pwc-archive/papers-with-abstracts huggingface dataset:
Bring Your Own View: Graph Neural Networks for Link Prediction with Personalized Subgraph Selection
Authors: Qiaoyu Tan, Xin Zhang, Ninghao Liu, Daochen Zha, Li Li, Rui Chen, Soo-Hyun Choi, Xia Hu
Date: 2022-12-23 00:00:00
Tasks: Link Prediction

Graph neural networks (GNNs) have received remarkable success in link prediction (GNNLP) tasks. Existing efforts first predefine the subgraph for the whole dataset and then apply GNNs to encode edge representations by leveraging the neighborhood structure induced by the fixed subgraph. The prominence of GNNLP methods significantly relies on the adhoc subgraph. Since node connectivity in real-world graphs is complex, one shared subgraph is limited for all edges. Thus, the choices of subgraphs should be personalized to different edges. However, performing personalized subgraph selection is nontrivial since the potential selection space grows exponentially to the scale of edges. Besides, the inference edges are not available during training in link prediction scenarios, so the selection process needs to be inductive. To bridge the gap, we introduce a Personalized Subgraph Selector (PS2) as a plug-and-play framework to automatically, personally, and inductively identify optimal subgraphs for different edges when performing GNNLP. PS2 is instantiated as a bi-level optimization problem that can be efficiently solved differently. Coupling GNNLP models with PS2, we suggest a brand-new angle towards GNNLP training: by first identifying the optimal subgraphs for edges; and then focusing on training the inference model by using the sampled subgraphs. Comprehensive experiments endorse the effectiveness of our proposed method across various GNNLP backbones (GCN, GraphSage, NGCF, LightGCN, and SEAL) and diverse benchmarks (Planetoid, OGB, and Recommendation datasets). Our code is publicly available at \url{https://github.com/qiaoyu-tan/PS2}
Physics-Informed Gaussian Process Regression Generalizes Linear PDE Solvers
Authors: Marvin Pförtner, Ingo Steinwart, Philipp Hennig, Jonathan Wenger
Date: 2022-12-23 00:00:00
Tasks: Bayesian Inference, regression

Linear partial differential equations (PDEs) are an important, widely applied class of mechanistic models, describing physical processes such as heat transfer, electromagnetism, and wave propagation. In practice, specialized numerical methods based on discretization are used to solve PDEs. They generally use an estimate of the unknown model parameters and, if available, physical measurements for initialization. Such solvers are often embedded into larger scientific models with a downstream application and thus error quantification plays a key role. However, by ignoring parameter and measurement uncertainty, classical PDE solvers may fail to produce consistent estimates of their inherent approximation error. In this work, we approach this problem in a principled fashion by interpreting solving linear PDEs as physics-informed Gaussian process (GP) regression. Our framework is based on a key generalization of the Gaussian process inference theorem to observations made via an arbitrary bounded linear operator. Crucially, this probabilistic viewpoint allows to (1) quantify the inherent discretization error; (2) propagate uncertainty about the model parameters to the solution; and (3) condition on noisy measurements. Demonstrating the strength of this formulation, we prove that it strictly generalizes methods of weighted residuals, a central class of PDE solvers including collocation, finite volume, pseudospectral, and (generalized) Galerkin methods such as finite element and spectral methods. This class can thus be directly equipped with a structured error estimate. In summary, our results enable the seamless integration of mechanistic models as modular building blocks into probabilistic models by blurring the boundaries between numerical analysis and Bayesian inference.
HAC-Net: A Hybrid Attention-Based Convolutional Neural Network for Highly Accurate Protein-Ligand Binding Affinity Prediction
Authors: Gregory W. Kyro, Rafael I. Brent, Victor S. Batista
Date: 2022-12-23 00:00:00
Tasks: Drug Discovery, Property Prediction

Applying deep learning concepts from image detection and graph theory has greatly advanced protein-ligand binding affinity prediction, a challenge with enormous ramifications for both drug discovery and protein engineering. We build upon these advances by designing a novel deep learning architecture consisting of a 3-dimensional convolutional neural network utilizing channel-wise attention and two graph convolutional networks utilizing attention-based aggregation of node features. HAC-Net (Hybrid Attention-Based Convolutional Neural Network) obtains state-of-the-art results on the PDBbind v.2016 core set, the most widely recognized benchmark in the field. We extensively assess the generalizability of our model using multiple train-test splits, each of which maximizes differences between either protein structures, protein sequences, or ligand extended-connectivity fingerprints of complexes in the training and test sets. Furthermore, we perform 10-fold cross-validation with a similarity cutoff between SMILES strings of ligands in the training and test sets, and also evaluate the performance of HAC-Net on lower-quality data. We envision that this model can be extended to a broad range of supervised learning problems related to structure-based biomolecular property prediction. All of our software is available as open source at https://github.com/gregory-kyro/HAC-Net/, and the HACNet Python package is available through PyPI.
Using MM principles to deal with incomplete data in K-means clustering
Authors: Ali Beikmohammadi
Date: 2022-12-23 00:00:00
Tasks: Clustering

