pwc-archive/papers-with-abstracts huggingface dataset:
Tracking and Mapping in Medical Computer Vision: A Review
Authors: Adam Schmidt, Omid Mohareri, Simon DiMaio, Michael C. Yip, Septimiu E. Salcudean
Date: 2023-10-17 00:00:00

As computer vision algorithms increase in capability, their applications in clinical systems will become more pervasive. These applications include: diagnostics, such as colonoscopy and bronchoscopy; guiding biopsies, minimally invasive interventions, and surgery; automating instrument motion; and providing image guidance using pre-operative scans. Many of these applications depend on the specific visual nature of medical scenes and require designing algorithms to perform in this environment. In this review, we provide an update to the field of camera-based tracking and scene mapping in surgery and diagnostics in medical computer vision. We begin with describing our review process, which results in a final list of 515 papers that we cover. We then give a high-level summary of the state of the art and provide relevant background for those who need tracking and mapping for their clinical applications. After which, we review datasets provided in the field and the clinical needs that motivate their design. Then, we delve into the algorithmic side, and summarize recent developments. This summary should be especially useful for algorithm designers and to those looking to understand the capability of off-the-shelf methods. We maintain focus on algorithms for deformable environments while also reviewing the essential building blocks in rigid tracking and mapping since there is a large amount of crossover in methods. With the field summarized, we discuss the current state of the tracking and mapping methods along with needs for future algorithms, needs for quantification, and the viability of clinical applications. We then provide some research directions and questions. We conclude that new methods need to be designed or combined to support clinical applications in deformable environments, and more focus needs to be put into collecting datasets for training and evaluation.
Dynamic financial processes identification using sparse regressive reservoir computers
Authors: Fredy Vides, Idelfonso B. R. Nogueira, Lendy Banegas, Evelyn Flores
Date: 2023-10-18 00:00:00
Tasks: Time Series

In this document, we present key findings in structured matrix approximation theory, with applications to the regressive representation of dynamic financial processes. Initially, we explore a comprehensive approach involving generic nonlinear time delay embedding for time series data extracted from a financial or economic system under examination. Subsequently, we employ sparse least-squares and structured matrix approximation methods to discern approximate representations of the output coupling matrices. These representations play a pivotal role in establishing the regressive models corresponding to the recursive structures inherent in a given financial system. The document further introduces prototypical algorithms that leverage the aforementioned techniques. These algorithms are demonstrated through applications in approximate identification and predictive simulation of dynamic financial and economic processes, encompassing scenarios that may or may not exhibit chaotic behavior.
Simple Mechanisms for Representing, Indexing and Manipulating Concepts
Authors: Yuanzhi Li, Raghu Meka, Rina Panigrahy, Kulin Shah
Date: 2023-10-18 00:00:00

Deep networks typically learn concepts via classifiers, which involves setting up a model and training it via gradient descent to fit the concept-labeled data. We will argue instead that learning a concept could be done by looking at its moment statistics matrix to generate a concrete representation or signature of that concept. These signatures can be used to discover structure across the set of concepts and could recursively produce higher-level concepts by learning this structure from those signatures. When the concepts are `intersected', signatures of the concepts can be used to find a common theme across a number of related `intersected' concepts. This process could be used to keep a dictionary of concepts so that inputs could correctly identify and be routed to the set of concepts involved in the (latent) generation of the input.
A Tale of Pronouns: Interpretability Informs Gender Bias Mitigation for Fairer Instruction-Tuned Machine Translation
Authors: Giuseppe Attanasio, Flor Miriam Plaza-del-Arco, Debora Nozza, Anne Lauscher
Date: 2023-10-18 00:00:00
Tasks: Fairness, Few-Shot Learning, Machine Translation, Translation

