pwc-archive/papers-with-abstracts huggingface dataset:
PhagoStat a scalable and interpretable end to end framework for efficient quantification of cell phagocytosis in neurodegenerative disease studies
Authors: Mehdi Ounissi, Morwena Latouche, Daniel Racoceanu
Date: 2023-04-26 00:00:00
Tasks: Cell Segmentation

Quantifying the phagocytosis of dynamic, unstained cells is essential for evaluating neurodegenerative diseases. However, measuring rapid cell interactions and distinguishing cells from background make this task very challenging when processing time-lapse phase-contrast video microscopy. In this study, we introduce an end-to-end, scalable, and versatile real-time framework for quantifying and analyzing phagocytic activity. Our proposed pipeline is able to process large data-sets and includes a data quality verification module to counteract perturbations such as microscope movements and frame blurring. We also propose an explainable cell segmentation module to improve the interpretability of DL methods compared to black-box algorithms. This includes two interpretable DL capabilities: visual explanation and model simplification. We demonstrate that interpretability in DL is not the opposite of high performance, by additionally providing essential DL algorithm optimization insights and solutions. Besides, incorporating interpretable modules results in an efficient architecture design and optimized execution time. We apply our pipeline to analyze microglial cell phagocytosis in FTD and obtain statistically reliable results showing that FTD mutant cells are larger and more aggressive than control cells. The method has been tested and validated on public benchmarks by generating state-of-the art performances. To stimulate translational approaches and future studies, we release an open-source end-to-end pipeline and a unique microglial cells phagocytosis dataset for immune system characterization in neurodegenerative diseases research. This pipeline and the associated dataset will consistently crystallize future advances in this field, promoting the development of interpretable algorithms dedicated to the domain of neurodegenerative diseases' characterization. github.com/ounissimehdi/PhagoStat
Automated Whole Slide Imaging for Label-Free Histology using Photon Absorption Remote Sensing Microscopy
Authors: James E. D. Tweel, Benjamin R. Ecclestone, Marian Boktor, Deepak Dinakaran, John R. Mackey, Parsin Haji Reza
Date: 2023-04-26 00:00:00
Tasks: Diagnostic, Virtual Staining, whole slide images

The field of histology relies heavily on antiquated tissue processing and staining techniques that limit the efficiency of pathologic diagnoses of cancer and other diseases. Current staining and advanced labeling methods are often destructive and mutually incompatible, requiring new tissue sections for each stain. This prolongs the diagnostic process and depletes valuable biopsy samples. In this study, we present an alternative label-free histology platform using the first transmission-mode Photon Absorption Remote Sensing microscope. Optimized for automated whole slide scanning of unstained tissue samples, the system provides slide images at magnifications up to 40x that are fully compatible with existing digital pathology tools. The scans capture high quality and high-resolution images with subcellular diagnostic detail. After imaging, samples remain suitable for histochemical, immunohistochemical, and other staining techniques. Scattering and absorption (radiative and non-radiative) contrasts are shown in whole slide images of malignant human breast and skin tissues samples. Clinically relevant features are highlighted, and close correspondence and analogous contrast is demonstrated with one-to-one gold standard H&E stained images. Our previously reported pix2pix virtual staining model is applied to an entire whole slide image, showcasing the potential of this approach in whole slide label-free H&E emulation. This work is a critical advance for integrating label-free optical methods into standard histopathology workflows, both enhancing diagnostic efficiency, and broadening the number of stains that can be applied while preserving valuable tissue samples.
Maximizing Model Generalization for Machine Condition Monitoring with Self-Supervised Learning and Federated Learning
Authors: Matthew Russell, Peng Wang
Date: 2023-04-27 00:00:00
Tasks: Domain Adaptation, Federated Learning, Self-Supervised Learning, Transfer Learning

