pwc-archive/papers-with-abstracts huggingface dataset:
Accelerated Markov Chain Monte Carlo Using Adaptive Weighting Scheme
Authors: Yanbo Wang, Wenyu Chen, Shimin Shan
Date: 2024-08-23 00:00:00

Gibbs sampling is one of the most commonly used Markov Chain Monte Carlo (MCMC) algorithms due to its simplicity and efficiency. It cycles through the latent variables, sampling each one from its distribution conditional on the current values of all the other variables. Conventional Gibbs sampling is based on the systematic scan (with a deterministic order of variables). In contrast, in recent years, Gibbs sampling with random scan has shown its advantage in some scenarios. However, almost all the analyses of Gibbs sampling with the random scan are based on uniform selection of variables. In this paper, we focus on a random scan Gibbs sampling method that selects each latent variable non-uniformly. Firstly, we show that this non-uniform scan Gibbs sampling leaves the target posterior distribution invariant. Then we explore how to determine the selection probability for latent variables. In particular, we construct an objective as a function of the selection probability and solve the constrained optimization problem. We further derive an analytic solution of the selection probability, which can be estimated easily. Our algorithm relies on the simple intuition that choosing the variable updates according to their marginal probabilities enhances the mixing time of the Markov chain. Finally, we validate the effectiveness of the proposed Gibbs sampler by conducting a set of experiments on real-world applications.
Disentangling, Amplifying, and Debiasing: Learning Disentangled Representations for Fair Graph Neural Networks
Authors: Yeon-Chang Lee, Hojung Shin, Sang-Wook Kim
Date: 2024-08-23 00:00:00
Tasks: Attribute, Disentanglement, Fairness, Graph Representation Learning, Representation Learning

Graph Neural Networks (GNNs) have become essential tools for graph representation learning in various domains, such as social media and healthcare. However, they often suffer from fairness issues due to inherent biases in node attributes and graph structure, leading to unfair predictions. To address these challenges, we propose a novel GNN framework, DAB-GNN, that Disentangles, Amplifies, and deBiases attribute, structure, and potential biases in the GNN mechanism. DAB-GNN employs a disentanglement and amplification module that isolates and amplifies each type of bias through specialized disentanglers, followed by a debiasing module that minimizes the distance between subgroup distributions. Extensive experiments on five datasets demonstrate that DAB-GNN significantly outperforms ten state-of-the-art competitors in terms of achieving an optimal balance between accuracy and fairness. The codebase of DAB-GNN is available at https://github.com/Bigdasgit/DAB-GNN
Multi-Faceted Question Complexity Estimation Targeting Topic Domain-Specificity
Authors: Sujay R, Suki Perumal, Yash Nagraj, Anushka Ghei, Srinivas K S
Date: 2024-08-23 00:00:00
Tasks: Information Retrieval, Question Generation, Question-Generation, Retrieval, Specificity

Question difficulty estimation remains a multifaceted challenge in educational and assessment settings. Traditional approaches often focus on surface-level linguistic features or learner comprehension levels, neglecting the intricate interplay of factors contributing to question complexity. This paper presents a novel framework for domain-specific question difficulty estimation, leveraging a suite of NLP techniques and knowledge graph analysis. We introduce four key parameters: Topic Retrieval Cost, Topic Salience, Topic Coherence, and Topic Superficiality, each capturing a distinct facet of question complexity within a given subject domain. These parameters are operationalized through topic modelling, knowledge graph analysis, and information retrieval techniques. A model trained on these features demonstrates the efficacy of our approach in predicting question difficulty. By operationalizing these parameters, our framework offers a novel approach to question complexity estimation, paving the way for more effective question generation, assessment design, and adaptive learning systems across diverse academic disciplines.
HGNAS: Hardware-Aware Graph Neural Architecture Search for Edge Devices
Authors: Ao Zhou, Jianlei Yang, Yingjie Qi, Tong Qiao, Yumeng Shi, Cenlin Duan, Weisheng Zhao, Chunming Hu
Date: 2024-08-23 00:00:00
Tasks: GPU, Neural Architecture Search