Recent instruction fine-tuned models can solve multiple NLP tasks when prompted to do so, with machine translation (MT) being a prominent use case. However, current research often focuses on standard performance benchmarks, leaving compelling fairness and ethical considerations behind. In MT, this might lead to misgendered translations, resulting, among other harms, in the perpetuation of stereotypes and prejudices. In this work, we address this gap by investigating whether and to what extent such models exhibit gender bias in machine translation and how we can mitigate it. Concretely, we compute established gender bias metrics on the WinoMT corpus from English to German and Spanish. We discover that IFT models default to male-inflected translations, even disregarding female occupational stereotypes. Next, using interpretability methods, we unveil that models systematically overlook the pronoun indicating the gender of a target occupation in misgendered translations. Finally, based on this finding, we propose an easy-to-implement and effective bias mitigation solution based on few-shot learning that leads to significantly fairer translations.
Automatic prediction of mortality in patients with mental illness using electronic health records
Authors: Sean Kim, Samuel Kim
Date: 2023-10-18 00:00:00
Tasks: Feature Importance

Mental disorders impact the lives of millions of people globally, not only impeding their day-to-day lives but also markedly reducing life expectancy. This paper addresses the persistent challenge of predicting mortality in patients with mental diagnoses using predictive machine-learning models with electronic health records (EHR). Data from patients with mental disease diagnoses were extracted from the well-known clinical MIMIC-III data set utilizing demographic, prescription, and procedural information. Four machine learning algorithms (Logistic Regression, Random Forest, Support Vector Machine, and K-Nearest Neighbors) were used, with results indicating that Random Forest and Support Vector Machine models outperformed others, with AUC scores of 0.911. Feature importance analysis revealed that drug prescriptions, particularly Morphine Sulfate, play a pivotal role in prediction. We applied a variety of machine learning algorithms to predict 30-day mortality followed by feature importance analysis. This study can be used to assist hospital workers in identifying at-risk patients to reduce excess mortality.
MMD-based Variable Importance for Distributional Random Forest
Authors: Clément Bénard, Jeffrey Näf, Julie Josse
Date: 2023-10-18 00:00:00

Distributional Random Forest (DRF) is a flexible forest-based method to estimate the full conditional distribution of a multivariate output of interest given input variables. In this article, we introduce a variable importance algorithm for DRFs, based on the well-established drop and relearn principle and MMD distance. While traditional importance measures only detect variables with an influence on the output mean, our algorithm detects variables impacting the output distribution more generally. We show that the introduced importance measure is consistent, exhibits high empirical performance on both real and simulated data, and outperforms competitors. In particular, our algorithm is highly efficient to select variables through recursive feature elimination, and can therefore provide small sets of variables to build accurate estimates of conditional output distributions.
An Online Learning Theory of Brokerage
Authors: Nataša Bolić, Tommaso Cesari, Roberto Colomboni
Date: 2023-10-18 00:00:00
Tasks: Learning Theory

We investigate brokerage between traders from an online learning perspective. At any round $t$, two traders arrive with their private valuations, and the broker proposes a trading price. Unlike other bilateral trade problems already studied in the online learning literature, we focus on the case where there are no designated buyer and seller roles: each trader will attempt to either buy or sell depending on the current price of the good. We assume the agents' valuations are drawn i.i.d. from a fixed but unknown distribution. If the distribution admits a density bounded by some constant $M$, then, for any time horizon $T$: $\bullet$ If the agents' valuations are revealed after each interaction, we provide an algorithm achieving regret $M \log T$ and show this rate is optimal, up to constant factors. $\bullet$ If only their willingness to sell or buy at the proposed price is revealed after each interaction, we provide an algorithm achieving regret $\sqrt{M T}$ and show this rate is optimal, up to constant factors. Finally, if we drop the bounded density assumption, we show that the optimal rate degrades to $\sqrt{T}$ in the first case, and the problem becomes unlearnable in the second.
On the latent dimension of deep autoencoders for reduced order modeling of PDEs parametrized by random fields
Authors: Nicola Rares Franco, Daniel Fraulin, Andrea Manzoni, Paolo Zunino
Date: 2023-10-18 00:00:00

