pwc-archive/papers-with-abstracts huggingface dataset:
Unsupervised ensemble-based phenotyping helps enhance the discoverability of genes related to heart morphology
Authors: Rodrigo Bonazzola, Enzo Ferrante, Nishant Ravikumar, Yan Xia, Bernard Keavney, Sven Plein, Tanveer Syeda-Mahmood, Alejandro F Frangi
Date: 2023-01-07 00:00:00

Recent genome-wide association studies (GWAS) have been successful in identifying associations between genetic variants and simple cardiac parameters derived from cardiac magnetic resonance (CMR) images. However, the emergence of big databases including genetic data linked to CMR, facilitates investigation of more nuanced patterns of shape variability. Here, we propose a new framework for gene discovery entitled Unsupervised Phenotype Ensembles (UPE). UPE builds a redundant yet highly expressive representation by pooling a set of phenotypes learned in an unsupervised manner, using deep learning models trained with different hyperparameters. These phenotypes are then analyzed via (GWAS), retaining only highly confident and stable associations across the ensemble. We apply our approach to the UK Biobank database to extract left-ventricular (LV) geometric features from image-derived three-dimensional meshes. We demonstrate that our approach greatly improves the discoverability of genes influencing LV shape, identifying 11 loci with study-wide significance and 8 with suggestive significance. We argue that our approach would enable more extensive discovery of gene associations with image-derived phenotypes for other organs or image modalities.
How to Allocate your Label Budget? Choosing between Active Learning and Learning to Reject in Anomaly Detection
Authors: Lorenzo Perini, Daniele Giannuzzi, Jesse Davis
Date: 2023-01-07 00:00:00
Tasks: Active Learning, Anomaly Detection

Anomaly detection attempts at finding examples that deviate from the expected behaviour. Usually, anomaly detection is tackled from an unsupervised perspective because anomalous labels are rare and difficult to acquire. However, the lack of labels makes the anomaly detector have high uncertainty in some regions, which usually results in poor predictive performance or low user trust in the predictions. One can reduce such uncertainty by collecting specific labels using Active Learning (AL), which targets examples close to the detector's decision boundary. Alternatively, one can increase the user trust by allowing the detector to abstain from making highly uncertain predictions, which is called Learning to Reject (LR). One way to do this is by thresholding the detector's uncertainty based on where its performance is low, which requires labels to be evaluated. Although both AL and LR need labels, they work with different types of labels: AL seeks strategic labels, which are evidently biased, while LR requires i.i.d. labels to evaluate the detector's performance and set the rejection threshold. Because one usually has a unique label budget, deciding how to optimally allocate it is challenging. In this paper, we propose a mixed strategy that, given a budget of labels, decides in multiple rounds whether to use the budget to collect AL labels or LR labels. The strategy is based on a reward function that measures the expected gain when allocating the budget to either side. We evaluate our strategy on 18 benchmark datasets and compare it to some baselines.
REaaS: Enabling Adversarially Robust Downstream Classifiers via Robust Encoder as a Service
Authors: Wenjie Qu, Jinyuan Jia, Neil Zhenqiang Gong
Date: 2023-01-07 00:00:00
Tasks: Self-Supervised Learning

Encoder as a service is an emerging cloud service. Specifically, a service provider first pre-trains an encoder (i.e., a general-purpose feature extractor) via either supervised learning or self-supervised learning and then deploys it as a cloud service API. A client queries the cloud service API to obtain feature vectors for its training/testing inputs when training/testing its classifier (called downstream classifier). A downstream classifier is vulnerable to adversarial examples, which are testing inputs with carefully crafted perturbation that the downstream classifier misclassifies. Therefore, in safety and security critical applications, a client aims to build a robust downstream classifier and certify its robustness guarantees against adversarial examples. What APIs should the cloud service provide, such that a client can use any certification method to certify the robustness of its downstream classifier against adversarial examples while minimizing the number of queries to the APIs? How can a service provider pre-train an encoder such that clients can build more certifiably robust downstream classifiers? We aim to answer the two questions in this work. For the first question, we show that the cloud service only needs to provide two APIs, which we carefully design, to enable a client to certify the robustness of its downstream classifier with a minimal number of queries to the APIs. For the second question, we show that an encoder pre-trained using a spectral-norm regularization term enables clients to build more robust downstream classifiers.
k-Means SubClustering: A Differentially Private Algorithm with Improved Clustering Quality
Authors: Devvrat Joshi, Janvi Thakkar
Date: 2023-01-07 00:00:00
Tasks: Clustering