Graph Neural Networks (GNNs) are becoming increasingly popular for graph-based learning tasks such as point cloud processing due to their state-of-the-art (SOTA) performance. Nevertheless, the research community has primarily focused on improving model expressiveness, lacking consideration of how to design efficient GNN models for edge scenarios with real-time requirements and limited resources. Examining existing GNN models reveals varied execution across platforms and frequent Out-Of-Memory (OOM) problems, highlighting the need for hardware-aware GNN design. To address this challenge, this work proposes a novel hardware-aware graph neural architecture search framework tailored for resource constraint edge devices, namely HGNAS. To achieve hardware awareness, HGNAS integrates an efficient GNN hardware performance predictor that evaluates the latency and peak memory usage of GNNs in milliseconds. Meanwhile, we study GNN memory usage during inference and offer a peak memory estimation method, enhancing the robustness of architecture evaluations when combined with predictor outcomes. Furthermore, HGNAS constructs a fine-grained design space to enable the exploration of extreme performance architectures by decoupling the GNN paradigm. In addition, the multi-stage hierarchical search strategy is leveraged to facilitate the navigation of huge candidates, which can reduce the single search time to a few GPU hours. To the best of our knowledge, HGNAS is the first automated GNN design framework for edge devices, and also the first work to achieve hardware awareness of GNNs across different platforms. Extensive experiments across various applications and edge devices have proven the superiority of HGNAS. It can achieve up to a 10.6x speedup and an 82.5% peak memory reduction with negligible accuracy loss compared to DGCNN on ModelNet40.
SAMBO-RL: Shifts-aware Model-based Offline Reinforcement Learning
Authors: Wang Luo, Haoran Li, ZiCheng Zhang, Congying Han, Jiayu Lv, Tiande Guo
Date: 2024-08-23 00:00:00
Tasks: reinforcement-learning, Reinforcement Learning

Model-based Offline Reinforcement Learning trains policies based on offline datasets and model dynamics, without direct real-world environment interactions. However, this method is inherently challenged by distribution shift. Previous approaches have primarily focused on tackling this issue directly leveraging off-policy mechanisms and heuristic uncertainty in model dynamics, but they resulted in inconsistent objectives and lacked a unified theoretical foundation. This paper offers a comprehensive analysis that disentangles the problem into two key components: model bias and policy shift. We provide both theoretical insights and empirical evidence to demonstrate how these factors lead to inaccuracies in value function estimation and impose implicit restrictions on policy learning. To address these challenges, we derive adjustment terms for model bias and policy shift within a unified probabilistic inference framework. These adjustments are seamlessly integrated into the vanilla reward function to create a novel Shifts-aware Reward (SAR), aiming at refining value learning and facilitating policy training. Furthermore, we introduce Shifts-aware Model-based Offline Reinforcement Learning (SAMBO-RL), a practical framework that efficiently trains classifiers to approximate the SAR for policy optimization. Empirically, we show that SAR effectively mitigates distribution shift, and SAMBO-RL demonstrates superior performance across various benchmarks, underscoring its practical effectiveness and validating our theoretical analysis.
Uncertainty-Aware Mean Opinion Score Prediction
Authors: Hui Wang, Shiwan Zhao, Jiaming Zhou, Xiguang Zheng, Haoqin Sun, Xuechen Wang, Yong Qin
Date: 2024-08-23 00:00:00
Tasks: Prediction