Among many clustering algorithms, the K-means clustering algorithm is widely used because of its simple algorithm and fast convergence. However, this algorithm suffers from incomplete data, where some samples have missed some of their attributes. To solve this problem, we mainly apply MM principles to restore the symmetry of the data, so that K-means could work well. We give the pseudo-code of the algorithm and use the standard datasets for experimental verification. The source code for the experiments is publicly available in the following link: \url{https://github.com/AliBeikmohammadi/MM-Optimization/blob/main/mini-project/MM%20K-means.ipynb}.
Relational Local Explanations
Authors: Vadim Borisov, Gjergji Kasneci
Date: 2022-12-23 00:00:00

The majority of existing post-hoc explanation approaches for machine learning models produce independent, per-variable feature attribution scores, ignoring a critical inherent characteristics of homogeneously structured data, such as visual or text data: there exist latent inter-variable relationships between features. In response, we develop a novel model-agnostic and permutation-based feature attribution approach based on the relational analysis between input variables. As a result, we are able to gain a broader insight into the predictions and decisions of machine learning models. Experimental evaluations of our framework in comparison with state-of-the-art attribution techniques on various setups involving both image and text data modalities demonstrate the effectiveness and validity of our method.
Piecewise-Velocity Model for Learning Continuous-time Dynamic Node Representations
Authors: Abdulkadir Çelikkanat, Nikolaos Nakis, Morten Mørup
Date: 2022-12-23 00:00:00
Tasks: Graph Representation Learning, Link Prediction, Representation Learning

Networks have become indispensable and ubiquitous structures in many fields to model the interactions among different entities, such as friendship in social networks or protein interactions in biological graphs. A major challenge is to understand the structure and dynamics of these systems. Although networks evolve through time, most existing graph representation learning methods target only static networks. Whereas approaches have been developed for the modeling of dynamic networks, there is a lack of efficient continuous time dynamic graph representation learning methods that can provide accurate network characterization and visualization in low dimensions while explicitly accounting for prominent network characteristics such as homophily and transitivity. In this paper, we propose the Piecewise-Velocity Model (PiVeM) for the representation of continuous-time dynamic networks. It learns dynamic embeddings in which the temporal evolution of nodes is approximated by piecewise linear interpolations based on a latent distance model with piecewise constant node-specific velocities. The model allows for analytically tractable expressions of the associated Poisson process likelihood with scalable inference invariant to the number of events. We further impose a scalable Kronecker structured Gaussian Process prior to the dynamics accounting for community structure, temporal smoothness, and disentangled (uncorrelated) latent embedding dimensions optimally learned to characterize the network dynamics. We show that PiVeM can successfully represent network structure and dynamics in ultra-low two-dimensional spaces. It outperforms relevant state-of-art methods in downstream tasks such as link prediction. In summary, PiVeM enables easily interpretable dynamic network visualizations and characterizations that can further improve our understanding of the intrinsic dynamics of time-evolving networks.
The choice of scaling technique matters for classification performance
Authors: Lucas B. V. de Amorim, George D. C. Cavalcanti, Rafael M. O. Cruz
Date: 2022-12-23 00:00:00
Tasks: Classification

Dataset scaling, also known as normalization, is an essential preprocessing step in a machine learning pipeline. It is aimed at adjusting attributes scales in a way that they all vary within the same range. This transformation is known to improve the performance of classification models, but there are several scaling techniques to choose from, and this choice is not generally done carefully. In this paper, we execute a broad experiment comparing the impact of 5 scaling techniques on the performances of 20 classification algorithms among monolithic and ensemble models, applying them to 82 publicly available datasets with varying imbalance ratios. Results show that the choice of scaling technique matters for classification performance, and the performance difference between the best and the worst scaling technique is relevant and statistically significant in most cases. They also indicate that choosing an inadequate technique can be more detrimental to classification performance than not scaling the data at all. We also show how the performance variation of an ensemble model, considering different scaling techniques, tends to be dictated by that of its base model. Finally, we discuss the relationship between a model's sensitivity to the choice of scaling technique and its performance and provide insights into its applicability on different model deployment scenarios. Full results and source code for the experiments in this paper are available in a GitHub repository.\footnote{https://github.com/amorimlb/scaling\_matters}
Rule Learning by Modularity
Authors: Albert Nössig, Tobias Hell, Georg Moser
Date: 2022-12-23 00:00:00

