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Molecular discovery, when formulated as an optimization problem, presents significant computational challenges because optimization objectives can be non-differentiable. Evolutionary Algorithms (EAs), often used to optimize black-box objectives in molecular discovery, traverse chemical space by performing random mutations and crossovers, leading to a large number of expensive objective evaluations. In this work, we ameliorate this shortcoming by incorporating chemistry-aware Large Language Models (LLMs) into EAs. Namely, we redesign crossover and mutation operations in EAs using LLMs trained on large corpora of chemical information. We perform extensive empirical studies on both commercial and open-source models on multiple tasks involving property optimization, molecular rediscovery, and structure-based drug design, demonstrating that the joint usage of LLMs with EAs yields superior performance over all baseline models across single- and multi-objective settings. We demonstrate that our algorithm improves both the quality of the final solution and convergence speed, thereby reducing the number of required objective evaluations. Our code is available at //github.com/zoom-wang112358/MOLLEO

Detecting undesired process behavior is one of the main tasks of process mining and various conformance-checking techniques have been developed to this end. These techniques typically require a normative process model as input, specifically designed for the processes to be analyzed. Such models are rarely available, though, and their creation involves considerable manual effort.However, reference process models serve as best-practice templates for organizational processes in a plethora of domains, containing valuable knowledge about general behavioral relations in well-engineered processes. These general models can thus mitigate the need for dedicated models by providing a basis to check for undesired behavior. Still, finding a perfectly matching reference model for a real-life event log is unrealistic because organizational needs can vary, despite similarities in process execution. Furthermore, event logs may encompass behavior related to different reference models, making traditional conformance checking impractical as it requires aligning process executions to individual models. To still use reference models for conformance checking, we propose a framework for mining declarative best-practice constraints from a reference model collection, automatically selecting constraints that are relevant for a given event log, and checking for best-practice violations. We demonstrate the capability of our framework to detect best-practice violations through an evaluation based on real-world process model collections and event logs.

We introduce a novel approach for the reconstruction of tubular shapes from skeletal representations. Our method processes all skeletal points as a whole, eliminating the need for splitting input structure into multiple segments. We represent the tubular shape as a truncated signed distance function (TSDF) in a voxel hashing manner, in which the signed distance between a voxel center and the object is computed through a simple geometric algorithm. Our method does not involve any surface sampling scheme or solving large matrix equations, and therefore is a faster and more elegant solution for tubular shape reconstruction compared to other approaches. Experiments demonstrate the efficiency and effectiveness of the proposed method. Code is avaliable at //github.com/wlsdzyzl/Dragon.

Models for multiphysics problems often contain strong nonlinearities. Including fracture contact mechanics introduces discontinuities at the transition between open and closed or sliding and sticking fractures. The resulting system of equations is highly challenging to solve. The na\"ive choice of Newton's method frequently fails to converge, calling for more refined solution techniques such as line search methods. When dealing with strong nonlinearities and discontinuities, a global line search based on the magnitude of the residual of all equations is at best costly to evaluate and at worst fails to converge. We therefore suggest a cheap and reliable approach tailored to the discontinuities. Utilising adaptive variable scaling, the algorithm uses a line search to identify the transition between contact states. Then, a solution update weight is chosen to ensure that no fracture cells move too far beyond the transition. We demonstrate the algorithm on a series of test cases for poromechanics and thermoporomechanics in fractured porous media. We consider both single- and multifracture cases and study the importance of proper scaling of variables and equations.

Video sequences offer valuable temporal information, but existing large multimodal models (LMMs) fall short in understanding extremely long videos. Many works address this by reducing the number of visual tokens using visual resamplers. Alternatively, in this paper, we approach this problem from the perspective of the language model. By simply extrapolating the context length of the language backbone, we enable LMMs to comprehend orders of magnitude more visual tokens without any video training. We call this phenomenon long context transfer and carefully ablate its properties. To effectively measure LMMs' ability to generalize to long contexts in the vision modality, we develop V-NIAH (Visual Needle-In-A-Haystack), a purely synthetic long vision benchmark inspired by the language model's NIAH test. Our proposed Long Video Assistant (LongVA) can process 2000 frames or over 200K visual tokens without additional complexities. With its extended context length, LongVA achieves state-of-the-art performance on Video-MME among 7B-scale models by densely sampling more input frames. Our work is open-sourced at //github.com/EvolvingLMMs-Lab/LongVA.

