Reasoning system dynamics is one of the most important analytical approaches for many scientific studies. With the initial state of a system as input, the recent graph neural networks (GNNs)-based methods are capable of predicting the future state distant in time with high accuracy. Although these methods have diverse designs in modeling the coordinates and interacting forces of the system, we show that they actually share a common paradigm that learns the integration of the velocity over the interval between the initial and terminal coordinates. However, their integrand is constant w.r.t. time. Inspired by this observation, we propose a new approach to predict the integration based on several velocity estimations with Newton-Cotes formulas and prove its effectiveness theoretically. Extensive experiments on several benchmarks empirically demonstrate consistent and significant improvement compared with the state-of-the-art methods.
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神經網絡（Neural Networks）是世界上三個最古老的神經建模學會的檔案期刊:國際神經網絡學會(INNS)、歐洲神經網絡學會(ENNS)和日本神經網絡學會(JNNS)。神經網絡提供了一個論壇，以發展和培育一個國際社會的學者和實踐者感興趣的所有方面的神經網絡和相關方法的計算智能。神經網絡歡迎高質量論文的提交，有助于全面的神經網絡研究，從行為和大腦建模，學習算法，通過數學和計算分析，系統的工程和技術應用，大量使用神經網絡的概念和技術。這一獨特而廣泛的范圍促進了生物和技術研究之間的思想交流，并有助于促進對生物啟發的計算智能感興趣的跨學科社區的發展。因此，神經網絡編委會代表的專家領域包括心理學，神經生物學，計算機科學，工程，數學，物理。該雜志發表文章、信件和評論以及給編輯的信件、社論、時事、軟件調查和專利信息。文章發表在五個部分之一:認知科學，神經科學，學習系統，數學和計算分析、工程和應用。
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Double descent presents a counter-intuitive aspect within the machine learning domain, and researchers have observed its manifestation in various models and tasks. While some theoretical explanations have been proposed for this phenomenon in specific contexts, an accepted theory to account for its occurrence in deep learning remains yet to be established. In this study, we revisit the phenomenon of double descent and demonstrate that its occurrence is strongly influenced by the presence of noisy data. Through conducting a comprehensive analysis of the feature space of learned representations, we unveil that double descent arises in imperfect models trained with noisy data. We argue that double descent is a consequence of the model first learning the noisy data until interpolation and then adding implicit regularization via over-parameterization acquiring therefore capability to separate the information from the noise.
CurvPy is an open-source Python library for automated curve fitting and regression analysis, aiming to make advanced statistical and machine learning techniques more accessible. This paper explores the mathematical foundations and implementation of key CurvPy components for optimization, smoothing, imputation, summarization, visualization, regression, evaluation, and tuning. The methodology leverages well-established statistical and computational algorithms adapted through both simplification and exposure of advanced options to balance usability and customizability. Mathematical techniques utilized include least squares estimation, Savitzky-Golay filtering, matrix completion, gradient descent optimization, regularization, basis function regression, and standard model evaluation metrics.
Testing complex simulation models can be expensive and time consuming. Current state-of-the-art methods that explore this problem are fully-supervised; i.e. they require that all examples are labeled. On the other hand, the GenClu system (introduced in this paper) takes a semi-supervised approach; i.e. (a) only a small subset of information is actually labeled (via simulation) and (b) those labels are then spread across the rest of the data. When applied to five open-source simulation models of cyber-physical systems, GenClu's test generation can be multiple orders of magnitude faster than the prior state of the art. Further, when assessed via mutation testing, tests generated by GenClu were as good or better than anything else tested here. Hence, we recommend semi-supervised methods over prior methods (evolutionary search and fully-supervised learning).
Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds ($1\textrm{fs}=10^{-15}\textrm{s}$). MD is often used to compute equilibrium properties, which requires sampling from an equilibrium distribution such as the Boltzmann distribution. However, many important processes, such as binding and folding, occur over timescales of milliseconds or beyond, and cannot be efficiently sampled with conventional MD. Furthermore, new MD simulations need to be performed for each molecular system studied. We present Timewarp, an enhanced sampling method which uses a normalising flow as a proposal distribution in a Markov chain Monte Carlo method targeting the Boltzmann distribution. The flow is trained offline on MD trajectories and learns to make large steps in time, simulating the molecular dynamics of $10^{5} - 10^{6}\:\textrm{fs}$. Crucially, Timewarp is transferable between molecular systems: once trained, we show that it generalises to unseen small peptides (2-4 amino acids) at all-atom resolution, exploring their metastable states and providing wall-clock acceleration of sampling compared to standard MD. Our method constitutes an important step towards general, transferable algorithms for accelerating MD.