Deep Learning (DL) can diagnose faults and assess machine health from raw condition monitoring data without manually designed statistical features. However, practical manufacturing applications remain extremely difficult for existing DL methods. Machine data is often unlabeled and from very few health conditions (e.g., only normal operating data). Furthermore, models often encounter shifts in domain as process parameters change and new categories of faults emerge. Traditional supervised learning may struggle to learn compact, discriminative representations that generalize to these unseen target domains since it depends on having plentiful classes to partition the feature space with decision boundaries. Transfer Learning (TL) with domain adaptation attempts to adapt these models to unlabeled target domains but assumes similar underlying structure that may not be present if new faults emerge. This study proposes focusing on maximizing the feature generality on the source domain and applying TL via weight transfer to copy the model to the target domain. Specifically, Self-Supervised Learning (SSL) with Barlow Twins may produce more discriminative features for monitoring health condition than supervised learning by focusing on semantic properties of the data. Furthermore, Federated Learning (FL) for distributed training may also improve generalization by efficiently expanding the effective size and diversity of training data by sharing information across multiple client machines. Results show that Barlow Twins outperforms supervised learning in an unlabeled target domain with emerging motor faults when the source training data contains very few distinct categories. Incorporating FL may also provide a slight advantage by diffusing knowledge of health conditions between machines.
Resampling Gradients Vanish in Differentiable Sequential Monte Carlo Samplers
Authors: Johannes Zenn, Robert Bamler
Date: 2023-04-27 00:00:00

Annealed Importance Sampling (AIS) moves particles along a Markov chain from a tractable initial distribution to an intractable target distribution. The recently proposed Differentiable AIS (DAIS) (Geffner and Domke, 2021; Zhang et al., 2021) enables efficient optimization of the transition kernels of AIS and of the distributions. However, we observe a low effective sample size in DAIS, indicating degenerate distributions. We thus propose to extend DAIS by a resampling step inspired by Sequential Monte Carlo. Surprisingly, we find empirically-and can explain theoretically-that it is not necessary to differentiate through the resampling step which avoids gradient variance issues observed in similar approaches for Particle Filters (Maddison et al., 2017; Naesseth et al., 2018; Le et al., 2018).
Dynamic Pricing and Advertising with Demand Learning
Authors: Shipra Agrawal, Yiding Feng, Wei Tang
Date: 2023-04-27 00:00:00
Proceeding: NeurIPS 2023 11

We consider a novel pricing and advertising framework, where a seller not only sets product price but also designs flexible 'advertising schemes' to influence customers' valuation of the product. We impose no structural restriction on the seller's feasible advertising strategies and allow her to advertise the product by disclosing or concealing any information. Following the literature in information design, this fully flexible advertising can be modeled as the seller being able to choose any information policy that signals the product quality/characteristic to the customers. Customers observe the advertising signal and infer a Bayesian belief over the products. We aim to investigate two questions in this work: (1) What is the value of advertising? To what extent can advertising enhance a seller's revenue? (2) Without any apriori knowledge of the customers' demand function, how can a seller adaptively learn and optimize both pricing and advertising strategies using past purchase responses? To study the first question, we introduce and study the value of advertising - a revenue gap between using advertising vs not advertising, and we provide a crisp tight characterization for this notion for a broad family of problems. For the second question, we study the seller's dynamic pricing and advertising problem with demand uncertainty. Our main result for this question is a computationally efficient online algorithm that achieves an optimal $O(T^{2/3}(m\log T)^{1/3})$ regret rate when the valuation function is linear in the product quality. Here $m$ is the cardinality of the discrete product quality domain and $T$ is the time horizon. This result requires some mild regularity assumptions on the valuation function, but no Lipschitz or smoothness assumption on the customers' demand function. We also obtain several improved results for the widely considered special case of additive valuations.
Functional Diffusion Maps
Authors: María Barroso, Carlos María Alaíz, Ángela Fernández, Jose Luis Torrecilla
Date: 2023-04-27 00:00:00
Tasks: Dimensionality Reduction

