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Anomaly detection in computational workflows is critical for ensuring system reliability and security. However, traditional rule-based methods struggle to detect novel anomalies. This paper leverages large language models (LLMs) for workflow anomaly detection by exploiting their ability to learn complex data patterns. Two approaches are investigated: 1) supervised fine-tuning (SFT), where pre-trained LLMs are fine-tuned on labeled data for sentence classification to identify anomalies, and 2) in-context learning (ICL) where prompts containing task descriptions and examples guide LLMs in few-shot anomaly detection without fine-tuning. The paper evaluates the performance, efficiency, generalization of SFT models, and explores zero-shot and few-shot ICL prompts and interpretability enhancement via chain-of-thought prompting. Experiments across multiple workflow datasets demonstrate the promising potential of LLMs for effective anomaly detection in complex executions., Comment: 12 pages, 14 figures, paper is accepted by SC'24, source code, see: https://github.com/PoSeiDon-Workflows/LLM_AD

The threat of geomagnetic disturbances (GMDs) to the reliable operation of the bulk energy system has spurred the development of effective strategies for mitigating their impacts. One such approach involves placing transformer neutral blocking devices, which interrupt the path of geomagnetically induced currents (GICs) to limit their impact. The high cost of these devices and the sparsity of transformers that experience high GICs during GMD events, however, calls for a sparse placement strategy that involves high computational cost. To address this challenge, we developed a physics-informed heterogeneous graph neural network (PIHGNN) for solving the graph-based dc-blocker placement problem. Our approach combines a heterogeneous graph neural network (HGNN) with a physics-informed neural network (PINN) to capture the diverse types of nodes and edges in ac/dc networks and incorporates the physical laws of the power grid. We train the PIHGNN model using a surrogate power flow model and validate it using case studies. Results demonstrate that PIHGNN can effectively and efficiently support the deployment of GIC dc-current blockers, ensuring the continued supply of electricity to meet societal demands. Our approach has the potential to contribute to the development of more reliable and resilient power grids capable of withstanding the growing threat that GMDs pose., Comment: Paper is accepted by PSCC 2024

A computational workflow, also known as workflow, consists of tasks that are executed in a certain order to attain a specific computational campaign. Computational workflows are commonly employed in science domains, such as physics, chemistry, genomics, to complete large-scale experiments in distributed and heterogeneous computing environments. However, running computations at such a large scale makes the workflow applications prone to failures and performance degradation, which can slowdown, stall, and ultimately lead to workflow failure. Learning how these workflows behave under normal and anomalous conditions can help us identify the causes of degraded performance and subsequently trigger appropriate actions to resolve them. However, learning in such circumstances is a challenging task because of the large volume of high-quality historical data needed to train accurate and reliable models. Generating such datasets not only takes a lot of time and effort but it also requires a lot of resources to be devoted to data generation for training purposes. Active learning is a promising approach to this problem. It is an approach where the data is generated as required by the machine learning model and thus it can potentially reduce the training data needed to derive accurate models. In this work, we present an active learning approach that is supported by an experimental framework, Poseidon-X, that utilizes a modern workflow management system and two cloud testbeds. We evaluate our approach using three computational workflows. For one workflow we run an end-to-end live active learning experiment, for the other two we evaluate our active learning algorithms using pre-captured data traces provided by the Flow-Bench benchmark. Our findings indicate that active learning not only saves resources, but it also improves the accuracy of the detection of anomalies.

Molecular generation, an essential method for identifying new drug structures, has been supported by advancements in machine learning and computational technology. However, challenges remain in multi-objective generation, model adaptability, and practical application in drug discovery. In this study, we developed a versatile 'plug-in' molecular generation model that incorporates multiple objectives related to target affinity, drug-likeness, and synthesizability, facilitating its application in various drug development contexts. We improved the Particle Swarm Optimization (PSO) in the context of drug discoveries, and identified PSO-ENP as the optimal variant for multi-objective molecular generation and optimization through comparative experiments. The model also incorporates a novel target-ligand affinity predictor, enhancing the model's utility by supporting three-dimensional information and improving synthetic feasibility. Case studies focused on generating and optimizing drug-like big marine natural products were performed, underscoring PSO-ENP's effectiveness and demonstrating its considerable potential for practical drug discovery applications.

Anomaly detection is the task of identifying abnormal behavior of a system. Anomaly detection in computational workflows is of special interest because of its wide implications in various domains such as cybersecurity, finance, and social networks. However, anomaly detection in computational workflows~(often modeled as graphs) is a relatively unexplored problem and poses distinct challenges. For instance, when anomaly detection is performed on graph data, the complex interdependency of nodes and edges, the heterogeneity of node attributes, and edge types must be accounted for. Although the use of graph neural networks can help capture complex inter-dependencies, the scarcity of labeled anomalous examples from workflow executions is still a significant challenge. To address this problem, we introduce an autoencoder-driven self-supervised learning~(SSL) approach that learns a summary statistic from unlabeled workflow data and estimates the normal behavior of the computational workflow in the latent space. In this approach, we combine generative and contrastive learning objectives to detect outliers in the summary statistics. We demonstrate that by estimating the distribution of normal behavior in the latent space, we can outperform state-of-the-art anomaly detection methods on our benchmark datasets.

