pwc-archive/papers-with-abstracts huggingface dataset:
Uncertainty Quantification Using Ensemble Learning and Monte Carlo Sampling for Performance Prediction and Monitoring in Cell Culture Processes
Authors: Thanh Tung Khuat, Robert Bassett, Ellen Otte, Bogdan Gabrys
Date: 2024-09-03 00:00:00
Tasks: Ensemble Learning, Specificity, Uncertainty Quantification

Biopharmaceutical products, particularly monoclonal antibodies (mAbs), have gained prominence in the pharmaceutical market due to their high specificity and efficacy. As these products are projected to constitute a substantial portion of global pharmaceutical sales, the application of machine learning models in mAb development and manufacturing is gaining momentum. This paper addresses the critical need for uncertainty quantification in machine learning predictions, particularly in scenarios with limited training data. Leveraging ensemble learning and Monte Carlo simulations, our proposed method generates additional input samples to enhance the robustness of the model in small training datasets. We evaluate the efficacy of our approach through two case studies: predicting antibody concentrations in advance and real-time monitoring of glucose concentrations during bioreactor runs using Raman spectra data. Our findings demonstrate the effectiveness of the proposed method in estimating the uncertainty levels associated with process performance predictions and facilitating real-time decision-making in biopharmaceutical manufacturing. This contribution not only introduces a novel approach for uncertainty quantification but also provides insights into overcoming challenges posed by small training datasets in bioprocess development. The evaluation demonstrates the effectiveness of our method in addressing key challenges related to uncertainty estimation within upstream cell cultivation, illustrating its potential impact on enhancing process control and product quality in the dynamic field of biopharmaceuticals.
Federated Prediction-Powered Inference from Decentralized Data
Authors: Ping Luo, Xiaoge Deng, Ziqing Wen, Tao Sun, Dongsheng Li
Date: 2024-09-03 00:00:00
Tasks: Federated Learning, Prediction, valid

In various domains, the increasing application of machine learning allows researchers to access inexpensive predictive data, which can be utilized as auxiliary data for statistical inference. Although such data are often unreliable compared to gold-standard datasets, Prediction-Powered Inference (PPI) has been proposed to ensure statistical validity despite the unreliability. However, the challenge of `data silos' arises when the private gold-standard datasets are non-shareable for model training, leading to less accurate predictive models and invalid inferences. In this paper, we introduces the Federated Prediction-Powered Inference (Fed-PPI) framework, which addresses this challenge by enabling decentralized experimental data to contribute to statistically valid conclusions without sharing private information. The Fed-PPI framework involves training local models on private data, aggregating them through Federated Learning (FL), and deriving confidence intervals using PPI computation. The proposed framework is evaluated through experiments, demonstrating its effectiveness in producing valid confidence intervals.
Toward Capturing Genetic Epistasis From Multivariate Genome-Wide Association Studies Using Mixed-Precision Kernel Ridge Regression
Authors: Hatem Ltaief, Rabab Alomairy, Qinglei Cao, Jie Ren, Lotfi Slim, Thorsten Kurth, Benedikt Dorschner, Salim Bougouffa, Rached Abdelkhalak, David E. Keyes
Date: 2024-09-03 00:00:00
Tasks: CPU, GPU

We exploit the widening margin in tensor-core performance between [FP64/FP32/FP16/INT8,FP64/FP32/FP16/FP8/INT8] on NVIDIA [Ampere,Hopper] GPUs to boost the performance of output accuracy-preserving mixed-precision computation of Genome-Wide Association Studies (GWAS) of 305K patients from the UK BioBank, the largest-ever GWAS cohort studied for genetic epistasis using a multivariate approach. Tile-centric adaptive-precision linear algebraic techniques motivated by reducing data motion gain enhanced significance with low-precision GPU arithmetic. At the core of Kernel Ridge Regression (KRR) techniques for GWAS lie compute-bound cubic-complexity matrix operations that inhibit scaling to aspirational dimensions of the population, genotypes, and phenotypes. We accelerate KRR matrix generation by redesigning the computation for Euclidean distances to engage INT8 tensor cores while exploiting symmetry.We accelerate solution of the regularized KRR systems by deploying a new four-precision Cholesky-based solver, which, at 1.805 mixed-precision ExaOp/s on a nearly full Alps system, outperforms the state-of-the-art CPU-only REGENIE GWAS software by five orders of magnitude.
A sparse PAC-Bayesian approach for high-dimensional quantile prediction
Authors: The Tien Mai
Date: 2024-09-03 00:00:00
Tasks: Econometrics, quantile regression, regression