Mean Opinion Score (MOS) prediction has made significant progress in specific domains. However, the unstable performance of MOS prediction models across diverse samples presents ongoing challenges in the practical application of these systems. In this paper, we point out that the absence of uncertainty modeling is a significant limitation hindering MOS prediction systems from applying to the real and open world. We analyze the sources of uncertainty in the MOS prediction task and propose to establish an uncertainty-aware MOS prediction system that models aleatory uncertainty and epistemic uncertainty by heteroscedastic regression and Monte Carlo dropout separately. The experimental results show that the system captures uncertainty well and is capable of performing selective prediction and out-of-domain detection. Such capabilities significantly enhance the practical utility of MOS systems in diverse real and open-world environments.
Data-Driven Parametrization of Molecular Mechanics Force Fields for Expansive Chemical Space Coverage
Authors: Tianze Zheng, Ailun Wang, Xu Han, Yu Xia, Xingyuan Xu, Jiawei Zhan, Yu Liu, Yang Chen, Zhi Wang, Xiaojie Wu, Sheng Gong, Wen Yan
Date: 2024-08-23 00:00:00
Tasks: Computational Efficiency, Drug Discovery, Graph Neural Network

A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges. In this study, we address this issue using a modern data-driven approach, developing ByteFF, an Amber-compatible force field for drug-like molecules. To create ByteFF, we generated an expansive and highly diverse molecular dataset at the B3LYP-D3(BJ)/DZVP level of theory. This dataset includes 2.4 million optimized molecular fragment geometries with analytical Hessian matrices, along with 3.2 million torsion profiles. We then trained an edge-augmented, symmetry-preserving molecular graph neural network (GNN) on this dataset, employing a carefully optimized training strategy. Our model predicts all bonded and non-bonded MM force field parameters for drug-like molecules simultaneously across a broad chemical space. ByteFF demonstrates state-of-the-art performance on various benchmark datasets, excelling in predicting relaxed geometries, torsional energy profiles, and conformational energies and forces. Its exceptional accuracy and expansive chemical space coverage make ByteFF a valuable tool for multiple stages of computational drug discovery.
Robust Predictions with Ambiguous Time Delays: A Bootstrap Strategy
Authors: Jiajie Wang, Zhiyuan Jerry Lin, Wen Chen
Date: 2024-08-23 00:00:00
Tasks: Time Series

In contemporary data-driven environments, the generation and processing of multivariate time series data is an omnipresent challenge, often complicated by time delays between different time series. These delays, originating from a multitude of sources like varying data transmission dynamics, sensor interferences, and environmental changes, introduce significant complexities. Traditional Time Delay Estimation methods, which typically assume a fixed constant time delay, may not fully capture these variabilities, compromising the precision of predictive models in diverse settings. To address this issue, we introduce the Time Series Model Bootstrap (TSMB), a versatile framework designed to handle potentially varying or even nondeterministic time delays in time series modeling. Contrary to traditional approaches that hinge on the assumption of a single, consistent time delay, TSMB adopts a nonparametric stance, acknowledging and incorporating time delay uncertainties. TSMB significantly bolsters the performance of models that are trained and make predictions using this framework, making it highly suitable for a wide range of dynamic and interconnected data environments.
Contrastive Representation Learning for Dynamic Link Prediction in Temporal Networks
Authors: Amirhossein Nouranizadeh, Fatemeh Tabatabaei Far, Mohammad Rahmati
Date: 2024-08-22 00:00:00
Tasks: Contrastive Learning, Dynamic Link Prediction, Graph Neural Network, Graph Reconstruction, Link Prediction, Representation Learning

Evolving networks are complex data structures that emerge in a wide range of systems in science and engineering. Learning expressive representations for such networks that encode their structural connectivity and temporal evolution is essential for downstream data analytics and machine learning applications. In this study, we introduce a self-supervised method for learning representations of temporal networks and employ these representations in the dynamic link prediction task. While temporal networks are typically characterized as a sequence of interactions over the continuous time domain, our study focuses on their discrete-time versions. This enables us to balance the trade-off between computational complexity and precise modeling of the interactions. We propose a recurrent message-passing neural network architecture for modeling the information flow over time-respecting paths of temporal networks. The key feature of our method is the contrastive training objective of the model, which is a combination of three loss functions: link prediction, graph reconstruction, and contrastive predictive coding losses. The contrastive predictive coding objective is implemented using infoNCE losses at both local and global scales of the input graphs. We empirically show that the additional self-supervised losses enhance the training and improve the model's performance in the dynamic link prediction task. The proposed method is tested on Enron, COLAB, and Facebook datasets and exhibits superior results compared to existing models.
ADRS-CNet: An adaptive dimensionality reduction selection and classification network for DNA storage clustering algorithms
Authors: Bowen Liu, Jiankun Li
Date: 2024-08-22 00:00:00
Tasks: Clustering, Dimensionality Reduction