Nowadays many real-world datasets can be considered as functional, in the sense that the processes which generate them are continuous. A fundamental property of this type of data is that in theory they belong to an infinite-dimensional space. Although in practice we usually receive finite observations, they are still high-dimensional and hence dimensionality reduction methods are crucial. In this vein, the main state-of-the-art method for functional data analysis is Functional PCA. Nevertheless, this classic technique assumes that the data lie in a linear manifold, and hence it could have problems when this hypothesis is not fulfilled. In this research, attention has been placed on a non-linear manifold learning method: Diffusion Maps. The article explains how to extend this multivariate method to functional data and compares its behavior against Functional PCA over different simulated and real examples.
Pseudo-Hamiltonian neural networks for learning partial differential equations
Authors: Sølve Eidnes, Kjetil Olsen Lye
Date: 2023-04-27 00:00:00

Pseudo-Hamiltonian neural networks (PHNN) were recently introduced for learning dynamical systems that can be modelled by ordinary differential equations. In this paper, we extend the method to partial differential equations. The resulting model is comprised of up to three neural networks, modelling terms representing conservation, dissipation and external forces, and discrete convolution operators that can either be learned or be given as input. We demonstrate numerically the superior performance of PHNN compared to a baseline model that models the full dynamics by a single neural network. Moreover, since the PHNN model consists of three parts with different physical interpretations, these can be studied separately to gain insight into the system, and the learned model is applicable also if external forces are removed or changed.
Learning Neural Constitutive Laws From Motion Observations for Generalizable PDE Dynamics
Authors: Pingchuan Ma, Peter Yichen Chen, Bolei Deng, Joshua B. Tenenbaum, Tao Du, Chuang Gan, Wojciech Matusik
Date: 2023-04-27 00:00:00
Tasks: Out-of-Distribution Generalization

We propose a hybrid neural network (NN) and PDE approach for learning generalizable PDE dynamics from motion observations. Many NN approaches learn an end-to-end model that implicitly models both the governing PDE and constitutive models (or material models). Without explicit PDE knowledge, these approaches cannot guarantee physical correctness and have limited generalizability. We argue that the governing PDEs are often well-known and should be explicitly enforced rather than learned. Instead, constitutive models are particularly suitable for learning due to their data-fitting nature. To this end, we introduce a new framework termed "Neural Constitutive Laws" (NCLaw), which utilizes a network architecture that strictly guarantees standard constitutive priors, including rotation equivariance and undeformed state equilibrium. We embed this network inside a differentiable simulation and train the model by minimizing a loss function based on the difference between the simulation and the motion observation. We validate NCLaw on various large-deformation dynamical systems, ranging from solids to fluids. After training on a single motion trajectory, our method generalizes to new geometries, initial/boundary conditions, temporal ranges, and even multi-physics systems. On these extremely out-of-distribution generalization tasks, NCLaw is orders-of-magnitude more accurate than previous NN approaches. Real-world experiments demonstrate our method's ability to learn constitutive laws from videos.
LibCity: A Unified Library Towards Efficient and Comprehensive Urban Spatial-Temporal Prediction
Authors: Jiawei Jiang, Chengkai Han, Wenjun Jiang, Wayne Xin Zhao, Jingyuan Wang
Date: 2023-04-27 00:00:00
Tasks: Prediction

As deep learning technology advances and more urban spatial-temporal data accumulates, an increasing number of deep learning models are being proposed to solve urban spatial-temporal prediction problems. However, there are limitations in the existing field, including open-source data being in various formats and difficult to use, few papers making their code and data openly available, and open-source models often using different frameworks and platforms, making comparisons challenging. A standardized framework is urgently needed to implement and evaluate these methods. To address these issues, we propose LibCity, an open-source library that offers researchers a credible experimental tool and a convenient development framework. In this library, we have reproduced 65 spatial-temporal prediction models and collected 55 spatial-temporal datasets, allowing researchers to conduct comprehensive experiments conveniently. By enabling fair model comparisons, designing a unified data storage format, and simplifying the process of developing new models, LibCity is poised to make significant contributions to the spatial-temporal prediction field.
On the Generalization Error of Meta Learning for the Gibbs Algorithm
Authors: Yuheng Bu, Harsha Vardhan Tetali, Gholamali Aminian, Miguel Rodrigues, Gregory Wornell
Date: 2023-04-27 00:00:00
Tasks: Meta-Learning