In this paper, we present a modular methodology that combines state-of-the-art methods in (stochastic) machine learning with traditional methods in rule learning to provide efficient and scalable algorithms for the classification of vast data sets, while remaining explainable. Apart from evaluating our approach on the common large scale data sets MNIST, Fashion-MNIST and IMDB, we present novel results on explainable classifications of dental bills. The latter case study stems from an industrial collaboration with Allianz Private Krankenversicherungs-Aktiengesellschaft which is an insurance company offering diverse services in Germany.
Introduction to Machine Learning for Physicians: A Survival Guide for Data Deluge
Authors: Ričards Marcinkevičs, Ece Ozkan, Julia E. Vogt
Date: 2022-12-23 00:00:00

Many modern research fields increasingly rely on collecting and analysing massive, often unstructured, and unwieldy datasets. Consequently, there is growing interest in machine learning and artificial intelligence applications that can harness this `data deluge'. This broad nontechnical overview provides a gentle introduction to machine learning with a specific focus on medical and biological applications. We explain the common types of machine learning algorithms and typical tasks that can be solved, illustrating the basics with concrete examples from healthcare. Lastly, we provide an outlook on open challenges, limitations, and potential impacts of machine-learning-powered medicine.
Statistical Distance Based Deterministic Offspring Selection in SMC Methods
Authors: Oskar Kviman, Hazal Koptagel, Harald Melin, Jens Lagergren
Date: 2022-12-23 00:00:00
Tasks: Heuristic Search

Over the years, sequential Monte Carlo (SMC) and, equivalently, particle filter (PF) theory has gained substantial attention from researchers. However, the performance of the resampling methodology, also known as offspring selection, has not advanced recently. We propose two deterministic offspring selection methods, which strive to minimize the Kullback-Leibler (KL) divergence and the total variation (TV) distance, respectively, between the particle distribution prior and subsequent to the offspring selection. By reducing the statistical distance between the selected offspring and the joint distribution, we obtain a heuristic search procedure that performs superior to a maximum likelihood search in precisely those contexts where the latter performs better than an SMC. For SMC and particle Markov chain Monte Carlo (pMCMC), our proposed offspring selection methods always outperform or compare favorably with the two state-of-the-art resampling schemes on two models commonly used as benchmarks from the literature.
Exploring the Optimized Value of Each Hyperparameter in Various Gradient Descent Algorithms
Authors: Abel C. H. Chen
Date: 2022-12-23 00:00:00
Tasks: Model Optimization

In the recent years, various gradient descent algorithms including the methods of gradient descent, gradient descent with momentum, adaptive gradient (AdaGrad), root-mean-square propagation (RMSProp) and adaptive moment estimation (Adam) have been applied to the parameter optimization of several deep learning models with higher accuracies or lower errors. These optimization algorithms may need to set the values of several hyperparameters which include a learning rate, momentum coefficients, etc. Furthermore, the convergence speed and solution accuracy may be influenced by the values of hyperparameters. Therefore, this study proposes an analytical framework to use mathematical models for analyzing the mean error of each objective function based on various gradient descent algorithms. Moreover, the suitable value of each hyperparameter could be determined by minimizing the mean error. The principles of hyperparameter value setting have been generalized based on analysis results for model optimization. The experimental results show that higher efficiency convergences and lower errors can be obtained by the proposed method.
Investigation of reinforcement learning for shape optimization of profile extrusion dies
Authors: Clemens Fricke, Daniel Wolff, Marco Kemmerling, Stefanie Elgeti
Date: 2022-12-23 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning (RL)

Profile extrusion is a continuous production process for manufacturing plastic profiles from molten polymer. Especially interesting is the design of the die, through which the melt is pressed to attain the desired shape. However, due to an inhomogeneous velocity distribution at the die exit or residual stresses inside the extrudate, the final shape of the manufactured part often deviates from the desired one. To avoid these deviations, the shape of the die can be computationally optimized, which has already been investigated in the literature using classical optimization approaches. A new approach in the field of shape optimization is the utilization of Reinforcement Learning (RL) as a learning-based optimization algorithm. RL is based on trial-and-error interactions of an agent with an environment. For each action, the agent is rewarded and informed about the subsequent state of the environment. While not necessarily superior to classical, e.g., gradient-based or evolutionary, optimization algorithms for one single problem, RL techniques are expected to perform especially well when similar optimization tasks are repeated since the agent learns a more general strategy for generating optimal shapes instead of concentrating on just one single problem. In this work, we investigate this approach by applying it to two 2D test cases. The flow-channel geometry can be modified by the RL agent using so-called Free-Form Deformation, a method where the computational mesh is embedded into a transformation spline, which is then manipulated based on the control-point positions. In particular, we investigate the impact of utilizing different agents on the training progress and the potential of wall time saving by utilizing multiple environments during training.
Deep Unfolding-based Weighted Averaging for Federated Learning in Heterogeneous Environments
Authors: Ayano Nakai-Kasai, Tadashi Wadayama
Date: 2022-12-23 00:00:00
Tasks: Federated Learning