Quantile regression, a robust method for estimating conditional quantiles, has advanced significantly in fields such as econometrics, statistics, and machine learning. In high-dimensional settings, where the number of covariates exceeds sample size, penalized methods like lasso have been developed to address sparsity challenges. Bayesian methods, initially connected to quantile regression via the asymmetric Laplace likelihood, have also evolved, though issues with posterior variance have led to new approaches, including pseudo/score likelihoods. This paper presents a novel probabilistic machine learning approach for high-dimensional quantile prediction. It uses a pseudo-Bayesian framework with a scaled Student-t prior and Langevin Monte Carlo for efficient computation. The method demonstrates strong theoretical guarantees, through PAC-Bayes bounds, that establish non-asymptotic oracle inequalities, showing minimax-optimal prediction error and adaptability to unknown sparsity. Its effectiveness is validated through simulations and real-world data, where it performs competitively against established frequentist and Bayesian techniques.
Optimizing Mortality Prediction for ICU Heart Failure Patients: Leveraging XGBoost and Advanced Machine Learning with the MIMIC-III Database
Authors: Negin Ashrafi, Armin Abdollahi, Jiahong Zhang, Maryam Pishgar
Date: 2024-09-03 00:00:00
Tasks: Feature Importance, feature selection, Hyperparameter Optimization, Mortality Prediction

Heart failure affects millions of people worldwide, significantly reducing quality of life and leading to high mortality rates. Despite extensive research, the relationship between heart failure and mortality rates among ICU patients is not fully understood, indicating the need for more accurate prediction models. This study analyzed data from 1,177 patients over 18 years old from the MIMIC-III database, identified using ICD-9 codes. Preprocessing steps included handling missing data, removing duplicates, treating skewness, and using oversampling techniques to address data imbalances. Through rigorous feature selection using Variance Inflation Factor (VIF), expert clinical input, and ablation studies, 46 key features were identified to enhance model performance. Our analysis compared several machine learning models, including Logistic Regression, Support Vector Machine (SVM), Random Forest, LightGBM, and XGBoost. XGBoost emerged as the superior model, achieving a test AUC-ROC of 0.9228 (95\% CI 0.8748 - 0.9613), significantly outperforming our previous work (AUC-ROC of 0.8766) and the best results reported in existing literature (AUC-ROC of 0.824). The improved model's success is attributed to advanced feature selection methods, robust preprocessing techniques, and comprehensive hyperparameter optimization through Grid-Search. SHAP analysis and feature importance evaluations based on XGBoost highlighted key variables like leucocyte count and RDW, providing valuable insights into the clinical factors influencing mortality risk. This framework offers significant support for clinicians, enabling them to identify high-risk ICU heart failure patients and improve patient outcomes through timely and informed interventions.
Graphons of Line Graphs
Authors: Sevvandi Kandanaarachchi, Cheng Soon Ong
Date: 2024-09-03 00:00:00

We consider the problem of estimating graph limits, known as graphons, from observations of sequences of sparse finite graphs. In this paper we show a simple method that can shed light on a subset of sparse graphs. The method involves mapping the original graphs to their line graphs. We show that graphs satisfying a particular property, which we call the square-degree property are sparse, but give rise to dense line graphs. This enables the use of results on graph limits of dense graphs to derive convergence. In particular, star graphs satisfy the square-degree property resulting in dense line graphs and non-zero graphons of line graphs. We demonstrate empirically that we can distinguish different numbers of stars (which are sparse) by the graphons of their corresponding line graphs. Whereas in the original graphs, the different number of stars all converge to the zero graphon due to sparsity. Similarly, superlinear preferential attachment graphs give rise to dense line graphs almost surely. In contrast, dense graphs, including Erdos-Renyi graphs make the line graphs sparse, resulting in the zero graphon.
CTG-KrEW: Generating Synthetic Structured Contextually Correlated Content by Conditional Tabular GAN with K-Means Clustering and Efficient Word Embedding
Authors: Riya Samanta, Bidyut Saha, Soumya K. Ghosh, Sajal K. Das
Date: 2024-09-03 00:00:00
Tasks: Attribute, CPU

