pwc-archive/papers-with-abstracts huggingface dataset:
ERNet: Unsupervised Collective Extraction and Registration in Neuroimaging Data
Authors: Yao Su, Zhentian Qian, Lifang He, Xiangnan Kong
Date: 2022-12-06 00:00:00
Tasks: Brain Image Segmentation, Image Registration, Image Segmentation, Medical Image Registration, Medical Image Segmentation

Brain extraction and registration are important preprocessing steps in neuroimaging data analysis, where the goal is to extract the brain regions from MRI scans (i.e., extraction step) and align them with a target brain image (i.e., registration step). Conventional research mainly focuses on developing methods for the extraction and registration tasks separately under supervised settings. The performance of these methods highly depends on the amount of training samples and visual inspections performed by experts for error correction. However, in many medical studies, collecting voxel-level labels and conducting manual quality control in high-dimensional neuroimages (e.g., 3D MRI) are very expensive and time-consuming. Moreover, brain extraction and registration are highly related tasks in neuroimaging data and should be solved collectively. In this paper, we study the problem of unsupervised collective extraction and registration in neuroimaging data. We propose a unified end-to-end framework, called ERNet (Extraction-Registration Network), to jointly optimize the extraction and registration tasks, allowing feedback between them. Specifically, we use a pair of multi-stage extraction and registration modules to learn the extraction mask and transformation, where the extraction network improves the extraction accuracy incrementally and the registration network successively warps the extracted image until it is well-aligned with the target image. Experiment results on real-world datasets show that our proposed method can effectively improve the performance on extraction and registration tasks in neuroimaging data. Our code and data can be found at https://github.com/ERNetERNet/ERNet
Supervised Tractogram Filtering using Geometric Deep Learning
Authors: Pietro Astolfi, Ruben Verhagen, Laurent Petit, Emanuele Olivetti, Silvio Sarubbo, Jonathan Masci, Davide Boscaini, Paolo Avesani
Date: 2022-12-06 00:00:00
Tasks: Deep Learning, GPU

A tractogram is a virtual representation of the brain white matter. It is composed of millions of virtual fibers, encoded as 3D polylines, which approximate the white matter axonal pathways. To date, tractograms are the most accurate white matter representation and thus are used for tasks like presurgical planning and investigations of neuroplasticity, brain disorders, or brain networks. However, it is a well-known issue that a large portion of tractogram fibers is not anatomically plausible and can be considered artifacts of the tracking procedure. With Verifyber, we tackle the problem of filtering out such non-plausible fibers using a novel fully-supervised learning approach. Differently from other approaches based on signal reconstruction and/or brain topology regularization, we guide our method with the existing anatomical knowledge of the white matter. Using tractograms annotated according to anatomical principles, we train our model, Verifyber, to classify fibers as either anatomically plausible or non-plausible. The proposed Verifyber model is an original Geometric Deep Learning method that can deal with variable size fibers, while being invariant to fiber orientation. Our model considers each fiber as a graph of points, and by learning features of the edges between consecutive points via the proposed sequence Edge Convolution, it can capture the underlying anatomical properties. The output filtering results highly accurate and robust across an extensive set of experiments, and fast; with a 12GB GPU, filtering a tractogram of 1M fibers requires less than a minute. Verifyber implementation and trained models are available at https://github.com/FBK-NILab/verifyber.
MobilePTX: Sparse Coding for Pneumothorax Detection Given Limited Training Examples
Authors: Darryl Hannan, Steven C. Nesbit, Ximing Wen, Glen Smith, Qiao Zhang, Alberto Goffi, Vincent Chan, Michael J. Morris, John C. Hunninghake, Nicholas E. Villalobos, Edward Kim, Rosina O. Weber, Christopher J. MacLellan
Date: 2022-12-06 00:00:00
Tasks: Pneumothorax Detection

Point-of-Care Ultrasound (POCUS) refers to clinician-performed and interpreted ultrasonography at the patient's bedside. Interpreting these images requires a high level of expertise, which may not be available during emergencies. In this paper, we support POCUS by developing classifiers that can aid medical professionals by diagnosing whether or not a patient has pneumothorax. We decomposed the task into multiple steps, using YOLOv4 to extract relevant regions of the video and a 3D sparse coding model to represent video features. Given the difficulty in acquiring positive training videos, we trained a small-data classifier with a maximum of 15 positive and 32 negative examples. To counteract this limitation, we leveraged subject matter expert (SME) knowledge to limit the hypothesis space, thus reducing the cost of data collection. We present results using two lung ultrasound datasets and demonstrate that our model is capable of achieving performance on par with SMEs in pneumothorax identification. We then developed an iOS application that runs our full system in less than 4 seconds on an iPad Pro, and less than 8 seconds on an iPhone 13 Pro, labeling key regions in the lung sonogram to provide interpretable diagnoses.
ABN: Anti-Blur Neural Networks for Multi-Stage Deformable Image Registration
Authors: Yao Su, Xin Dai, Lifang He, Xiangnan Kong
Date: 2022-12-06 00:00:00
Tasks: Deformable Medical Image Registration, Image Registration, Medical Image Registration