DNA storage technology offers new possibilities for addressing massive data storage due to its high storage density, long-term preservation, low maintenance cost, and compact size. To improve the reliability of stored information, base errors and missing storage sequences are challenges that must be faced. Currently, clustering and comparison of sequenced sequences are employed to recover the original sequence information as much as possible. Nonetheless, extracting DNA sequences of different lengths as features leads to the curse of dimensionality, which needs to be overcome. To address this, techniques like PCA, UMAP, and t-SNE are commonly employed to project high-dimensional features into low-dimensional space. Considering that these methods exhibit varying effectiveness in dimensionality reduction when dealing with different datasets, this paper proposes training a multilayer perceptron model to classify input DNA sequence features and adaptively select the most suitable dimensionality reduction method to enhance subsequent clustering results. Through testing on open-source datasets and comparing our approach with various baseline methods, experimental results demonstrate that our model exhibits superior classification performance and significantly improves clustering outcomes. This displays that our approach effectively mitigates the impact of the curse of dimensionality on clustering models.
Quantum Convolutional Neural Networks are (Effectively) Classically Simulable
Authors: Pablo Bermejo, Paolo Braccia, Manuel S. Rudolph, Zoë Holmes, Lukasz Cincio, M. Cerezo
Date: 2024-08-22 00:00:00
Tasks: Quantum Machine Learning

Quantum Convolutional Neural Networks (QCNNs) are widely regarded as a promising model for Quantum Machine Learning (QML). In this work we tie their heuristic success to two facts. First, that when randomly initialized, they can only operate on the information encoded in low-bodyness measurements of their input states. And second, that they are commonly benchmarked on "locally-easy'' datasets whose states are precisely classifiable by the information encoded in these low-bodyness observables subspace. We further show that the QCNN's action on this subspace can be efficiently classically simulated by a classical algorithm equipped with Pauli shadows on the dataset. Indeed, we present a shadow-based simulation of QCNNs on up-to $1024$ qubits for phases of matter classification. Our results can then be understood as highlighting a deeper symptom of QML: Models could only be showing heuristic success because they are benchmarked on simple problems, for which their action can be classically simulated. This insight points to the fact that non-trivial datasets are a truly necessary ingredient for moving forward with QML. To finish, we discuss how our results can be extrapolated to classically simulate other architectures.
New Bounds on Quantum Sample Complexity of Measurement Classes
Authors: Mohsen Heidari, Wojciech Szpankowski
Date: 2024-08-22 00:00:00

This paper studies quantum supervised learning for classical inference from quantum states. In this model, a learner has access to a set of labeled quantum samples as the training set. The objective is to find a quantum measurement that predicts the label of the unseen samples. The hardness of learning is measured via sample complexity under a quantum counterpart of the well-known probably approximately correct (PAC). Quantum sample complexity is expected to be higher than classical one, because of the measurement incompatibility and state collapse. Recent efforts showed that the sample complexity of learning a finite quantum concept class $\mathcal{C}$ scales as $O(|\mathcal{C}|)$. This is significantly higher than the classical sample complexity that grows logarithmically with the class size. This work improves the sample complexity bound to $O(V_{\mathcal{C}^*} \log |\mathcal{C}^*|)$, where $\mathcal{C}^*$ is the set of extreme points of the convex closure of $\mathcal{C}$ and $V_{\mathcal{C}^*}$ is the shadow-norm of this set. We show the tightness of our bound for the class of bounded Hilbert-Schmidt norm, scaling as $O(\log |\mathcal{C}^*|)$. Our approach is based on a new quantum empirical risk minimization (ERM) algorithm equipped with a shadow tomography method.
Improving Radiography Machine Learning Workflows via Metadata Management for Training Data Selection
Authors: Mirabel Reid, Christine Sweeney, Oleg Korobkin
Date: 2024-08-22 00:00:00
Tasks: Feature Engineering, Management

