Quasi-2D Coulomb systems are of fundamental importance and have attracted much attention in many areas nowadays. Their reduced symmetry gives rise to interesting collective behaviors, but also brings great challenges for particle-based simulations. Here, we propose a novel algorithm framework to address the $\mathcal O(N^2)$ simulation complexity associated with the long-range nature of Coulomb interactions. First, we introduce an efficient Sum-of-Exponentials (SOE) approximation for the long-range kernel associated with Ewald splitting, achieving uniform convergence in terms of inter-particle distance, which reduces the complexity to $\mathcal{O}(N^{7/5})$. We then introduce a random batch sampling method in the periodic dimensions, the stochastic approximation is proven to be both unbiased and with reduced variance via a tailored importance sampling strategy, further reducing the computational cost to $\mathcal{O}(N)$. The performance of our algorithm is demonstrated via varies numerical examples. Notably, it achieves a speedup of $2\sim 3$ orders of magnitude comparing with Ewald2D method, enabling molecular dynamics (MD) simulations with up to $10^6$ particles on a single core. The present approach is therefore well-suited for large-scale particle-based simulations of Coulomb systems under confinement, making it possible to investigate the role of Coulomb interaction in many practical situations.
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Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the inherent graph structure of PPI networks. This paper reviews various graph-based methodologies, and discusses their applications in PPI prediction. We classify these approaches into two primary groups based on their model structures. The first category employs Graph Neural Networks (GNN) or Graph Convolutional Networks (GCN), while the second category utilizes Graph Attention Networks (GAT), Graph Auto-Encoders and Graph-BERT. We highlight the distinctive methodologies of each approach in managing the graph-structured data inherent in PPI networks and anticipate future research directions in this domain.
Large Language Models (LLMs) have demonstrated exceptional performance in biochemical tasks, especially the molecule caption translation task, which aims to bridge the gap between molecules and natural language texts. However, previous methods in adapting LLMs to the molecule-caption translation task required extra domain-specific pre-training stages, suffered weak alignment between molecular and textual spaces, or imposed stringent demands on the scale of LLMs. To resolve the challenges, we propose In-Context Molecule Adaptation (ICMA), as a new paradigm allowing LLMs to learn the molecule-text alignment from context examples via In-Context Molecule Tuning. Specifically, ICMA incorporates the following three stages: Hybrid Context Retrieval, Post-retrieval Re-ranking, and In-context Molecule Tuning. Initially, Hybrid Context Retrieval utilizes BM25 Caption Retrieval and Molecule Graph Retrieval to retrieve informative context examples. Additionally, we also propose Post-retrieval Re-ranking with Sequence Reversal and Random Walk to further improve the quality of retrieval results. Finally, In-Context Molecule Tuning unlocks the in-context molecule learning capability of LLMs with retrieved examples and adapts the parameters of LLMs for the molecule-caption translation task. Experimental results demonstrate that ICMT can empower LLMs to achieve state-of-the-art or comparable performance without extra training corpora and intricate structures, showing that LLMs are inherently in-context molecule learners.
Hyperproperties express the relationship between multiple executions of a system. This is needed in many AI-related fields, such as knowledge representation and planning, to capture system properties related to knowledge, information flow, and privacy. In this paper, we study the monitoring of complex hyperproperties at runtime. Previous work in this area has either focused on the simpler problem of monitoring trace properties (which are sets of traces, while hyperproperties are sets of sets of traces) or on monitoring first-order hyperproperties, which are expressible in temporal logics with first-order quantification over traces, such as HyperLTL. We present the first monitoring algorithm for the much more expressive class of second-order hyperproperties. Second-order hyperproperties include system properties like common knowledge, which cannot be expressed in first-order logics like HyperLTL. We introduce Hyper$^2$LTL$_f$, a temporal logic over finite traces that allows for second-order quantification over sets of traces. We study the monitoring problem in two fundamental execution models: (1) the parallel model, where a fixed number of traces is monitored in parallel, and (2) the sequential model, where an unbounded number of traces is observed sequentially, one trace after the other. For the parallel model, we show that the monitoring of the second-order hyperproperties of Hyper$^2$LTL$_f$ can be reduced to monitoring first-order hyperproperties. For the sequential model, we present a monitoring algorithm that handles second-order quantification efficiently, exploiting optimizations based on the monotonicity of subformulas, graph-based storing of executions, and fixpoint hashing. We present experimental results from a range of benchmarks, including examples from common knowledge and planning.
Prompt Tuning is emerging as a scalable and cost-effective method to fine-tune Pretrained Language Models (PLMs), which are often referred to as Large Language Models (LLMs). This study benchmarks the performance and computational efficiency of Prompt Tuning and baselines for multi-label text classification. This is applied to the challenging task of classifying companies into an investment firm's proprietary industry taxonomy, supporting their thematic investment strategy. Text-to-text classification is frequently reported to outperform task-specific classification heads, but has several limitations when applied to a multi-label classification problem where each label consists of multiple tokens: (a) Generated labels may not match any label in the label taxonomy; (b) The fine-tuning process lacks permutation invariance and is sensitive to the order of the provided labels; (c) The model provides binary decisions rather than appropriate confidence scores. Limitation (a) is addressed by applying constrained decoding using Trie Search, which slightly improves classification performance. All limitations (a), (b), and (c) are addressed by replacing the PLM's language head with a classification head, which is referred to as Prompt Tuned Embedding Classification (PTEC). This improves performance significantly, while also reducing computational costs during inference. In our industrial application, the training data is skewed towards well-known companies. We confirm that the model's performance is consistent across both well-known and less-known companies. Our overall results indicate the continuing need to adapt state-of-the-art methods to domain-specific tasks, even in the era of PLMs with strong generalization abilities. We release our codebase and a benchmarking dataset at //github.com/EQTPartners/PTEC.