We analyze the generalization ability of joint-training meta learning algorithms via the Gibbs algorithm. Our exact characterization of the expected meta generalization error for the meta Gibbs algorithm is based on symmetrized KL information, which measures the dependence between all meta-training datasets and the output parameters, including task-specific and meta parameters. Additionally, we derive an exact characterization of the meta generalization error for the super-task Gibbs algorithm, in terms of conditional symmetrized KL information within the super-sample and super-task framework introduced in Steinke and Zakynthinou (2020) and Hellstrom and Durisi (2022) respectively. Our results also enable us to provide novel distribution-free generalization error upper bounds for these Gibbs algorithms applicable to meta learning.
Learning to Extrapolate: A Transductive Approach
Authors: Aviv Netanyahu, Abhishek Gupta, Max Simchowitz, Kaiqing Zhang, Pulkit Agrawal
Date: 2023-04-27 00:00:00
Tasks: Imitation Learning

Machine learning systems, especially with overparameterized deep neural networks, can generalize to novel test instances drawn from the same distribution as the training data. However, they fare poorly when evaluated on out-of-support test points. In this work, we tackle the problem of developing machine learning systems that retain the power of overparameterized function approximators while enabling extrapolation to out-of-support test points when possible. This is accomplished by noting that under certain conditions, a "transductive" reparameterization can convert an out-of-support extrapolation problem into a problem of within-support combinatorial generalization. We propose a simple strategy based on bilinear embeddings to enable this type of combinatorial generalization, thereby addressing the out-of-support extrapolation problem under certain conditions. We instantiate a simple, practical algorithm applicable to various supervised learning and imitation learning tasks.
A Best-of-Both-Worlds Algorithm for Constrained MDPs with Long-Term Constraints
Authors: Jacopo Germano, Francesco Emanuele Stradi, Gianmarco Genalti, Matteo Castiglioni, Alberto Marchesi, Nicola Gatti
Date: 2023-04-27 00:00:00
Tasks: Autonomous Driving, Recommendation Systems

We study online learning in episodic constrained Markov decision processes (CMDPs), where the learner aims at collecting as much reward as possible over the episodes, while satisfying some long-term constraints during the learning process. Rewards and constraints can be selected either stochastically or adversarially, and the transition function is not known to the learner. While online learning in classical (unconstrained) MDPs has received considerable attention over the last years, the setting of CMDPs is still largely unexplored. This is surprising, since in real-world applications, such as, e.g., autonomous driving, automated bidding, and recommender systems, there are usually additional constraints and specifications that an agent has to obey during the learning process. In this paper, we provide the first best-of-both-worlds algorithm for CMDPs with long-term constraints, in the flavor of Balseiro et al. (2023). Our algorithm is capable of handling settings in which rewards and constraints are selected either stochastically or adversarially, without requiring any knowledge of the underling process. Moreover, our algorithm matches state-of-the-art regret and constraint violation bounds for settings in which constraints are selected stochastically, while it is the first to provide guarantees in the case in which they are chosen adversarially.
A Measurement of the Kuiper Belt's Mean Plane From Objects Classified By Machine Learning
Authors: Ian C. Matheson, Renu Malhotra
Date: 2023-04-27 00:00:00

Mean plane measurements of the Kuiper Belt from observational data are of interest for their potential to test dynamical models of the solar system. Recent measurements have yielded inconsistent results. Here we report a measurement of the Kuiper Belt's mean plane with a sample size more than twice as large as in previous measurements. The sample of interest is the non-resonant Kuiper belt objects, which we identify by using machine learning on the observed Kuiper Belt population whose orbits are well-determined. We estimate the measurement error with a Monte Carlo procedure. We find that the overall mean plane of the non-resonant Kuiper Belt (semimajor axis range 35-150 au) and also that of the classical Kuiper Belt (semimajor axis range 42-48 au) are both close to (within about 0.7 degrees) but distinguishable from the invariable plane of the solar system to greater than 99.7% confidence. When binning the sample into smaller semimajor axis bins, we find the measured mean plane mostly consistent with both the invariable plane and the theoretically expected Laplace surface forced by the known planets. Statistically significant discrepancies are found only in the semimajor axis ranges 40.3-42 au and 45-50 au; these ranges are in proximity to a secular resonance and Neptune's 2:1 mean motion resonance where the theory for the Laplace surface is likely to be inaccurate. These results do not support a previously reported anomalous warp at semimajor axes above 50 au.
A Method for Classifying Snow Using Ski-Mounted Strain Sensors
Authors: Florian McLelland, Floris van Breugel
Date: 2023-04-27 00:00:00
Tasks: Dimensionality Reduction