In today's data-driven world, the sensitivity of information has been a significant concern. With this data and additional information on the person's background, one can easily infer an individual's private data. Many differentially private iterative algorithms have been proposed in interactive settings to protect an individual's privacy from these inference attacks. The existing approaches adapt the method to compute differentially private(DP) centroids by iterative Llyod's algorithm and perturbing the centroid with various DP mechanisms. These DP mechanisms do not guarantee convergence of differentially private iterative algorithms and degrade the quality of the cluster. Thus, in this work, we further extend the previous work on 'Differentially Private k-Means Clustering With Convergence Guarantee' by taking it as our baseline. The novelty of our approach is to sub-cluster the clusters and then select the centroid which has a higher probability of moving in the direction of the future centroid. At every Lloyd's step, the centroids are injected with the noise using the exponential DP mechanism. The results of the experiments indicate that our approach outperforms the current state-of-the-art method, i.e., the baseline algorithm, in terms of clustering quality while maintaining the same differential privacy requirements. The clustering quality significantly improved by 4.13 and 2.83 times than baseline for the Wine and Breast_Cancer dataset, respectively.
Perceptual-Neural-Physical Sound Matching
Authors: Han Han, Vincent Lostanlen, Mathieu Lagrange
Date: 2023-01-07 00:00:00
Tasks: Attribute, Audio Synthesis, Decoder

Sound matching algorithms seek to approximate a target waveform by parametric audio synthesis. Deep neural networks have achieved promising results in matching sustained harmonic tones. However, the task is more challenging when targets are nonstationary and inharmonic, e.g., percussion. We attribute this problem to the inadequacy of loss function. On one hand, mean square error in the parametric domain, known as "P-loss", is simple and fast but fails to accommodate the differing perceptual significance of each parameter. On the other hand, mean square error in the spectrotemporal domain, known as "spectral loss", is perceptually motivated and serves in differentiable digital signal processing (DDSP). Yet, spectral loss is a poor predictor of pitch intervals and its gradient may be computationally expensive; hence a slow convergence. Against this conundrum, we present Perceptual-Neural-Physical loss (PNP). PNP is the optimal quadratic approximation of spectral loss while being as fast as P-loss during training. We instantiate PNP with physical modeling synthesis as decoder and joint time-frequency scattering transform (JTFS) as spectral representation. We demonstrate its potential on matching synthetic drum sounds in comparison with other loss functions.
Deep Learning for Mean Field Games with non-separable Hamiltonians
Authors: Mouhcine Assouli, Badr Missaoui
Date: 2023-01-07 00:00:00
Tasks: Deep Learning

This paper introduces a new method based on Deep Galerkin Methods (DGMs) for solving high-dimensional stochastic Mean Field Games (MFGs). We achieve this by using two neural networks to approximate the unknown solutions of the MFG system and forward-backward conditions. Our method is efficient, even with a small number of iterations, and is capable of handling up to 300 dimensions with a single layer, which makes it faster than other approaches. In contrast, methods based on Generative Adversarial Networks (GANs) cannot solve MFGs with non-separable Hamiltonians. We demonstrate the effectiveness of our approach by applying it to a traffic flow problem, which was previously solved using the Newton iteration method only in the deterministic case. We compare the results of our method to analytical solutions and previous approaches, showing its efficiency. We also prove the convergence of our neural network approximation with a single hidden layer using the universal approximation theorem.
GAN-Based Content Generation of Maps for Strategy Games
Authors: Vasco Nunes, João Dias, Pedro A. Santos
Date: 2023-01-07 00:00:00