Conditional Tabular Generative Adversarial Networks (CTGAN) and their various derivatives are attractive for their ability to efficiently and flexibly create synthetic tabular data, showcasing strong performance and adaptability. However, there are certain critical limitations to such models. The first is their inability to preserve the semantic integrity of contextually correlated words or phrases. For instance, skillset in freelancer profiles is one such attribute where individual skills are semantically interconnected and indicative of specific domain interests or qualifications. The second challenge of traditional approaches is that, when applied to generate contextually correlated tabular content, besides generating semantically shallow content, they consume huge memory resources and CPU time during the training stage. To address these problems, we introduce a novel framework, CTGKrEW (Conditional Tabular GAN with KMeans Clustering and Word Embedding), which is adept at generating realistic synthetic tabular data where attributes are collections of semantically and contextually coherent words. CTGKrEW is trained and evaluated using a dataset from Upwork, a realworld freelancing platform. Comprehensive experiments were conducted to analyze the variability, contextual similarity, frequency distribution, and associativity of the generated data, along with testing the framework's system feasibility. CTGKrEW also takes around 99\% less CPU time and 33\% less memory footprints than the conventional approach. Furthermore, we developed KrEW, a web application to facilitate the generation of realistic data containing skill-related information. This application, available at https://riyasamanta.github.io/krew.html, is freely accessible to both the general public and the research community.
AQ-PINNs: Attention-Enhanced Quantum Physics-Informed Neural Networks for Carbon-Efficient Climate Modeling
Authors: Siddhant Dutta, Nouhaila Innan, Sadok Ben Yahia, Muhammad Shafique
Date: 2024-09-03 00:00:00
Tasks: Tensor Networks

The growing computational demands of artificial intelligence (AI) in addressing climate change raise significant concerns about inefficiencies and environmental impact, as highlighted by the Jevons paradox. We propose an attention-enhanced quantum physics-informed neural networks model (AQ-PINNs) to tackle these challenges. This approach integrates quantum computing techniques into physics-informed neural networks (PINNs) for climate modeling, aiming to enhance predictive accuracy in fluid dynamics governed by the Navier-Stokes equations while reducing the computational burden and carbon footprint. By harnessing variational quantum multi-head self-attention mechanisms, our AQ-PINNs achieve a 51.51% reduction in model parameters compared to classical multi-head self-attention methods while maintaining comparable convergence and loss. It also employs quantum tensor networks to enhance representational capacity, which can lead to more efficient gradient computations and reduced susceptibility to barren plateaus. Our AQ-PINNs represent a crucial step towards more sustainable and effective climate modeling solutions.
On-chain Validation of Tracking Data Messages (TDM) Using Distributed Deep Learning on a Proof of Stake (PoS) Blockchain
Authors: Yasir Latif, Anirban Chowdhury, Samya Bagchi
Date: 2024-09-03 00:00:00
Tasks: POS

Trustless tracking of Resident Space Objects (RSOs) is crucial for Space Situational Awareness (SSA), especially during adverse situations. The importance of transparent SSA cannot be overstated, as it is vital for ensuring space safety and security. In an era where RSO location information can be easily manipulated, the risk of RSOs being used as weapons is a growing concern. The Tracking Data Message (TDM) is a standardized format for broadcasting RSO observations. However, the varying quality of observations from diverse sensors poses challenges to SSA reliability. While many countries operate space assets, relatively few have SSA capabilities, making it crucial to ensure the accuracy and reliability of the data. Current practices assume complete trust in the transmitting party, leaving SSA capabilities vulnerable to adversarial actions such as spoofing TDMs. This work introduces a trustless mechanism for TDM validation and verification using deep learning over blockchain. By leveraging the trustless nature of blockchain, our approach eliminates the need for a central authority, establishing consensus-based truth. We propose a state-of-the-art, transformer-based orbit propagator that outperforms traditional methods like SGP4, enabling cross-validation of multiple observations for a single RSO. This deep learning-based transformer model can be distributed over a blockchain, allowing interested parties to host a node that contains a part of the distributed deep learning model. Our system comprises decentralised observers and validators within a Proof of Stake (PoS) blockchain. Observers contribute TDM data along with a stake to ensure honesty, while validators run the propagation and validation algorithms. The system rewards observers for contributing verified TDMs and penalizes those submitting unverifiable data.
Data-driven topology design based on principal component analysis for 3D structural design problems
Authors: Jun Yang, Kentaro Yaji, Shintaro Yamasaki
Date: 2024-09-03 00:00:00
Tasks: Sensitivity