Deep Learning is having a remarkable impact on the design of Reduced Order Models (ROMs) for Partial Differential Equations (PDEs), where it is exploited as a powerful tool for tackling complex problems for which classical methods might fail. In this respect, deep autoencoders play a fundamental role, as they provide an extremely flexible tool for reducing the dimensionality of a given problem by leveraging on the nonlinear capabilities of neural networks. Indeed, starting from this paradigm, several successful approaches have already been developed, which are here referred to as Deep Learning-based ROMs (DL-ROMs). Nevertheless, when it comes to stochastic problems parameterized by random fields, the current understanding of DL-ROMs is mostly based on empirical evidence: in fact, their theoretical analysis is currently limited to the case of PDEs depending on a finite number of (deterministic) parameters. The purpose of this work is to extend the existing literature by providing some theoretical insights about the use of DL-ROMs in the presence of stochasticity generated by random fields. In particular, we derive explicit error bounds that can guide domain practitioners when choosing the latent dimension of deep autoencoders. We evaluate the practical usefulness of our theory by means of numerical experiments, showing how our analysis can significantly impact the performance of DL-ROMs.
Contributing Components of Metabolic Energy Models to Metabolic Cost Estimations in Gait
Authors: Markus Gambietz, Marlies Nitschke, Jörg Miehling, Anne Koelewijn
Date: 2023-10-18 00:00:00
Tasks: feature selection, Sensitivity

Objective: As metabolic cost is a primary factor influencing humans' gait, we want to deepen our understanding of metabolic energy expenditure models. Therefore, this paper identifies the parameters and input variables, such as muscle or joint states, that contribute to accurate metabolic cost estimations. Methods: We explored the parameters of four metabolic energy expenditure models in a Monte Carlo sensitivity analysis. Then, we analysed the model parameters by their calculated sensitivity indices, physiological context, and the resulting metabolic rates during the gait cycle. The parameter combination with the highest accuracy in the Monte Carlo simulations represented a quasi-optimized model. In the second step, we investigated the importance of input parameters and variables by analysing the accuracy of neural networks trained with different input features. Results: Power-related parameters were most influential in the sensitivity analysis and the neural network-based feature selection. We observed that the quasi-optimized models produced negative metabolic rates, contradicting muscle physiology. Neural network-based models showed promising abilities but have been unable to match the accuracy of traditional metabolic energy expenditure models. Conclusion: We showed that power-related metabolic energy expenditure model parameters and inputs are most influential during gait. Furthermore, our results suggest that neural network-based metabolic energy expenditure models are viable. However, bigger datasets are required to achieve better accuracy. Significance: As there is a need for more accurate metabolic energy expenditure models, we explored which musculoskeletal parameters are essential when developing a model to estimate metabolic energy.
Differential Equation Scaling Limits of Shaped and Unshaped Neural Networks
Authors: Mufan Bill Li, Mihai Nica
Date: 2023-10-18 00:00:00

Recent analyses of neural networks with shaped activations (i.e. the activation function is scaled as the network size grows) have led to scaling limits described by differential equations. However, these results do not a priori tell us anything about "ordinary" unshaped networks, where the activation is unchanged as the network size grows. In this article, we find similar differential equation based asymptotic characterization for two types of unshaped networks. Firstly, we show that the following two architectures converge to the same infinite-depth-and-width limit at initialization: (i) a fully connected ResNet with a $d^{-1/2}$ factor on the residual branch, where $d$ is the network depth. (ii) a multilayer perceptron (MLP) with depth $d \ll$ width $n$ and shaped ReLU activation at rate $d^{-1/2}$. Secondly, for an unshaped MLP at initialization, we derive the first order asymptotic correction to the layerwise correlation. In particular, if $\rho_\ell$ is the correlation at layer $\ell$, then $q_t = \ell^2 (1 - \rho_\ell)$ with $t = \frac{\ell}{n}$ converges to an SDE with a singularity at $t=0$. These results together provide a connection between shaped and unshaped network architectures, and opens up the possibility of studying the effect of normalization methods and how it connects with shaping activation functions.
Transformers for scientific data: a pedagogical review for astronomers
Authors: Dimitrios Tanoglidis, Bhuvnesh Jain, Helen Qu
Date: 2023-10-18 00:00:00
Tasks: Astronomy, Time Series