Maps are a very important component of strategy games, and a time-consuming task if done by hand. Maps generated by traditional PCG techniques such as Perlin noise or tile-based PCG techniques look unnatural and unappealing, thus not providing the best user experience for the players. However it is possible to have a generator that can create realistic and natural images of maps, given that it is trained how to do so. We propose a model for the generation of maps based on Generative Adversarial Networks (GAN). In our implementation we tested out different variants of GAN-based networks on a dataset of heightmaps. We conducted extensive empirical evaluation to determine the advantages and properties of each approach. The results obtained are promising, showing that it is indeed possible to generate realistic looking maps using this type of approach.
"It's a Match!" -- A Benchmark of Task Affinity Scores for Joint Learning
Authors: Raphael Azorin, Massimo Gallo, Alessandro Finamore, Dario Rossi, Pietro Michiardi
Date: 2023-01-07 00:00:00
Tasks: Benchmarking, Multi-Task Learning

While the promises of Multi-Task Learning (MTL) are attractive, characterizing the conditions of its success is still an open problem in Deep Learning. Some tasks may benefit from being learned together while others may be detrimental to one another. From a task perspective, grouping cooperative tasks while separating competing tasks is paramount to reap the benefits of MTL, i.e., reducing training and inference costs. Therefore, estimating task affinity for joint learning is a key endeavor. Recent work suggests that the training conditions themselves have a significant impact on the outcomes of MTL. Yet, the literature is lacking of a benchmark to assess the effectiveness of tasks affinity estimation techniques and their relation with actual MTL performance. In this paper, we take a first step in recovering this gap by (i) defining a set of affinity scores by both revisiting contributions from previous literature as well presenting new ones and (ii) benchmarking them on the Taskonomy dataset. Our empirical campaign reveals how, even in a small-scale scenario, task affinity scoring does not correlate well with actual MTL performance. Yet, some metrics can be more indicative than others.
Machine Learning to Estimate Gross Loss of Jewelry for Wax Patterns
Authors: Mihir Jain, Kashish Jain, Sandip Mane
Date: 2023-01-07 00:00:00
Tasks: Decision Making

In mass manufacturing of jewellery, the gross loss is estimated before manufacturing to calculate the wax weight of the pattern that would be investment casted to make multiple identical pieces of jewellery. Machine learning is a technology that is a part of AI which helps create a model with decision-making capabilities based on a large set of user-defined data. In this paper, the authors found a way to use Machine Learning in the jewellery industry to estimate this crucial Gross Loss. Choosing a small data set of manufactured rings and via regression analysis, it was found out that there is a potential of reducing the error in estimation from +-2-3 to +-0.5 using ML Algorithms from historic data and attributes collected from the CAD file during the design phase itself. To evaluate the approach's viability, additional study must be undertaken with a larger data set.
Sublinear Time Algorithms for Several Geometric Optimization (With Outliers) Problems In Machine Learning
Authors: Hu Ding
Date: 2023-01-07 00:00:00
Tasks: LEMMA

In this paper, we study several important geometric optimization problems arising in machine learning. First, we revisit the Minimum Enclosing Ball (MEB) problem in Euclidean space $\mathbb{R}^d$. The problem has been extensively studied before, but real-world machine learning tasks often need to handle large-scale datasets so that we cannot even afford linear time algorithms. Motivated by the recent studies on {\em beyond worst-case analysis}, we introduce the notion of stability for MEB, which is natural and easy to understand. Roughly speaking, an instance of MEB is stable, if the radius of the resulting ball cannot be significantly reduced by removing a small fraction of the input points. Under the stability assumption, we present two sampling algorithms for computing radius-approximate MEB with sample complexities independent of the number of input points $n$. In particular, the second algorithm has the sample complexity even independent of the dimensionality $d$. We also consider the general case without the stability assumption. We present a hybrid algorithm that can output either a radius-approximate MEB or a covering-approximate MEB. Our algorithm improves the running time and the number of passes for the previous sublinear MEB algorithms. Our method relies on two novel techniques, the Uniform-Adaptive Sampling method and Sandwich Lemma. Furthermore, we observe that these two techniques can be generalized to design sublinear time algorithms for a broader range of geometric optimization problems with outliers in high dimensions, including MEB with outliers, one-class and two-class linear SVMs with outliers, $k$-center clustering with outliers, and flat fitting with outliers. Our proposed algorithms also work fine for kernels.
The 3D Structural Phenotype of the Glaucomatous Optic Nerve Head and its Relationship with The Severity of Visual Field Damage
Authors: Fabian A. Braeu, Thanadet Chuangsuwanich, Tin A. Tun, Shamira A. Perera, Rahat Husain, Aiste Kadziauskiene, Leopold Schmetterer, Alexandre H. Thiéry, George Barbastathis, Tin Aung, Michaël J. A. Girard
Date: 2023-01-07 00:00:00

