pwc-archive/papers-with-abstracts huggingface dataset:
Interpretation of High-Dimensional Regression Coefficients by Comparison with Linearized Compressing Features
Authors: Joachim Schaeffer, Jinwook Rhyu, Robin Droop, Rolf Findeisen, Richard Braatz
Date: 2024-11-18 00:00:00
Tasks: regression

Linear regression is often deemed inherently interpretable; however, challenges arise for high-dimensional data. We focus on further understanding how linear regression approximates nonlinear responses from high-dimensional functional data, motivated by predicting cycle life for lithium-ion batteries. We develop a linearization method to derive feature coefficients, which we compare with the closest regression coefficients of the path of regression solutions. We showcase the methods on battery data case studies where a single nonlinear compressing feature, $g\colon \mathbb{R}^p \to \mathbb{R}$, is used to construct a synthetic response, $\mathbf{y} \in \mathbb{R}$. This unifying view of linear regression and compressing features for high-dimensional functional data helps to understand (1) how regression coefficients are shaped in the highly regularized domain and how they relate to linearized feature coefficients and (2) how the shape of regression coefficients changes as a function of regularization to approximate nonlinear responses by exploiting local structures.
Higher Order Graph Attention Probabilistic Walk Networks
Authors: Thomas Bailie, Yun Sing Koh, Karthik Mukkavilli
Date: 2024-11-18 00:00:00
Tasks: Diversity, Graph Attention, Node Classification

Graphs inherently capture dependencies between nodes or variables through their topological structure, with paths between any two nodes indicating a sequential dependency on the nodes traversed. Message Passing Neural Networks (MPNNs) leverage these latent relationships embedded in graph structures, and have become widely adopted across diverse applications. However, many existing methods predominantly rely on local information within the $1$-hop neighborhood. This approach has notable limitations; for example, $1$-hop aggregation schemes inherently lose long-distance information, and are limited in expressive power as defined by the $k$-Weisfeiler-Leman ($k$-WL) isomorphism test. To address these issues, we propose the Higher Order Graphical Attention (HoGA) module, which assigns weights to variable-length paths sampled based on feature-vector diversity, effectively reconstructing the $k$-hop neighborhood. HoGA represents higher-order relationships as a robust form of self-attention, applicable to any single-hop attention mechanism. In empirical studies, applying HoGA to existing attention-based models consistently leads to significant accuracy improvements on benchmark node classification datasets. Furthermore, we observe that the performance degradation typically associated with additional message-passing steps may be mitigated.
Prediction-Guided Active Experiments
Authors: Ruicheng Ao, Hongyu Chen, David Simchi-Levi
Date: 2024-11-18 00:00:00
Tasks: Prediction

In this work, we introduce a new framework for active experimentation, the Prediction-Guided Active Experiment (PGAE), which leverages predictions from an existing machine learning model to guide sampling and experimentation. Specifically, at each time step, an experimental unit is sampled according to a designated sampling distribution, and the actual outcome is observed based on an experimental probability. Otherwise, only a prediction for the outcome is available. We begin by analyzing the non-adaptive case, where full information on the joint distribution of the predictor and the actual outcome is assumed. For this scenario, we derive an optimal experimentation strategy by minimizing the semi-parametric efficiency bound for the class of regular estimators. We then introduce an estimator that meets this efficiency bound, achieving asymptotic optimality. Next, we move to the adaptive case, where the predictor is continuously updated with newly sampled data. We show that the adaptive version of the estimator remains efficient and attains the same semi-parametric bound under certain regularity assumptions. Finally, we validate PGAE's performance through simulations and a semi-synthetic experiment using data from the US Census Bureau. The results underscore the PGAE framework's effectiveness and superiority compared to other existing methods.
Machine Learning Evaluation Metric Discrepancies across Programming Languages and Their Components: Need for Standardization
Authors: Mohammad R. Salmanpour, Morteza Alizadeh, Ghazal Mousavi, Saba Sadeghi, Sajad Amiri, Mehrdad Oveisi, Arman Rahmim, Ilker Hacihaliloglu
Date: 2024-11-18 00:00:00
Tasks: Binary Classification, Clustering, Multi-class Classification, Segmentation, Translation