The deep learning architecture associated with ChatGPT and related generative AI products is known as transformers. Initially applied to Natural Language Processing, transformers and the self-attention mechanism they exploit have gained widespread interest across the natural sciences. The goal of this pedagogical and informal review is to introduce transformers to scientists. The review includes the mathematics underlying the attention mechanism, a description of the original transformer architecture, and a section on applications to time series and imaging data in astronomy. We include a Frequently Asked Questions section for readers who are curious about generative AI or interested in getting started with transformers for their research problem.
Understanding Reward Ambiguity Through Optimal Transport Theory in Inverse Reinforcement Learning
Authors: Ali Baheri
Date: 2023-10-18 00:00:00
Tasks: reinforcement-learning

In inverse reinforcement learning (IRL), the central objective is to infer underlying reward functions from observed expert behaviors in a way that not only explains the given data but also generalizes to unseen scenarios. This ensures robustness against reward ambiguity where multiple reward functions can equally explain the same expert behaviors. While significant efforts have been made in addressing this issue, current methods often face challenges with high-dimensional problems and lack a geometric foundation. This paper harnesses the optimal transport (OT) theory to provide a fresh perspective on these challenges. By utilizing the Wasserstein distance from OT, we establish a geometric framework that allows for quantifying reward ambiguity and identifying a central representation or centroid of reward functions. These insights pave the way for robust IRL methodologies anchored in geometric interpretations, offering a structured approach to tackle reward ambiguity in high-dimensional settings.
Applications of ML-Based Surrogates in Bayesian Approaches to Inverse Problems
Authors: Pelin Ersin, Emma Hayes, Peter Matthews, Paramjyoti Mohapatra, Elisa Negrini, Karl Schulz
Date: 2023-10-18 00:00:00
Tasks: Computational Efficiency

Neural networks have become a powerful tool as surrogate models to provide numerical solutions for scientific problems with increased computational efficiency. This efficiency can be advantageous for numerically challenging problems where time to solution is important or when evaluation of many similar analysis scenarios is required. One particular area of scientific interest is the setting of inverse problems, where one knows the forward dynamics of a system are described by a partial differential equation and the task is to infer properties of the system given (potentially noisy) observations of these dynamics. We consider the inverse problem of inferring the location of a wave source on a square domain, given a noisy solution to the 2-D acoustic wave equation. Under the assumption of Gaussian noise, a likelihood function for source location can be formulated, which requires one forward simulation of the system per evaluation. Using a standard neural network as a surrogate model makes it computationally feasible to evaluate this likelihood several times, and so Markov Chain Monte Carlo methods can be used to evaluate the posterior distribution of the source location. We demonstrate that this method can accurately infer source-locations from noisy data.
Conformal Drug Property Prediction with Density Estimation under Covariate Shift
Authors: Siddhartha Laghuvarapu, Zhen Lin, Jimeng Sun
Date: 2023-10-18 00:00:00
Tasks: Conformal Prediction, Density Estimation, Drug Design, Drug Discovery, Prediction, Property Prediction, valid