Collaborative filtering (CF) is an essential technique in recommender systems that provides personalized recommendations by only leveraging user-item interactions. However, most CF methods represent users and items as fixed points in the latent space, lacking the ability to capture uncertainty. While probabilistic embedding is proposed to intergrate uncertainty, they suffer from several limitations when introduced to graph-based recommender systems. Graph convolutional network framework would confuse the semantic of uncertainty in the nodes, and similarity measured by Kullback-Leibler (KL) divergence suffers from degradation problem and demands an exponential number of samples. To address these challenges, we propose a novel approach, called the Wasserstein dependent Graph Attention network (W-GAT), for collaborative filtering with uncertainty. We utilize graph attention network and Wasserstein distance to learn Gaussian embedding for each user and item. Additionally, our method incorporates Wasserstein-dependent mutual information further to increase the similarity between positive pairs. Experimental results on three benchmark datasets show the superiority of W-GAT compared to several representative baselines. Extensive experimental analysis validates the effectiveness of W-GAT in capturing uncertainty by modeling the range of user preferences and categories associated with items.

The recent surge in generative AI technologies, such as large language models and diffusion models, has boosted the development of AI applications in various domains, including science, finance, and education. Concurrently, adaptive learning, a concept that has gained substantial interest in the educational sphere, has proven its efficacy in enhancing students' learning efficiency. In this position paper, we aim to shed light on the intersectional studies of these two methods, which combine generative AI with adaptive learning concepts. By presenting discussions about the benefits, challenges, and potentials in this field, we argue that this union will contribute significantly to the development of the next-stage learning format in education.

Detecting dynamic patterns of task-specific responses shared across heterogeneous datasets is an essential and challenging problem in many scientific applications in medical science and neuroscience. In our motivating example of rodent electrophysiological data, identifying the dynamical patterns in neuronal activity associated with ongoing cognitive demands and behavior is key to uncovering the neural mechanisms of memory. One of the greatest challenges in investigating a cross-subject biological process is that the systematic heterogeneity across individuals could significantly undermine the power of existing machine learning methods to identify the underlying biological dynamics. In addition, many technically challenging neurobiological experiments are conducted on only a handful of subjects where rich longitudinal data are available for each subject. The low sample sizes of such experiments could further reduce the power to detect common dynamic patterns among subjects. In this paper, we propose a novel heterogeneous data integration framework based on optimal transport to extract shared patterns in complex biological processes. The key advantages of the proposed method are that it can increase discriminating power in identifying common patterns by reducing heterogeneity unrelated to the signal by aligning the extracted latent spatiotemporal information across subjects. Our approach is effective even with a small number of subjects, and does not require auxiliary matching information for the alignment. In particular, our method can align longitudinal data across heterogeneous subjects in a common latent space to capture the dynamics of shared patterns while utilizing temporal dependency within subjects.

Translational distance-based knowledge graph embedding has shown progressive improvements on the link prediction task, from TransE to the latest state-of-the-art RotatE. However, N-1, 1-N and N-N predictions still remain challenging. In this work, we propose a novel translational distance-based approach for knowledge graph link prediction. The proposed method includes two-folds, first we extend the RotatE from 2D complex domain to high dimension space with orthogonal transforms to model relations for better modeling capacity. Second, the graph context is explicitly modeled via two directed context representations. These context representations are used as part of the distance scoring function to measure the plausibility of the triples during training and inference. The proposed approach effectively improves prediction accuracy on the difficult N-1, 1-N and N-N cases for knowledge graph link prediction task. The experimental results show that it achieves better performance on two benchmark data sets compared to the baseline RotatE, especially on data set (FB15k-237) with many high in-degree connection nodes.

We propose a new method for event extraction (EE) task based on an imitation learning framework, specifically, inverse reinforcement learning (IRL) via generative adversarial network (GAN). The GAN estimates proper rewards according to the difference between the actions committed by the expert (or ground truth) and the agent among complicated states in the environment. EE task benefits from these dynamic rewards because instances and labels yield to various extents of difficulty and the gains are expected to be diverse -- e.g., an ambiguous but correctly detected trigger or argument should receive high gains -- while the traditional RL models usually neglect such differences and pay equal attention on all instances. Moreover, our experiments also demonstrate that the proposed framework outperforms state-of-the-art methods, without explicit feature engineering.