This study evaluates metrics for tasks such as classification, regression, clustering, correlation analysis, statistical tests, segmentation, and image-to-image (I2I) translation. Metrics were compared across Python libraries, R packages, and Matlab functions to assess their consistency and highlight discrepancies. The findings underscore the need for a unified roadmap to standardize metrics, ensuring reliable and reproducible ML evaluations across platforms. This study examined a wide range of evaluation metrics across various tasks and found only some to be consistent across platforms, such as (i) Accuracy, Balanced Accuracy, Cohens Kappa, F-beta Score, MCC, Geometric Mean, AUC, and Log Loss in binary classification; (ii) Accuracy, Cohens Kappa, and F-beta Score in multi-class classification; (iii) MAE, MSE, RMSE, MAPE, Explained Variance, Median AE, MSLE, and Huber in regression; (iv) Davies-Bouldin Index and Calinski-Harabasz Index in clustering; (v) Pearson, Spearman, Kendall's Tau, Mutual Information, Distance Correlation, Percbend, Shepherd, and Partial Correlation in correlation analysis; (vi) Paired t-test, Chi-Square Test, ANOVA, Kruskal-Wallis Test, Shapiro-Wilk Test, Welchs t-test, and Bartlett's test in statistical tests; (vii) Accuracy, Precision, and Recall in 2D segmentation; (viii) Accuracy in 3D segmentation; (ix) MAE, MSE, RMSE, and R-Squared in 2D-I2I translation; and (x) MAE, MSE, and RMSE in 3D-I2I translation. Given observation of discrepancies in a number of metrics (e.g. precision, recall and F1 score in binary classification, WCSS in clustering, multiple statistical tests, and IoU in segmentation, amongst multiple metrics), this study concludes that ML evaluation metrics require standardization and recommends that future research use consistent metrics for different tasks to effectively compare ML techniques and solutions.
The Generalization Error of Machine Learning Algorithms
Authors: Samir M. Perlaza, Xinying Zou
Date: 2024-11-18 00:00:00

In this paper, the method of gaps, a technique for deriving closed-form expressions in terms of information measures for the generalization error of machine learning algorithms is introduced. The method relies on two central observations: $(a)$~The generalization error is an average of the variation of the expected empirical risk with respect to changes on the probability measure (used for expectation); and~$(b)$~these variations, also referred to as gaps, exhibit closed-form expressions in terms of information measures. The expectation of the empirical risk can be either with respect to a measure on the models (with a fixed dataset) or with respect to a measure on the datasets (with a fixed model), which results in two variants of the method of gaps. The first variant, which focuses on the gaps of the expected empirical risk with respect to a measure on the models, appears to be the most general, as no assumptions are made on the distribution of the datasets. The second variant develops under the assumption that datasets are made of independent and identically distributed data points. All existing exact expressions for the generalization error of machine learning algorithms can be obtained with the proposed method. Also, this method allows obtaining numerous new exact expressions, which improves the understanding of the generalization error; establish connections with other areas in statistics, e.g., hypothesis testing; and potentially, might guide algorithm designs.
On the Efficiency of ERM in Feature Learning
Authors: Ayoub El Hanchi, Chris J. Maddison, Murat A. Erdogdu
Date: 2024-11-18 00:00:00

Given a collection of feature maps indexed by a set $\mathcal{T}$, we study the performance of empirical risk minimization (ERM) on regression problems with square loss over the union of the linear classes induced by these feature maps. This setup aims at capturing the simplest instance of feature learning, where the model is expected to jointly learn from the data an appropriate feature map and a linear predictor. We start by studying the asymptotic quantiles of the excess risk of sequences of empirical risk minimizers. Remarkably, we show that when the set $\mathcal{T}$ is not too large and when there is a unique optimal feature map, these quantiles coincide, up to a factor of two, with those of the excess risk of the oracle procedure, which knows a priori this optimal feature map and deterministically outputs an empirical risk minimizer from the associated optimal linear class. We complement this asymptotic result with a non-asymptotic analysis that quantifies the decaying effect of the global complexity of the set $\mathcal{T}$ on the excess risk of ERM, and relates it to the size of the sublevel sets of the suboptimality of the feature maps. As an application of our results, we obtain new guarantees on the performance of the best subset selection procedure in sparse linear regression under general assumptions.
Neural and Time-Series Approaches for Pricing Weather Derivatives: Performance and Regime Adaptation Using Satellite Data
Authors: Marco Hening Tallarico, Pablo Olivares
Date: 2024-11-18 00:00:00
Tasks: Time Series