$\bf{Purpose}$: To describe the 3D structural changes in both connective and neural tissues of the optic nerve head (ONH) that occur concurrently at different stages of glaucoma using traditional and AI-driven approaches. $\bf{Methods}$: We included 213 normal, 204 mild glaucoma (mean deviation [MD] $\ge$ -6.00 dB), 118 moderate glaucoma (MD of -6.01 to -12.00 dB), and 118 advanced glaucoma patients (MD < -12.00 dB). All subjects had their ONHs imaged in 3D with Spectralis optical coherence tomography. To describe the 3D structural phenotype of glaucoma as a function of severity, we used two different approaches: (1) We extracted human-defined 3D structural parameters of the ONH including retinal nerve fiber layer (RNFL) thickness, lamina cribrosa (LC) shape and depth at different stages of glaucoma; (2) we also employed a geometric deep learning method (i.e. PointNet) to identify the most important 3D structural features that differentiate ONHs from different glaucoma severity groups without any human input. $\bf{Results}$: We observed that the majority of ONH structural changes occurred in the early glaucoma stage, followed by a plateau effect in the later stages. Using PointNet, we also found that 3D ONH structural changes were present in both neural and connective tissues. In both approaches, we observed that structural changes were more prominent in the superior and inferior quadrant of the ONH, particularly in the RNFL, the prelamina, and the LC. As the severity of glaucoma increased, these changes became more diffuse (i.e. widespread), particularly in the LC. $\bf{Conclusions}$: In this study, we were able to uncover complex 3D structural changes of the ONH in both neural and connective tissues as a function of glaucoma severity. We hope to provide new insights into the complex pathophysiology of glaucoma that might help clinicians in their daily clinical care.
Why do Nearest Neighbor Language Models Work?
Authors: Frank F. Xu, Uri Alon, Graham Neubig
Date: 2023-01-07 00:00:00
Tasks: Retrieval

Language models (LMs) compute the probability of a text by sequentially computing a representation of an already-seen context and using this representation to predict the next word. Currently, most LMs calculate these representations through a neural network consuming the immediate previous context. However recently, retrieval-augmented LMs have shown to improve over standard neural LMs, by accessing information retrieved from a large datastore, in addition to their standard, parametric, next-word prediction. In this paper, we set out to understand why retrieval-augmented language models, and specifically why k-nearest neighbor language models (kNN-LMs) perform better than standard parametric LMs, even when the k-nearest neighbor component retrieves examples from the same training set that the LM was originally trained on. To this end, we perform a careful analysis of the various dimensions over which kNN-LM diverges from standard LMs, and investigate these dimensions one by one. Empirically, we identify three main reasons why kNN-LM performs better than standard LMs: using a different input representation for predicting the next tokens, approximate kNN search, and the importance of softmax temperature for the kNN distribution. Further, we incorporate these insights into the model architecture or the training procedure of the standard parametric LM, improving its results without the need for an explicit retrieval component. The code is available at https://github.com/frankxu2004/knnlm-why.
ExcelFormer: A neural network surpassing GBDTs on tabular data
Authors: Jintai Chen, Jiahuan Yan, Qiyuan Chen, Danny Ziyi Chen, Jian Wu, Jimeng Sun
Date: 2023-01-07 00:00:00
Tasks: Data Augmentation, Model Selection, Prediction