Understanding the structure, quantity, and type of snow in mountain landscapes is crucial for assessing avalanche safety, interpreting satellite imagery, building accurate hydrology models, and choosing the right pair of skis for your weekend trip. Currently, such characteristics of snowpack are measured using a combination of remote satellite imagery, weather stations, and laborious point measurements and descriptions provided by local forecasters, guides, and backcountry users. Here, we explore how characteristics of the top layer of snowpack could be estimated while skiing using strain sensors mounted to the top surface of an alpine ski. We show that with two strain gauges and an inertial measurement unit it is feasible to correctly assign one of three qualitative labels (powder, slushy, or icy/groomed snow) to each 10 second segment of a trajectory with 97% accuracy, independent of skiing style. Our algorithm uses a combination of a data-driven linear model of the ski-snow interaction, dimensionality reduction, and a Naive Bayes classifier. Comparisons of classifier performance between strain gauges suggest that the optimal placement of strain gauges is halfway between the binding and the tip/tail of the ski, in the cambered section just before the point where the unweighted ski would touch the snow surface. The ability to classify snow, potentially in real-time, using skis opens the door to applications that range from citizen science efforts to map snow surface characteristics in the backcountry, and develop skis with automated stiffness tuning based on the snow type.
Learning Absorption Rates in Glucose-Insulin Dynamics from Meal Covariates
Authors: Ke Alexander Wang, Matthew E. Levine, Jiaxin Shi, Emily B. Fox
Date: 2023-04-27 00:00:00

Traditional models of glucose-insulin dynamics rely on heuristic parameterizations chosen to fit observations within a laboratory setting. However, these models cannot describe glucose dynamics in daily life. One source of failure is in their descriptions of glucose absorption rates after meal events. A meal's macronutritional content has nuanced effects on the absorption profile, which is difficult to model mechanistically. In this paper, we propose to learn the effects of macronutrition content from glucose-insulin data and meal covariates. Given macronutrition information and meal times, we use a neural network to predict an individual's glucose absorption rate. We use this neural rate function as the control function in a differential equation of glucose dynamics, enabling end-to-end training. On simulated data, our approach is able to closely approximate true absorption rates, resulting in better forecast than heuristic parameterizations, despite only observing glucose, insulin, and macronutritional information. Our work readily generalizes to meal events with higher-dimensional covariates, such as images, setting the stage for glucose dynamics models that are personalized to each individual's daily life.
On Manifold Learning in Plato's Cave: Remarks on Manifold Learning and Physical Phenomena
Authors: Roy R. Lederman, Bogdan Toader
Date: 2023-04-27 00:00:00
Tasks: Dimensionality Reduction

Many techniques in machine learning attempt explicitly or implicitly to infer a low-dimensional manifold structure of an underlying physical phenomenon from measurements without an explicit model of the phenomenon or the measurement apparatus. This paper presents a cautionary tale regarding the discrepancy between the geometry of measurements and the geometry of the underlying phenomenon in a benign setting. The deformation in the metric illustrated in this paper is mathematically straightforward and unavoidable in the general case, and it is only one of several similar effects. While this is not always problematic, we provide an example of an arguably standard and harmless data processing procedure where this effect leads to an incorrect answer to a seemingly simple question. Although we focus on manifold learning, these issues apply broadly to dimensionality reduction and unsupervised learning.