This paper studies pricing of weather-derivative (WD) contracts on temperature and precipitation. For temperature-linked strangles in Toronto and Chicago, we benchmark a harmonic-regression/ARMA model against a feed-forward neural network (NN), finding that the NN reduces out-of-sample mean-squared error (MSE) and materially shifts December fair values relative to both the time-series model and the industry-standard Historic Burn Approach (HBA). For precipitation, we employ a compound Poisson--Gamma framework: shape and scale parameters are estimated via maximum likelihood estimation (MLE) and via a convolutional neural network (CNN) trained on 30-day rainfall sequences spanning multiple seasons. The CNN adaptively learns season-specific $(\alpha,\beta)$ mappings, thereby capturing heterogeneity across regimes that static i.i.d.\ fits miss. At valuation, we assume days are i.i.d.\ $\Gamma(\hat{\alpha},\hat{\beta})$ within each regime and apply a mean-count approximation (replacing the Poisson count by its mean ($n\hat{\lambda}$) to derive closed-form strangle prices. Exploratory analysis of 1981--2023 NASA POWER data confirms pronounced seasonal heterogeneity in $(\alpha,\beta)$ between summer and winter, demonstrating that static global fits are inadequate. Back-testing on Toronto and Chicago grids shows that our regime-adaptive CNN yields competitive valuations and underscores how model choice can shift strangle prices. Payoffs are evaluated analytically when possible and by simulation elsewhere, enabling a like-for-like comparison of forecasting and valuation methods.
SynCoTrain: A Dual Classifier PU-learning Framework for Synthesizability Prediction
Authors: Sasan Amariamir, Janine George, Philipp Benner
Date: 2024-11-18 00:00:00
Tasks: Computational Efficiency, Formation Energy

Material discovery is a cornerstone of modern science, driving advancements in diverse disciplines from biomedical technology to climate solutions. Predicting synthesizability, a critical factor in realizing novel materials, remains a complex challenge due to the limitations of traditional heuristics and thermodynamic proxies. While stability metrics such as formation energy offer partial insights, they fail to account for kinetic factors and technological constraints that influence synthesis outcomes. These challenges are further compounded by the scarcity of negative data, as failed synthesis attempts are often unpublished or context-specific. We present SynCoTrain, a semi-supervised machine learning model designed to predict the synthesizability of materials. SynCoTrain employs a co-training framework leveraging two complementary graph convolutional neural networks: SchNet and ALIGNN. By iteratively exchanging predictions between classifiers, SynCoTrain mitigates model bias and enhances generalizability. Our approach uses Positive and Unlabeled (PU) Learning to address the absence of explicit negative data, iteratively refining predictions through collaborative learning. The model demonstrates robust performance, achieving high recall on internal and leave-out test sets. By focusing on oxide crystals, a well-characterized material family with extensive experimental data, we establish SynCoTrain as a reliable tool for predicting synthesizability while balancing dataset variability and computational efficiency. This work highlights the potential of co-training to advance high-throughput materials discovery and generative research, offering a scalable solution to the challenge of synthesizability prediction.
Active learning for efficient discovery of optimal gene combinations in the combinatorial perturbation space
Authors: Jason Qin, Hans-Hermann Wessels, Carlos Fernandez-Granda, Yuhan Hao
Date: 2024-11-18 00:00:00
Tasks: Active Learning