Most machine learning models require many iterations of hyper-parameter tuning, feature engineering, and debugging to produce effective results. As machine learning models become more complicated, this pipeline becomes more difficult to manage effectively. In the physical sciences, there is an ever-increasing pool of metadata that is generated by the scientific research cycle. Tracking this metadata can reduce redundant work, improve reproducibility, and aid in the feature and training dataset engineering process. In this case study, we present a tool for machine learning metadata management in dynamic radiography. We evaluate the efficacy of this tool against the initial research workflow and discuss extensions to general machine learning pipelines in the physical sciences.
Wave-LSTM: Multi-scale analysis of somatic whole genome copy number profiles
Authors: Charles Gadd, Christopher Yau
Date: 2024-08-22 00:00:00
Tasks: Survival Prediction

Changes in the number of copies of certain parts of the genome, known as copy number alterations (CNAs), due to somatic mutation processes are a hallmark of many cancers. This genomic complexity is known to be associated with poorer outcomes for patients but describing its contribution in detail has been difficult. Copy number alterations can affect large regions spanning whole chromosomes or the entire genome itself but can also be localised to only small segments of the genome and no methods exist that allow this multi-scale nature to be quantified. In this paper, we address this using Wave-LSTM, a signal decomposition approach designed to capture the multi-scale structure of complex whole genome copy number profiles. Using wavelet-based source separation in combination with deep learning-based attention mechanisms. We show that Wave-LSTM can be used to derive multi-scale representations from copy number profiles which can be used to decipher sub-clonal structures from single-cell copy number data and to improve survival prediction performance from patient tumour profiles.
Domain-specific long text classification from sparse relevant information
Authors: Célia D'Cruz, Jean-Marc Bereder, Frédéric Precioso, Michel Riveill
Date: 2024-08-23 00:00:00
Tasks: Sentiment Analysis, text-classification, Text Classification

Large Language Models have undoubtedly revolutionized the Natural Language Processing field, the current trend being to promote one-model-for-all tasks (sentiment analysis, translation, etc.). However, the statistical mechanisms at work in the larger language models struggle to exploit the relevant information when it is very sparse, when it is a weak signal. This is the case, for example, for the classification of long domain-specific documents, when the relevance relies on a single relevant word or on very few relevant words from technical jargon. In the medical domain, it is essential to determine whether a given report contains critical information about a patient's condition. This critical information is often based on one or few specific isolated terms. In this paper, we propose a hierarchical model which exploits a short list of potential target terms to retrieve candidate sentences and represent them into the contextualized embedding of the target term(s) they contain. A pooling of the term(s) embedding(s) entails the document representation to be classified. We evaluate our model on one public medical document benchmark in English and on one private French medical dataset. We show that our narrower hierarchical model is better than larger language models for retrieving relevant long documents in a domain-specific context.
Which Prosodic Features Matter Most for Pragmatics?
Authors: Nigel G. Ward, Divette Marco, Olac Fuentes
Date: 2024-08-23 00:00:00
Tasks: Speech Synthesis

We investigate which prosodic features matter most in conveying prosodic functions. We use the problem of predicting human perceptions of pragmatic similarity among utterance pairs to evaluate the utility of prosodic features of different types. We find, for example, that duration-related features are more important than pitch-related features, and that utterance-initial features are more important than utterance-final features. Further, failure analysis indicates that modeling using pitch features only often fails to handle important pragmatic functions, and suggests that several generally-neglected acoustic and prosodic features are pragmatically significant, including nasality and vibrato. These findings can guide future basic research in prosody, and suggest how to improve speech synthesis evaluation, among other applications.