A computational workflow, also known as workflow, consists of tasks that must be executed in a specific order to attain a specific goal. Often, in fields such as biology, chemistry, physics, and data science, among others, these workflows are complex and are executed in large-scale, distributed, and heterogeneous computing environments prone to failures and performance degradation. Therefore, anomaly detection for workflows is an important paradigm that aims to identify unexpected behavior or errors in workflow execution. This crucial task to improve the reliability of workflow executions can be further assisted by machine learning-based techniques. However, such application is limited, in large part, due to the lack of open datasets and benchmarking. To address this gap, we make the following contributions in this paper: (1) we systematically inject anomalies and collect raw execution logs from workflows executing on distributed infrastructures; (2) we summarize the statistics of new datasets, and provide insightful analyses; (3) we convert workflows into tabular, graph and text data, and benchmark with supervised and unsupervised anomaly detection techniques correspondingly. The presented dataset and benchmarks allow examining the effectiveness and efficiency of scientific computational workflows and identifying potential research opportunities for improvement and generalization. The dataset and benchmark code are publicly available \url{https://poseidon-workflows.github.io/FlowBench/} under the MIT License., Comment: Work under review, updated with more workflow data

This paper studies the issues about the generalized inverses of tensors under the C-Product. The aim of this paper is threefold. Firstly, this paper present the definition of the Moore-Penrose inverse, Drazin inverse of tensors under the C-Product. Moreover, the inverse along a tensor is also introduced. Secondly, this paper gives some other expressions of the generalized inverses of tensors by using several decomposition forms of tensors. Finally, the algorithms for the Moore-Penrose inverse, Drazin inverse of tensors and the inverse along a tensor are established.

In this article, specific definitions of the Moore-Penrose inverse, Drazin inverse of the quaternion tensor and the inverse along two quaternion tensors are introduced under the T-product. Some characterizations, representations and properties of the defined inverses are investigated. Moreover, algorithms are established for computing the Moore-Penrose inverse, Drazin inverse of the quaternion tensor and the inverse along two quaternion tensors, respectively.

Comparing structured data from possibly different metric-measure spaces is a fundamental task in machine learning, with applications in, e.g., graph classification. The Gromov-Wasserstein (GW) discrepancy formulates a coupling between the structured data based on optimal transportation, tackling the incomparability between different structures by aligning the intra-relational geometries. Although efficient \emph{local} solvers such as conditional gradient and Sinkhorn are available, the inherent non-convexity still prevents a tractable evaluation, and the existing lower bounds are not tight enough for practical use. To address this issue, we take inspiration from the connection with the quadratic assignment problem, and propose the orthogonal Gromov-Wasserstein (OGW) discrepancy as a surrogate of GW. It admits an efficient and \emph{closed-form} lower bound with $\mathcal{O}(n^3)$ complexity, and directly extends to the fused Gromov-Wasserstein (FGW) distance, incorporating node features into the coupling. Extensive experiments on both the synthetic and real-world datasets show the tightness of our lower bounds, and both OGW and its lower bounds efficiently deliver accurate predictions and satisfactory barycenters for graph sets., Comment: Published as a conference paper in UAI 2022

Learning the similarity between structured data, especially the graphs, is one of the essential problems. Besides the approach like graph kernels, Gromov-Wasserstein (GW) distance recently draws big attention due to its flexibility to capture both topological and feature characteristics, as well as handling the permutation invariance. However, structured data are widely distributed for different data mining and machine learning applications. With privacy concerns, accessing the decentralized data is limited to either individual clients or different silos. To tackle these issues, we propose a privacy-preserving framework to analyze the GW discrepancy of node embedding learned locally from graph neural networks in a federated flavor, and then explicitly place local differential privacy (LDP) based on Multi-bit Encoder to protect sensitive information. Our experiments show that, with strong privacy protections guaranteed by the $\varepsilon$-LDP algorithm, the proposed framework not only preserves privacy in graph learning but also presents a noised structural metric under GW distance, resulting in comparable and even better performance in classification and clustering tasks. Moreover, we reason the rationale behind the LDP-based GW distance analytically and empirically.

Molecular fingerprints are the workhorse in ligand-based drug discovery. In recent years, an increasing number of research papers reported fascinating results on using deep neural networks to learn 2D molecular representations as fingerprints. It is anticipated that the integration of deep learning would also contribute to the prosperity of 3D fingerprints. Here, we unprecedentedly introduce deep learning into 3D small molecule fingerprints, presenting a new one we termed as the three-dimensional force fields fingerprint (TF3P). TF3P is learned by a deep capsular network whose training is in no need of labeled datasets for specific predictive tasks. TF3P can encode the 3D force fields information of molecules and demonstrates the stronger ability to capture 3D structural changes, to recognize molecules alike in 3D but not in 2D, and to identify similar targets inaccessible by other 2D or 3D fingerprints based on only ligands similarity. Furthermore, TF3P is compatible with both statistical models (e.g. similarity ensemble approach) and machine learning models. Altogether, we report TF3P as a new 3D small molecule fingerprint with a promising future in ligand-based drug discovery. All codes are written in Python and available at https://github.com/canisw/tf3p.

In this article one-sided (b, c)-inverses of arbitrary matrices as well as one-sided inverses along a (not necessarily square) matrix, will be studied. In adddition, the (b, c)-inverse and the inverse along an element will be also researched in the context of rectangular matrices., Comment: 38 pages, original research article

In this article, we define new classes of tensors called double $\overline{B}$-tensors, quasi-double $\overline{B}$-tensors and establish some of their properties. Using these properties, we construct new regions viz., double $\overline{B}$-intervals and quasi-double $\overline{B}$-intervals, which contain all the $H$-eigenvalues of real even order symmetric tensors. We prove that the double $\overline{B}$-intervals is contained in the quasi-double $\overline{B}$-intervals and quasi-double ${\overline{B}}$-intervals provide supplement information on the Brauer-type eigenvalues inclusion set of tensors. These are analogous to the double $\overline{B}$-intervals of matrices established by J. M. Pe\~na~[On an alternative to Gerschgorin circles and ovals of Cassini, Numer. Math. 95 (2003), no. 2, 337-345.], Comment: Comments are welcome