In drug discovery, it is vital to confirm the predictions of pharmaceutical properties from computational models using costly wet-lab experiments. Hence, obtaining reliable uncertainty estimates is crucial for prioritizing drug molecules for subsequent experimental validation. Conformal Prediction (CP) is a promising tool for creating such prediction sets for molecular properties with a coverage guarantee. However, the exchangeability assumption of CP is often challenged with covariate shift in drug discovery tasks: Most datasets contain limited labeled data, which may not be representative of the vast chemical space from which molecules are drawn. To address this limitation, we propose a method called CoDrug that employs an energy-based model leveraging both training data and unlabelled data, and Kernel Density Estimation (KDE) to assess the densities of a molecule set. The estimated densities are then used to weigh the molecule samples while building prediction sets and rectifying for distribution shift. In extensive experiments involving realistic distribution drifts in various small-molecule drug discovery tasks, we demonstrate the ability of CoDrug to provide valid prediction sets and its utility in addressing the distribution shift arising from de novo drug design models. On average, using CoDrug can reduce the coverage gap by over 35% when compared to conformal prediction sets not adjusted for covariate shift.
Exact and general decoupled solutions of the LMC Multitask Gaussian Process model
Authors: Olivier Truffinet, Karim Ammar, Jean-Philippe Argaud, Bertrand Bouriquet
Date: 2023-10-18 00:00:00

The Linear Model of Co-regionalization (LMC) is a very general model of multitask gaussian process for regression or classification. While its expressivity and conceptual simplicity are appealing, naive implementations have cubic complexity in the number of datapoints and number of tasks, making approximations mandatory for most applications. However, recent work has shown that under some conditions the latent processes of the model can be decoupled, leading to a complexity that is only linear in the number of said processes. We here extend these results, showing from the most general assumptions that the only condition necessary to an efficient exact computation of the LMC is a mild hypothesis on the noise model. We introduce a full parametrization of the resulting \emph{projected LMC} model, and an expression of the marginal likelihood enabling efficient optimization. We perform a parametric study on synthetic data to show the excellent performance of our approach, compared to an unrestricted exact LMC and approximations of the latter. Overall, the projected LMC appears as a credible and simpler alternative to state-of-the art models, which greatly facilitates some computations such as leave-one-out cross-validation and fantasization.
Nonparametric Discrete Choice Experiments with Machine Learning Guided Adaptive Design
Authors: Mingzhang Yin, Ruijiang Gao, Weiran Lin, Steven M. Shugan
Date: 2023-10-18 00:00:00

Designing products to meet consumers' preferences is essential for a business's success. We propose the Gradient-based Survey (GBS), a discrete choice experiment for multiattribute product design. The experiment elicits consumer preferences through a sequence of paired comparisons for partial profiles. GBS adaptively constructs paired comparison questions based on the respondents' previous choices. Unlike the traditional random utility maximization paradigm, GBS is robust to model misspecification by not requiring a parametric utility model. Cross-pollinating the machine learning and experiment design, GBS is scalable to products with hundreds of attributes and can design personalized products for heterogeneous consumers. We demonstrate the advantage of GBS in accuracy and sample efficiency compared to the existing parametric and nonparametric methods in simulations.
Iterative Methods for Vecchia-Laplace Approximations for Latent Gaussian Process Models
Authors: Pascal Kündig, Fabio Sigrist
Date: 2023-10-18 00:00:00

Latent Gaussian process (GP) models are flexible probabilistic non-parametric function models. Vecchia approximations are accurate approximations for GPs to overcome computational bottlenecks for large data, and the Laplace approximation is a fast method with asymptotic convergence guarantees to approximate marginal likelihoods and posterior predictive distributions for non-Gaussian likelihoods. Unfortunately, the computational complexity of combined Vecchia-Laplace approximations grows faster than linearly in the sample size when used in combination with direct solver methods such as the Cholesky decomposition. Computations with Vecchia-Laplace approximations can thus become prohibitively slow precisely when the approximations are usually the most accurate, i.e., on large data sets. In this article, we present iterative methods to overcome this drawback. Among other things, we introduce and analyze several preconditioners, derive new convergence results, and propose novel methods for accurately approximating predictive variances. We analyze our proposed methods theoretically and in experiments with simulated and real-world data. In particular, we obtain a speed-up of an order of magnitude compared to Cholesky-based calculations and a threefold increase in prediction accuracy in terms of the continuous ranked probability score compared to a state-of-the-art method on a large satellite data set. All methods are implemented in a free C++ software library with high-level Python and R packages.