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This paper presents a methodology for enhancing relation extraction from biomedical texts, focusing specifically on chemical-gene interactions. Leveraging the BioBERT model and a multi-layer fully connected network architecture, our approach integrates the ChemProt and DrugProt datasets using a novel merging strategy. Through extensive experimentation, we demonstrate significant performance improvements, particularly in CPR groups shared between the datasets. The findings underscore the importance of dataset merging in augmenting sample counts and improving model accuracy. Moreover, the study highlights the potential of automated information extraction in biomedical research and clinical practice.

We present a framework for constructing a first-order hyperbolic system whose solution approximates that of a desired higher-order evolution equation. Constructions of this kind have received increasing interest in recent years, and are potentially useful as either analytical or computational tools for understanding the corresponding higher-order equation. We perform a systematic analysis of a family of linear model equations and show that for each member of this family there is a stable hyperbolic approximation whose solution converges to that of the model equation in a certain limit. We then show through several examples that this approach can be applied successfully to a very wide range of nonlinear PDEs of practical interest.

We study the problem of training diffusion models to sample from a distribution with a given unnormalized density or energy function. We benchmark several diffusion-structured inference methods, including simulation-based variational approaches and off-policy methods (continuous generative flow networks). Our results shed light on the relative advantages of existing algorithms while bringing into question some claims from past work. We also propose a novel exploration strategy for off-policy methods, based on local search in the target space with the use of a replay buffer, and show that it improves the quality of samples on a variety of target distributions. Our code for the sampling methods and benchmarks studied is made public at //github.com/GFNOrg/gfn-diffusion as a base for future work on diffusion models for amortized inference.

This paper focuses on the numerical scheme for delay-type stochastic McKean-Vlasov equations (DSMVEs) driven by fractional Brownian motion with Hurst parameter $H\in (0,1/2)\cup (1/2,1)$. The existence and uniqueness of the solutions to such DSMVEs whose drift coefficients contain polynomial delay terms are proved by exploting the Banach fixed point theorem. Then the propagation of chaos between interacting particle system and non-interacting system in $\mathcal{L}^p$ sense is shown. We find that even if the delay term satisfies the polynomial growth condition, the unmodified classical Euler-Maruyama scheme still can approximate the corresponding interacting particle system without the particle corruption. The convergence rates are revealed for $H\in (0,1/2)\cup (1/2,1)$. Finally, as an example that closely fits the original equation, a stochastic opinion dynamics model with both extrinsic memory and intrinsic memory is simulated to illustrate the plausibility of the theoretical result.

We present BadGD, a unified theoretical framework that exposes the vulnerabilities of gradient descent algorithms through strategic backdoor attacks. Backdoor attacks involve embedding malicious triggers into a training dataset to disrupt the model's learning process. Our framework introduces three novel constructs: Max RiskWarp Trigger, Max GradWarp Trigger, and Max GradDistWarp Trigger, each designed to exploit specific aspects of gradient descent by distorting empirical risk, deterministic gradients, and stochastic gradients respectively. We rigorously define clean and backdoored datasets and provide mathematical formulations for assessing the distortions caused by these malicious backdoor triggers. By measuring the impact of these triggers on the model training procedure, our framework bridges existing empirical findings with theoretical insights, demonstrating how a malicious party can exploit gradient descent hyperparameters to maximize attack effectiveness. In particular, we show that these exploitations can significantly alter the loss landscape and gradient calculations, leading to compromised model integrity and performance. This research underscores the severe threats posed by such data-centric attacks and highlights the urgent need for robust defenses in machine learning. BadGD sets a new standard for understanding and mitigating adversarial manipulations, ensuring the reliability and security of AI systems.

