit cycle or quasiperiodic invariant torus. The intersections with each hyperplane of stochastic trajectories that remain near the deterministic cycle or torus over intermediate times may be approximated by a Gaussian distribution whose covariance matrix can be obtained from the solution to the corresponding boundary-value problem. In the case of limit cycles, the analysis improves upon results in the literature through the explicit use of state-space projections, transversality constraints, and symmetry-breaking parameters that ensure uniqueness of the solution despite the lack of hyperbolicity along the limit cycle. These same innovations are then generalized to the case of a quasiperiodic invariant torus of arbitrary dimension. In each case, a closed-form solution to the covariance boundary-value problem is found in terms of a convergent series. The methodology is validated against the results of numerical integration for two examples of stochastically perturbed limit cycles and one example of a stochastically perturbed two-dimensional quasiperiodic invariant torus. Finally, an implementation of the covariance boundary-value problem in the numerical continuation package coco is applied to analyze the small-noise limit near a two-dimensional quasiperiodic invariant torus in a nonlinear deterministic dynamical system in $\mathbb{R}^4$ that does not support closed-form analysis.
Constraint satisfaction or optimisation models -- even if they are formulated in high-level modelling languages -- need to be reduced into an equivalent format before they can be solved by the use of Quantum Computing. In this paper we show how Boolean and integer FlatZinc builtins over finite-domain integer variables can be equivalently reformulated as linear equations, linear inequalities or binary products of those variables, i.e. as finite-domain quadratic integer programs. Those quadratic integer programs can be further transformed into equivalent Quadratic Unconstrained Binary Optimisation problem models, i.e. a general format for optimisation problems to be solved on Quantum Computers especially on Quantum Annealers.
This paper presents a distributed model predictive control (DMPC) algorithm for a heterogeneous platoon using arbitrary communication topologies, as long as each vehicle is able to communicate with a preceding vehicle in the platoon. The proposed DMPC algorithm is able to accommodate any spacing policy that is affine in a vehicle's velocity, which includes constant distance or constant time headway spacing policies. By analyzing the total cost for the entire platoon, a sufficient condition is derived to guarantee platoon asymptotic stability. Simulation experiments with a platoon of 50 vehicles and hardware experiments with a platoon of four 1/10th scale vehicles validate the algorithm and compare performance under different spacing policies and communication topologies.
Scene context is well known to facilitate humans' perception of visible objects. In this paper, we investigate the role of context in Referring Expression Generation (REG) for objects in images, where existing research has often focused on distractor contexts that exert pressure on the generator. We take a new perspective on scene context in REG and hypothesize that contextual information can be conceived of as a resource that makes REG models more resilient and facilitates the generation of object descriptions, and object types in particular. We train and test Transformer-based REG models with target representations that have been artificially obscured with noise to varying degrees. We evaluate how properties of the models' visual context affect their processing and performance. Our results show that even simple scene contexts make models surprisingly resilient to perturbations, to the extent that they can identify referent types even when visual information about the target is completely missing.
Generalizing to longer sentences is important for recent Transformer-based language models. Besides algorithms manipulating explicit position features, the success of Transformers without position encodings (NoPE) provides a new way to overcome the challenge. In this paper, we study the length generalization property of NoPE. We find that although NoPE can extend to longer sequences than the commonly used explicit position encodings, it still has a limited context length. We identify a connection between the failure of NoPE's generalization and the distraction of attention distributions. We propose a parameter-efficient tuning for searching attention heads' best temperature hyper-parameters, which substantially expands NoPE's context size. Experiments on long sequence language modeling, the synthetic passkey retrieval task and real-world long context tasks show that NoPE can achieve competitive performances with state-of-the-art length generalization algorithms. The source code is publicly accessible
Pre-trained Language Models (PLMs) which are trained on large text corpus via self-supervised learning method, have yielded promising performance on various tasks in Natural Language Processing (NLP). However, though PLMs with huge parameters can effectively possess rich knowledge learned from massive training text and benefit downstream tasks at the fine-tuning stage, they still have some limitations such as poor reasoning ability due to the lack of external knowledge. Research has been dedicated to incorporating knowledge into PLMs to tackle these issues. In this paper, we present a comprehensive review of Knowledge-Enhanced Pre-trained Language Models (KE-PLMs) to provide a clear insight into this thriving field. We introduce appropriate taxonomies respectively for Natural Language Understanding (NLU) and Natural Language Generation (NLG) to highlight these two main tasks of NLP. For NLU, we divide the types of knowledge into four categories: linguistic knowledge, text knowledge, knowledge graph (KG), and rule knowledge. The KE-PLMs for NLG are categorized into KG-based and retrieval-based methods. Finally, we point out some promising future directions of KE-PLMs.
Molecular design and synthesis planning are two critical steps in the process of molecular discovery that we propose to formulate as a single shared task of conditional synthetic pathway generation. We report an amortized approach to generate synthetic pathways as a Markov decision process conditioned on a target molecular embedding. This approach allows us to conduct synthesis planning in a bottom-up manner and design synthesizable molecules by decoding from optimized conditional codes, demonstrating the potential to solve both problems of design and synthesis simultaneously. The approach leverages neural networks to probabilistically model the synthetic trees, one reaction step at a time, according to reactivity rules encoded in a discrete action space of reaction templates. We train these networks on hundreds of thousands of artificial pathways generated from a pool of purchasable compounds and a list of expert-curated templates. We validate our method with (a) the recovery of molecules using conditional generation, (b) the identification of synthesizable structural analogs, and (c) the optimization of molecular structures given oracle functions relevant to drug discovery.