Topology optimization is a structural design methodology widely utilized to address engineering challenges. However, sensitivity-based topology optimization methods struggle to solve optimization problems characterized by strong non-linearity. Leveraging the sensitivity-free nature and high capacity of deep generative models, data-driven topology design (DDTD) methodology is considered an effective solution to this problem. Despite this, the training effectiveness of deep generative models diminishes when input size exceeds a threshold while maintaining high degrees of freedom is crucial for accurately characterizing complex structures. To resolve the conflict between the both, we propose DDTD based on principal component analysis (PCA). Its core idea is to replace the direct training of deep generative models with material distributions by using a principal component score matrix obtained from PCA computation and to obtain the generated material distributions with new features through the restoration process. We apply the proposed PCA-based DDTD to the problem of minimizing the maximum stress in 3D structural mechanics and demonstrate it can effectively address the current challenges faced by DDTD that fail to handle 3D structural design problems. Various experiments are conducted to demonstrate the effectiveness and practicability of the proposed PCA-based DDTD.
Learning out-of-time-ordered correlators with classical kernel methods
Authors: John Tanner, Jason Pye, Jingbo Wang
Date: 2024-09-03 00:00:00
Tasks: Tensor Networks

Out-of-Time Ordered Correlators (OTOCs) are widely used to investigate information scrambling in quantum systems. However, directly computing OTOCs with classical computers is an expensive procedure. This is due to the need to classically simulate the dynamics of quantum many-body systems, which entails computational costs that scale rapidly with system size. Similarly, exact simulation of the dynamics with a quantum computer (QC) will either only be possible for short times with noisy intermediate-scale quantum (NISQ) devices, or will require a fault-tolerant QC which is currently beyond technological capabilities. This motivates a search for alternative approaches to determine OTOCs and related quantities. In this study, we explore four parameterised sets of Hamiltonians describing local one-dimensional quantum systems of interest in condensed matter physics. For each set, we investigate whether classical kernel methods (KMs) can accurately learn the XZ-OTOC and a particular sum of OTOCs, as functions of the Hamiltonian parameters. We frame the problem as a regression task, generating small batches of labelled data with classical tensor network methods for quantum many-body systems with up to 40 qubits. Using this data, we train a variety of standard kernel machines and observe that the Laplacian and radial basis function (RBF) kernels perform best, achieving a coefficient of determination (\(R^2\)) on the testing sets of at least 0.7167, with averages between 0.8112 and 0.9822 for the various sets of Hamiltonians, together with small root mean squared error and mean absolute error. Hence, after training, the models can replace further uses of tensor networks for calculating an OTOC function of a system within the parameterised sets. Accordingly, the proposed method can assist with extensive evaluations of an OTOC function.
Buffer-based Gradient Projection for Continual Federated Learning
Authors: Shenghong Dai, Jy-yong Sohn, Yicong Chen, S M Iftekharul Alam, Ravikumar Balakrishnan, Suman Banerjee, Nageen Himayat, Kangwook Lee
Date: 2024-09-03 00:00:00
Tasks: Federated Learning, Incremental Learning