The monotone Variational Inequality (VI) is a general model with important applications in various engineering and scientific domains. In numerous instances, the VI problems are accompanied by function constraints that can be data-driven, making the usual projection operator challenging to compute. This paper presents novel first-order methods for the function-constrained Variational Inequality (FCVI) problem in smooth or nonsmooth settings with possibly stochastic operators and constraints. We introduce the AdOpEx method, which employs an operator extrapolation on the KKT operator of the FCVI in a smooth deterministic setting. Since this operator is not uniformly Lipschitz continuous in the Lagrange multipliers, we employ an adaptive two-timescale algorithm leading to bounded multipliers and achieving the optimal $O(1/T)$ convergence rate. For the nonsmooth and stochastic VIs, we introduce design changes to the AdOpEx method and propose a novel P-OpEx method that takes partial extrapolation. It converges at the rate of $O(1/\sqrt{T})$ when both the operator and constraints are stochastic or nonsmooth. This method has suboptimal dependence on the noise and Lipschitz constants of function constraints. We propose a constraint extrapolation approach leading to the OpConEx method that improves this dependence by an order of magnitude. All our algorithms easily extend to saddle point problems with function constraints that couple the primal and dual variables while maintaining the same complexity results. To the best of our knowledge, all our complexity results are new in the literature

Learning to Optimize (L2O) stands at the intersection of traditional optimization and machine learning, utilizing the capabilities of machine learning to enhance conventional optimization techniques. As real-world optimization problems frequently share common structures, L2O provides a tool to exploit these structures for better or faster solutions. This tutorial dives deep into L2O techniques, introducing how to accelerate optimization algorithms, promptly estimate the solutions, or even reshape the optimization problem itself, making it more adaptive to real-world applications. By considering the prerequisites for successful applications of L2O and the structure of the optimization problems at hand, this tutorial provides a comprehensive guide for practitioners and researchers alike.

In this paper, we propose a weak Galerkin finite element method (WG) for solving singularly perturbed convection-diffusion problems on a Bakhvalov-type mesh in 2D. Our method is flexible and allows the use of discontinuous approximation functions on the meshe. An error estimate is devised in a suitable norm and the optimal convergence order is obtained. Finally, numerical experiments are given to support the theory and to show the efficiency of the proposed method.

This article presents a high-order accurate numerical method for the evaluation of singular volume integral operators, with attention focused on operators associated with the Poisson and Helmholtz equations in two dimensions. Following the ideas of the density interpolation method for boundary integral operators, the proposed methodology leverages Green's third identity and a local polynomial interpolant of the density function to recast the volume potential as a sum of single- and double-layer potentials and a volume integral with a regularized (bounded or smoother) integrand. The layer potentials can be accurately and efficiently evaluated everywhere in the plane by means of existing methods (e.g. the density interpolation method), while the regularized volume integral can be accurately evaluated by applying elementary quadrature rules. Compared to straightforwardly computing corrections for every singular and nearly-singular volume target, the method significantly reduces the amount of required specialized quadrature by pushing all singular and near-singular corrections to near-singular layer-potential evaluations at target points in a small neighborhood of the domain boundary. Error estimates for the regularization and quadrature approximations are provided. The method is compatible with well-established fast algorithms, being both efficient not only in the online phase but also to set-up. Numerical examples demonstrate the high-order accuracy and efficiency of the proposed methodology; applications to inhomogeneous scattering are presented.

The recent proliferation of knowledge graphs (KGs) coupled with incomplete or partial information, in the form of missing relations (links) between entities, has fueled a lot of research on knowledge base completion (also known as relation prediction). Several recent works suggest that convolutional neural network (CNN) based models generate richer and more expressive feature embeddings and hence also perform well on relation prediction. However, we observe that these KG embeddings treat triples independently and thus fail to cover the complex and hidden information that is inherently implicit in the local neighborhood surrounding a triple. To this effect, our paper proposes a novel attention based feature embedding that captures both entity and relation features in any given entity's neighborhood. Additionally, we also encapsulate relation clusters and multihop relations in our model. Our empirical study offers insights into the efficacy of our attention based model and we show marked performance gains in comparison to state of the art methods on all datasets.