Data organized in tabular format is ubiquitous in real-world applications, and users often craft tables with biased feature definitions and flexibly set prediction targets of their interests. Thus, a rapid development of a robust, effective, dataset-versatile, user-friendly tabular prediction approach is highly desired. While Gradient Boosting Decision Trees (GBDTs) and existing deep neural networks (DNNs) have been extensively utilized by professional users, they present several challenges for casual users, particularly: (i) the dilemma of model selection due to their different dataset preferences, and (ii) the need for heavy hyperparameter searching, failing which their performances are deemed inadequate. In this paper, we delve into this question: Can we develop a deep learning model that serves as a "sure bet" solution for a wide range of tabular prediction tasks, while also being user-friendly for casual users? We delve into three key drawbacks of deep tabular models, encompassing: (P1) lack of rotational variance property, (P2) large data demand, and (P3) over-smooth solution. We propose ExcelFormer, addressing these challenges through a semi-permeable attention module that effectively constrains the influence of less informative features to break the DNNs' rotational invariance property (for P1), data augmentation approaches tailored for tabular data (for P2), and attentive feedforward network to boost the model fitting capability (for P3). These designs collectively make ExcelFormer a "sure bet" solution for diverse tabular datasets. Extensive and stratified experiments conducted on real-world datasets demonstrate that our model outperforms previous approaches across diverse tabular data prediction tasks, and this framework can be friendly to casual users, offering ease of use without the heavy hyperparameter tuning.
Randomized Greedy Algorithms and Composable Coreset for k-Center Clustering with Outliers
Authors: Hu Ding, Ruomin Huang, Kai Liu, Haikuo Yu, Zixiu Wang
Date: 2023-01-07 00:00:00
Tasks: Clustering

In this paper, we study the problem of {\em $k$-center clustering with outliers}. The problem has many important applications in real world, but the presence of outliers can significantly increase the computational complexity. Though a number of methods have been developed in the past decades, it is still quite challenging to design quality guaranteed algorithm with low complexity for this problem. Our idea is inspired by the greedy method, Gonzalez's algorithm, that was developed for solving the ordinary $k$-center clustering problem. Based on some novel observations, we show that a simple randomized version of this greedy strategy actually can handle outliers efficiently. We further show that this randomized greedy approach also yields small coreset for the problem in doubling metrics (even if the doubling dimension is not given), which can greatly reduce the computational complexity. Moreover, together with the partial clustering framework proposed in arXiv:1703.01539 , we prove that our coreset method can be applied to distributed data with a low communication complexity. The experimental results suggest that our algorithms can achieve near optimal solutions and yield lower complexities comparing with the existing methods.
Faithful and Consistent Graph Neural Network Explanations with Rationale Alignment
Authors: Tianxiang Zhao, Dongsheng Luo, Xiang Zhang, Suhang Wang
Date: 2023-01-07 00:00:00
Tasks: Graph Neural Network, Inductive Bias

Uncovering rationales behind predictions of graph neural networks (GNNs) has received increasing attention over recent years. Instance-level GNN explanation aims to discover critical input elements, like nodes or edges, that the target GNN relies upon for making predictions. %These identified sub-structures can provide interpretations of GNN's behavior. Though various algorithms are proposed, most of them formalize this task by searching the minimal subgraph which can preserve original predictions. However, an inductive bias is deep-rooted in this framework: several subgraphs can result in the same or similar outputs as the original graphs. Consequently, they have the danger of providing spurious explanations and failing to provide consistent explanations. Applying them to explain weakly-performed GNNs would further amplify these issues. To address this problem, we theoretically examine the predictions of GNNs from the causality perspective. Two typical reasons for spurious explanations are identified: confounding effect of latent variables like distribution shift, and causal factors distinct from the original input. Observing that both confounding effects and diverse causal rationales are encoded in internal representations, \tianxiang{we propose a new explanation framework with an auxiliary alignment loss, which is theoretically proven to be optimizing a more faithful explanation objective intrinsically. Concretely for this alignment loss, a set of different perspectives are explored: anchor-based alignment, distributional alignment based on Gaussian mixture models, mutual-information-based alignment, etc. A comprehensive study is conducted both on the effectiveness of this new framework in terms of explanation faithfulness/consistency and on the advantages of these variants.