The advancement of novel combinatorial CRISPR screening technologies enables the identification of synergistic gene combinations on a large scale. This is crucial for developing novel and effective combination therapies, but the combinatorial space makes exhaustive experimentation infeasible. We introduce NAIAD, an active learning framework that efficiently discovers optimal gene pairs capable of driving cells toward desired cellular phenotypes. NAIAD leverages single-gene perturbation effects and adaptive gene embeddings that scale with the training data size, mitigating overfitting in small-sample learning while capturing complex gene interactions as more data is collected. Evaluated on four CRISPR combinatorial perturbation datasets totaling over 350,000 genetic interactions, NAIAD, trained on small datasets, outperforms existing models by up to 40\% relative to the second-best. NAIAD's recommendation system prioritizes gene pairs with the maximum predicted effects, resulting in the highest marginal gain in each AI-experiment round and accelerating discovery with fewer CRISPR experimental iterations. Our NAIAD framework (https://github.com/NeptuneBio/NAIAD) improves the identification of novel, effective gene combinations, enabling more efficient CRISPR library design and offering promising applications in genomics research and therapeutic development.
Compression of Higher Order Ambisonics with Multichannel RVQGAN
Authors: Toni Hirvonen, Mahmoud Namazi
Date: 2024-11-18 00:00:00
Tasks: Transfer Learning

A multichannel extension to the RVQGAN neural coding method is proposed, and realized for data-driven compression of third-order Ambisonics audio. The input- and output layers of the generator and discriminator models are modified to accept multiple (16) channels without increasing the model bitrate. We also propose a loss function for accounting for spatial perception in immersive reproduction, and transfer learning from single-channel models. Listening test results with 7.1.4 immersive playback show that the proposed extension is suitable for coding scene-based, 16-channel Ambisonics content with good quality at 16 kbps when trained and tested on the EigenScape database. The model has potential applications for learning other types of content and multichannel formats.
Transmission Line Outage Probability Prediction Under Extreme Events Using Peter-Clark Bayesian Structural Learning
Authors: Xiaolin Chen, Qiuhua Huang, Yuqi Zhou
Date: 2024-11-18 00:00:00

Recent years have seen a notable increase in the frequency and intensity of extreme weather events. With a rising number of power outages caused by these events, accurate prediction of power line outages is essential for safe and reliable operation of power grids. The Bayesian network is a probabilistic model that is very effective for predicting line outages under weather-related uncertainties. However, most existing studies in this area offer general risk assessments, but fall short of providing specific outage probabilities. In this work, we introduce a novel approach for predicting transmission line outage probabilities using a Bayesian network combined with Peter-Clark (PC) structural learning. Our approach not only enables precise outage probability calculations, but also demonstrates better scalability and robust performance, even with limited data. Case studies using data from BPA and NOAA show the effectiveness of this approach, while comparisons with several existing methods further highlight its advantages.
Introducing Milabench: Benchmarking Accelerators for AI
Authors: Pierre Delaunay, Xavier Bouthillier, Olivier Breuleux, Satya Ortiz-Gagné, Olexa Bilaniuk, Fabrice Normandin, Arnaud Bergeron, Bruno Carrez, Guillaume Alain, Soline Blanc, Frédéric Osterrath, Joseph Viviano, Roger Creus-Castanyer Darshan Patil, Rabiul Awal, Le Zhang
Date: 2024-11-18 00:00:00
Tasks: Benchmarking, Deep Learning

AI workloads, particularly those driven by deep learning, are introducing novel usage patterns to high-performance computing (HPC) systems that are not comprehensively captured by standard HPC benchmarks. As one of the largest academic research centers dedicated to deep learning, Mila identified the need to develop a custom benchmarking suite to address the diverse requirements of its community, which consists of over 1,000 researchers. This report introduces Milabench, the resulting benchmarking suite. Its design was informed by an extensive literature review encompassing 867 papers, as well as surveys conducted with Mila researchers. This rigorous process led to the selection of 26 primary benchmarks tailored for procurement evaluations, alongside 16 optional benchmarks for in-depth analysis. We detail the design methodology, the structure of the benchmarking suite, and provide performance evaluations using GPUs from NVIDIA, AMD, and Intel. The Milabench suite is open source and can be accessed at github.com/mila-iqia/milabench.
Artificial Intelligence Mangrove Monitoring System Based on Deep Learning and Sentinel-2 Satellite Data in the UAE (2017-2024)
Authors: Linlin Tan, Haishan Wu
Date: 2024-11-18 00:00:00
Tasks: Earth Observation