Federated learning is a collaborative model training method that iterates model updates by multiple clients and aggregation of the updates by a central server. Device and statistical heterogeneity of participating clients cause significant performance degradation so that an appropriate aggregation weight should be assigned to each client in the aggregation phase of the server. To adjust the aggregation weights, this paper employs deep unfolding, which is known as the parameter tuning method that leverages both learning capability using training data like deep learning and domain knowledge. This enables us to directly incorporate the heterogeneity of the environment of interest into the tuning of the aggregation weights. The proposed approach can be combined with various federated learning algorithms. The results of numerical experiments indicate that a higher test accuracy for unknown class-balanced data can be obtained with the proposed method than that with conventional heuristic weighting methods. The proposed method can handle large-scale learning models with the aid of pretrained models such that it can perform practical real-world tasks. Convergence rate of federated learning algorithms with the proposed method is also provided in this paper.
Look Around! A Neighbor Relation Graph Learning Framework for Real Estate Appraisal
Authors: Chih-Chia Li, Wei-Yao Wang, Wei-Wei Du, Wen-Chih Peng
Date: 2022-12-23 00:00:00
Tasks: Graph Learning, Relation

Real estate appraisal is a crucial issue for urban applications, which aims to value the properties on the market. Traditional methods perform appraisal based on the domain knowledge, but suffer from the efforts of hand-crafted design. Recently, several methods have been developed to automatize the valuation process by taking the property trading transaction into account when estimating the property value. However, existing methods only consider the real estate itself, ignoring the relation between the properties. Moreover, naively aggregating the information of neighbors fails to model the relationships between the transactions. To tackle these limitations, we propose a novel Neighbor Relation Graph Learning Framework (ReGram) by incorporating the relation between target transaction and surrounding neighbors with the attention mechanism. To model the influence between communities, we integrate the environmental information and the past price of each transaction from other communities. Moreover, since the target transactions in different regions share some similarities and differences of characteristics, we introduce a dynamic adapter to model the different distributions of the target transactions based on the input-related kernel weights. Extensive experiments on the real-world dataset with various scenarios demonstrate that ReGram robustly outperforms the state-of-the-art methods. Furthermore, comprehensive ablation studies were conducted to examine the effectiveness of each component in ReGram.
Stop using the elbow criterion for k-means and how to choose the number of clusters instead
Authors: Erich Schubert
Date: 2022-12-23 00:00:00
Tasks: Clustering

A major challenge when using k-means clustering often is how to choose the parameter k, the number of clusters. In this letter, we want to point out that it is very easy to draw poor conclusions from a common heuristic, the "elbow method". Better alternatives have been known in literature for a long time, and we want to draw attention to some of these easy to use options, that often perform better. This letter is a call to stop using the elbow method altogether, because it severely lacks theoretic support, and we want to encourage educators to discuss the problems of the method -- if introducing it in class at all -- and teach alternatives instead, while researchers and reviewers should reject conclusions drawn from the elbow method.
Autothrottle: A Practical Bi-Level Approach to Resource Management for SLO-Targeted Microservices
Authors: Zibo Wang, Pinghe Li, Chieh-Jan Mike Liang, Feng Wu, Francis Y. Yan
Date: 2022-12-23 00:00:00
Tasks: CPU, Management

Achieving resource efficiency while preserving end-user experience is non-trivial for cloud application operators. As cloud applications progressively adopt microservices, resource managers are faced with two distinct levels of system behavior: end-to-end application latency and per-service resource usage. Translating between the two levels, however, is challenging because user requests traverse heterogeneous services that collectively (but unevenly) contribute to the end-to-end latency. We present Autothrottle, a bi-level resource management framework for microservices with latency SLOs (service-level objectives). It architecturally decouples application SLO feedback from service resource control, and bridges them through the notion of performance targets. Specifically, an application-wide learning-based controller is employed to periodically set performance targets -- expressed as CPU throttle ratios -- for per-service heuristic controllers to attain. We evaluate Autothrottle on three microservice applications, with workload traces from production scenarios. Results show superior CPU savings, up to 26.21% over the best-performing baseline and up to 93.84% over all baselines.