The Laplace-Beltrami operator (LBO) emerges from studying manifolds equipped with a Riemannian metric. It is often called the Swiss army knife of geometry processing as it allows to capture intrinsic shape information and gives rise to heat diffusion, geodesic distances, and a multitude of shape descriptors. It also plays a central role in geometric deep learning. In this work, we explore Finsler manifolds as a generalization of Riemannian manifolds. We revisit the Finsler heat equation and derive a Finsler heat kernel and a Finsler-Laplace-Beltrami Operator (FLBO): a novel theoretically justified anisotropic Laplace-Beltrami operator (ALBO). In experimental evaluations we demonstrate that the proposed FLBO is a valuable alternative to the traditional Riemannian-based LBO and ALBOs for spatial filtering and shape correspondence estimation. We hope that the proposed Finsler heat kernel and the FLBO will inspire further exploration of Finsler geometry in the computer vision community.
Heterogeneous Graphs (HGs) can effectively model complex relationships in the real world by multi-type nodes and edges. In recent years, inspired by self-supervised learning, contrastive Heterogeneous Graphs Neural Networks (HGNNs) have shown great potential by utilizing data augmentation and discriminators for downstream tasks. However, data augmentation is still limited due to the discrete and abstract nature of graphs. To tackle the above limitations, we propose a novel \textit{Generative-Contrastive Heterogeneous Graph Neural Network (GC-HGNN)}. Specifically, we first propose a heterogeneous graph generative learning enhanced contrastive paradigm. This paradigm includes: 1) A contrastive view augmentation strategy by using masked autoencoder. 2) Position-aware and semantics-aware positive sample sampling strategy for generate hard negative samples. 3) A hierarchical contrastive learning strategy for capturing local and global information. Furthermore, the hierarchical contrastive learning and sampling strategies aim to constitute an enhanced discriminator under the generative-contrastive perspective. Finally, we compare our model with seventeen baselines on eight real-world datasets. Our model outperforms the latest contrastive and generative baselines on node classification and link prediction tasks. To reproduce our work, we have open-sourced our code at //github.com/xxx.
Graph Neural Networks (GNNs), despite achieving remarkable performance across different tasks, are theoretically bounded by the 1-Weisfeiler-Lehman test, resulting in limitations in terms of graph expressivity. Even though prior works on topological higher-order GNNs overcome that boundary, these models often depend on assumptions about sub-structures of graphs. Specifically, topological GNNs leverage the prevalence of cliques, cycles, and rings to enhance the message-passing procedure. Our study presents a novel perspective by focusing on simple paths within graphs during the topological message-passing process, thus liberating the model from restrictive inductive biases. We prove that by lifting graphs to path complexes, our model can generalize the existing works on topology while inheriting several theoretical results on simplicial complexes and regular cell complexes. Without making prior assumptions about graph sub-structures, our method outperforms earlier works in other topological domains and achieves state-of-the-art results on various benchmarks.
Few-shot Knowledge Graph (KG) completion is a focus of current research, where each task aims at querying unseen facts of a relation given its few-shot reference entity pairs. Recent attempts solve this problem by learning static representations of entities and references, ignoring their dynamic properties, i.e., entities may exhibit diverse roles within task relations, and references may make different contributions to queries. This work proposes an adaptive attentional network for few-shot KG completion by learning adaptive entity and reference representations. Specifically, entities are modeled by an adaptive neighbor encoder to discern their task-oriented roles, while references are modeled by an adaptive query-aware aggregator to differentiate their contributions. Through the attention mechanism, both entities and references can capture their fine-grained semantic meanings, and thus render more expressive representations. This will be more predictive for knowledge acquisition in the few-shot scenario. Evaluation in link prediction on two public datasets shows that our approach achieves new state-of-the-art results with different few-shot sizes.
Graph Neural Networks (GNN) has demonstrated the superior performance in many challenging applications, including the few-shot learning tasks. Despite its powerful capacity to learn and generalize from few samples, GNN usually suffers from severe over-fitting and over-smoothing as the model becomes deep, which limit the model scalability. In this work, we propose a novel Attentive GNN to tackle these challenges, by incorporating a triple-attention mechanism, \ie node self-attention, neighborhood attention, and layer memory attention. We explain why the proposed attentive modules can improve GNN for few-shot learning with theoretical analysis and illustrations. Extensive experiments show that the proposed Attentive GNN outperforms the state-of-the-art GNN-based methods for few-shot learning over the mini-ImageNet and Tiered-ImageNet datasets, with both inductive and transductive settings.
Interest in the field of Explainable Artificial Intelligence has been growing for decades and has accelerated recently. As Artificial Intelligence models have become more complex, and often more opaque, with the incorporation of complex machine learning techniques, explainability has become more critical. Recently, researchers have been investigating and tackling explainability with a user-centric focus, looking for explanations to consider trustworthiness, comprehensibility, explicit provenance, and context-awareness. In this chapter, we leverage our survey of explanation literature in Artificial Intelligence and closely related fields and use these past efforts to generate a set of explanation types that we feel reflect the expanded needs of explanation for today's artificial intelligence applications. We define each type and provide an example question that would motivate the need for this style of explanation. We believe this set of explanation types will help future system designers in their generation and prioritization of requirements and further help generate explanations that are better aligned to users' and situational needs.
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