Mangroves play a crucial role in maintaining coastal ecosystem health and protecting biodiversity. Therefore, continuous mapping of mangroves is essential for understanding their dynamics. Earth observation imagery typically provides a cost-effective way to monitor mangrove dynamics. However, there is a lack of regional studies on mangrove areas in the UAE. This study utilizes the UNet++ deep learning model combined with Sentinel-2 multispectral data and manually annotated labels to monitor the spatiotemporal dynamics of densely distributed mangroves (coverage greater than 70%) in the UAE from 2017 to 2024, achieving an mIoU of 87.8% on the validation set. Results show that the total mangrove area in the UAE in 2024 was approximately 9,142.21 hectares, an increase of 2,061.33 hectares compared to 2017, with carbon sequestration increasing by approximately 194,383.42 tons, equivalent to fixing about 713,367.36 tons of carbon dioxide. Abu Dhabi has the largest mangrove area and plays a dominant role in the UAE's mangrove growth, increasing by 1,855.6 hectares between 2017-2024, while other emirates have also contributed to mangrove expansion through stable and sustainable growth in mangrove areas. This comprehensive growth pattern reflects the collective efforts of all emirates in mangrove restoration.
Phenome-wide causal proteomics enhance systemic lupus erythematosus flare prediction: A study in Asian populations
Authors: Liying Chen, Ou Deng, Ting Fang, Mei Chen, Xvfeng Zhang, Ruichen Cong, Dingqi Lu, Runrun Zhang, Qun Jin, Xinchang Wang
Date: 2024-11-18 00:00:00
Tasks: 2k, Management

Objective: Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by unpredictable flares. This study aimed to develop a novel proteomics-based risk prediction model specifically for Asian SLE populations to enhance personalized disease management and early intervention. Methods: A longitudinal cohort study was conducted over 48 weeks, including 139 SLE patients monitored every 12 weeks. Patients were classified into flare (n = 53) and non-flare (n = 86) groups. Baseline plasma samples underwent data-independent acquisition (DIA) proteomics analysis, and phenome-wide Mendelian randomization (PheWAS) was performed to evaluate causal relationships between proteins and clinical predictors. Logistic regression (LR) and random forest (RF) models were used to integrate proteomic and clinical data for flare risk prediction. Results: Five proteins (SAA1, B4GALT5, GIT2, NAA15, and RPIA) were significantly associated with SLE Disease Activity Index-2K (SLEDAI-2K) scores and 1-year flare risk, implicating key pathways such as B-cell receptor signaling and platelet degranulation. SAA1 demonstrated causal effects on flare-related clinical markers, including hemoglobin and red blood cell counts. A combined model integrating clinical and proteomic data achieved the highest predictive accuracy (AUC = 0.769), surpassing individual models. SAA1 was highlighted as a priority biomarker for rapid flare discrimination. Conclusion: The integration of proteomic and clinical data significantly improves flare prediction in Asian SLE patients. The identification of key proteins and their causal relationships with flare-related clinical markers provides valuable insights for proactive SLE management and personalized therapeutic approaches.
LoRA Unlearns More and Retains More (Student Abstract)
Authors: Atharv Mittal
Date: 2024-11-16 00:00:00
Tasks: Computational Efficiency, Machine Unlearning

Due to increasing privacy regulations and regulatory compliance, Machine Unlearning (MU) has become essential. The goal of unlearning is to remove information related to a specific class from a model. Traditional approaches achieve exact unlearning by retraining the model on the remaining dataset, but incur high computational costs. This has driven the development of more efficient unlearning techniques, including model sparsification techniques, which boost computational efficiency, but degrade the model's performance on the remaining classes. To mitigate these issues, we propose a novel method, PruneLoRA which introduces a new MU paradigm, termed prune first, then adapt, then unlearn. LoRA (Hu et al. 2022) reduces the need for large-scale parameter updates by applying low-rank updates to the model. We leverage LoRA to selectively modify a subset of the pruned model's parameters, thereby reducing the computational cost, memory requirements and improving the model's ability to retain performance on the remaining classes. Experimental Results across various metrics showcase that our method outperforms other approximate MU methods and bridges the gap between exact and approximate unlearning. Our code is available at https://github.com/vlgiitr/LoRA-Unlearn.