Continual Federated Learning (CFL) is essential for enabling real-world applications where multiple decentralized clients adaptively learn from continuous data streams. A significant challenge in CFL is mitigating catastrophic forgetting, where models lose previously acquired knowledge when learning new information. Existing approaches often face difficulties due to the constraints of device storage capacities and the heterogeneous nature of data distributions among clients. While some CFL algorithms have addressed these challenges, they frequently rely on unrealistic assumptions about the availability of task boundaries (i.e., knowing when new tasks begin). To address these limitations, we introduce Fed-A-GEM, a federated adaptation of the A-GEM method (Chaudhry et al., 2019), which employs a buffer-based gradient projection approach. Fed-A-GEM alleviates catastrophic forgetting by leveraging local buffer samples and aggregated buffer gradients, thus preserving knowledge across multiple clients. Our method is combined with existing CFL techniques, enhancing their performance in the CFL context. Our experiments on standard benchmarks show consistent performance improvements across diverse scenarios. For example, in a task-incremental learning scenario using the CIFAR-100 dataset, our method can increase the accuracy by up to 27%. Our code is available at https://github.com/shenghongdai/Fed-A-GEM.
Policy Gradients for Optimal Parallel Tempering MCMC
Authors: Daniel Zhao, Natesh S. Pillai
Date: 2024-09-03 00:00:00

Parallel tempering is a meta-algorithm for Markov Chain Monte Carlo that uses multiple chains to sample from tempered versions of the target distribution, enhancing mixing in multi-modal distributions that are challenging for traditional methods. The effectiveness of parallel tempering is heavily influenced by the selection of chain temperatures. Here, we present an adaptive temperature selection algorithm that dynamically adjusts temperatures during sampling using a policy gradient approach. Experiments demonstrate that our method can achieve lower integrated autocorrelation times compared to traditional geometrically spaced temperatures and uniform acceptance rate schemes on benchmark distributions.
Smoothed Robust Phase Retrieval
Authors: Zhong Zheng, Lingzhou Xue
Date: 2024-09-03 00:00:00
Tasks: Retrieval

The phase retrieval problem in the presence of noise aims to recover the signal vector of interest from a set of quadratic measurements with infrequent but arbitrary corruptions, and it plays an important role in many scientific applications. However, the essential geometric structure of the nonconvex robust phase retrieval based on the $\ell_1$-loss is largely unknown to study spurious local solutions, even under the ideal noiseless setting, and its intrinsic nonsmooth nature also impacts the efficiency of optimization algorithms. This paper introduces the smoothed robust phase retrieval (SRPR) based on a family of convolution-type smoothed loss functions. Theoretically, we prove that the SRPR enjoys a benign geometric structure with high probability: (1) under the noiseless situation, the SRPR has no spurious local solutions, and the target signals are global solutions, and (2) under the infrequent but arbitrary corruptions, we characterize the stationary points of the SRPR and prove its benign landscape, which is the first landscape analysis of phase retrieval with corruption in the literature. Moreover, we prove the local linear convergence rate of gradient descent for solving the SRPR under the noiseless situation. Experiments on both simulated datasets and image recovery are provided to demonstrate the numerical performance of the SRPR.
Quantifying Emergence in Neural Networks: Insights from Pruning and Training Dynamics
Authors: Faisal AlShinaifi, Zeyad Almoaigel, Johnny Jingze Li, Abdulla Kuleib, Gabriel A. Silva
Date: 2024-09-03 00:00:00

Emergence, where complex behaviors develop from the interactions of simpler components within a network, plays a crucial role in enhancing neural network capabilities. We introduce a quantitative framework to measure emergence during the training process and examine its impact on network performance, particularly in relation to pruning and training dynamics. Our hypothesis posits that the degree of emergence, defined by the connectivity between active and inactive nodes, can predict the development of emergent behaviors in the network. Through experiments with feedforward and convolutional architectures on benchmark datasets, we demonstrate that higher emergence correlates with improved trainability and performance. We further explore the relationship between network complexity and the loss landscape, suggesting that higher emergence indicates a greater concentration of local minima and a more rugged loss landscape. Pruning, which reduces network complexity by removing redundant nodes and connections, is shown to enhance training efficiency and convergence speed, though it may lead to a reduction in final accuracy. These findings provide new insights into the interplay between emergence, complexity, and performance in neural networks, offering valuable implications for the design and optimization of more efficient architectures.