Knowledge graph embedding (KGE) is a increasingly popular technique that aims to represent entities and relations of knowledge graphs into low-dimensional semantic spaces for a wide spectrum of applications such as link prediction, knowledge reasoning and knowledge completion. In this paper, we provide a systematic review of existing KGE techniques based on representation spaces. Particularly, we build a fine-grained classification to categorise the models based on three mathematical perspectives of the representation spaces: (1) Algebraic perspective, (2) Geometric perspective, and (3) Analytical perspective. We introduce the rigorous definitions of fundamental mathematical spaces before diving into KGE models and their mathematical properties. We further discuss different KGE methods over the three categories, as well as summarise how spatial advantages work over different embedding needs. By collating the experimental results from downstream tasks, we also explore the advantages of mathematical space in different scenarios and the reasons behind them. We further state some promising research directions from a representation space perspective, with which we hope to inspire researchers to design their KGE models as well as their related applications with more consideration of their mathematical space properties.
In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.
Graph neural networks generalize conventional neural networks to graph-structured data and have received widespread attention due to their impressive representation ability. In spite of the remarkable achievements, the performance of Euclidean models in graph-related learning is still bounded and limited by the representation ability of Euclidean geometry, especially for datasets with highly non-Euclidean latent anatomy. Recently, hyperbolic space has gained increasing popularity in processing graph data with tree-like structure and power-law distribution, owing to its exponential growth property. In this survey, we comprehensively revisit the technical details of the current hyperbolic graph neural networks, unifying them into a general framework and summarizing the variants of each component. More importantly, we present various HGNN-related applications. Last, we also identify several challenges, which potentially serve as guidelines for further flourishing the achievements of graph learning in hyperbolic spaces.
Despite its great success, machine learning can have its limits when dealing with insufficient training data. A potential solution is the additional integration of prior knowledge into the training process which leads to the notion of informed machine learning. In this paper, we present a structured overview of various approaches in this field. We provide a definition and propose a concept for informed machine learning which illustrates its building blocks and distinguishes it from conventional machine learning. We introduce a taxonomy that serves as a classification framework for informed machine learning approaches. It considers the source of knowledge, its representation, and its integration into the machine learning pipeline. Based on this taxonomy, we survey related research and describe how different knowledge representations such as algebraic equations, logic rules, or simulation results can be used in learning systems. This evaluation of numerous papers on the basis of our taxonomy uncovers key methods in the field of informed machine learning.
Lots of learning tasks require dealing with graph data which contains rich relation information among elements. Modeling physics system, learning molecular fingerprints, predicting protein interface, and classifying diseases require that a model to learn from graph inputs. In other domains such as learning from non-structural data like texts and images, reasoning on extracted structures, like the dependency tree of sentences and the scene graph of images, is an important research topic which also needs graph reasoning models. Graph neural networks (GNNs) are connectionist models that capture the dependence of graphs via message passing between the nodes of graphs. Unlike standard neural networks, graph neural networks retain a state that can represent information from its neighborhood with an arbitrary depth. Although the primitive graph neural networks have been found difficult to train for a fixed point, recent advances in network architectures, optimization techniques, and parallel computation have enabled successful learning with them. In recent years, systems based on graph convolutional network (GCN) and gated graph neural network (GGNN) have demonstrated ground-breaking performance on many tasks mentioned above. In this survey, we provide a detailed review over existing graph neural network models, systematically categorize the applications, and propose four open problems for future research.
We introduce a multi-task setup of identifying and classifying entities, relations, and coreference clusters in scientific articles. We create SciERC, a dataset that includes annotations for all three tasks and develop a unified framework called Scientific Information Extractor (SciIE) for with shared span representations. The multi-task setup reduces cascading errors between tasks and leverages cross-sentence relations through coreference links. Experiments show that our multi-task model outperforms previous models in scientific information extraction without using any domain-specific features. We further show that the framework supports construction of a scientific knowledge graph, which we use to analyze information in scientific literature.
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