Deformable image registration, i.e., the task of aligning multiple images into one coordinate system by non-linear transformation, serves as an essential preprocessing step for neuroimaging data. Recent research on deformable image registration is mainly focused on improving the registration accuracy using multi-stage alignment methods, where the source image is repeatedly deformed in stages by a same neural network until it is well-aligned with the target image. Conventional methods for multi-stage registration can often blur the source image as the pixel/voxel values are repeatedly interpolated from the image generated by the previous stage. However, maintaining image quality such as sharpness during image registration is crucial to medical data analysis. In this paper, we study the problem of anti-blur deformable image registration and propose a novel solution, called Anti-Blur Network (ABN), for multi-stage image registration. Specifically, we use a pair of short-term registration and long-term memory networks to learn the nonlinear deformations at each stage, where the short-term registration network learns how to improve the registration accuracy incrementally and the long-term memory network combines all the previous deformations to allow an interpolation to perform on the raw image directly and preserve image sharpness. Extensive experiments on both natural and medical image datasets demonstrated that ABN can accurately register images while preserving their sharpness. Our code and data can be found at https://github.com/anonymous3214/ABN
Giga-SSL: Self-Supervised Learning for Gigapixel Images
Authors: Tristan Lazard, Marvin Lerousseau, Etienne Decencière, Thomas Walter
Date: 2022-12-06 00:00:00
Tasks: Multiple Instance Learning, Self-Supervised Learning, whole slide images

Whole slide images (WSI) are microscopy images of stained tissue slides routinely prepared for diagnosis and treatment selection in medical practice. WSI are very large (gigapixel size) and complex (made of up to millions of cells). The current state-of-the-art (SoTA) approach to classify WSI subdivides them into tiles, encodes them by pre-trained networks and applies Multiple Instance Learning (MIL) to train for specific downstream tasks. However, annotated datasets are often small, typically a few hundred to a few thousand WSI, which may cause overfitting and underperforming models. Conversely, the number of unannotated WSI is ever increasing, with datasets of tens of thousands (soon to be millions) of images available. While it has been previously proposed to use these unannotated data to identify suitable tile representations by self-supervised learning (SSL), downstream classification tasks still require full supervision because parts of the MIL architecture is not trained during tile level SSL pre-training. Here, we propose a strategy of slide level SSL to leverage the large number of WSI without annotations to infer powerful slide representations. Applying our method to The Cancer-Genome Atlas, one of the most widely used data resources in cancer research (16 TB image data), we are able to downsize the dataset to 23 MB without any loss in predictive power: we show that a linear classifier trained on top of these embeddings maintains or improves previous SoTA performances on various benchmark WSI classification tasks. Finally, we observe that training a classifier on these representations with tiny datasets (e.g. 50 slides) improved performances over SoTA by an average of +6.3 AUC points over all downstream tasks.
NeRDi: Single-View NeRF Synthesis with Language-Guided Diffusion as General Image Priors
Authors: Congyue Deng, Chiyu "Max'' Jiang, Charles R. Qi, Xinchen Yan, Yin Zhou, Leonidas Guibas, Dragomir Anguelov
Date: 2022-12-06 00:00:00
Proceeding: CVPR 2023 1
Tasks: 3D Generation, 3D geometry, 3D Reconstruction, NeRF

2D-to-3D reconstruction is an ill-posed problem, yet humans are good at solving this problem due to their prior knowledge of the 3D world developed over years. Driven by this observation, we propose NeRDi, a single-view NeRF synthesis framework with general image priors from 2D diffusion models. Formulating single-view reconstruction as an image-conditioned 3D generation problem, we optimize the NeRF representations by minimizing a diffusion loss on its arbitrary view renderings with a pretrained image diffusion model under the input-view constraint. We leverage off-the-shelf vision-language models and introduce a two-section language guidance as conditioning inputs to the diffusion model. This is essentially helpful for improving multiview content coherence as it narrows down the general image prior conditioned on the semantic and visual features of the single-view input image. Additionally, we introduce a geometric loss based on estimated depth maps to regularize the underlying 3D geometry of the NeRF. Experimental results on the DTU MVS dataset show that our method can synthesize novel views with higher quality even compared to existing methods trained on this dataset. We also demonstrate our generalizability in zero-shot NeRF synthesis for in-the-wild images.
Phase2vec: Dynamical systems embedding with a physics-informed convolutional network
Authors: Matthew Ricci, Noa Moriel, Zoe Piran, Mor Nitzan
Date: 2022-12-07 00:00:00
Tasks: Time Series, Time Series Analysis, Time Series Classification

Dynamical systems are found in innumerable forms across the physical and biological sciences, yet all these systems fall naturally into universal equivalence classes: conservative or dissipative, stable or unstable, compressible or incompressible. Predicting these classes from data remains an essential open challenge in computational physics at which existing time-series classification methods struggle. Here, we propose, \texttt{phase2vec}, an embedding method that learns high-quality, physically-meaningful representations of 2D dynamical systems without supervision. Our embeddings are produced by a convolutional backbone that extracts geometric features from flow data and minimizes a physically-informed vector field reconstruction loss. In an auxiliary training period, embeddings are optimized so that they robustly encode the equations of unseen data over and above the performance of a per-equation fitting method. The trained architecture can not only predict the equations of unseen data, but also, crucially, learns embeddings that respect the underlying semantics of the embedded physical systems. We validate the quality of learned embeddings investigating the extent to which physical categories of input data can be decoded from embeddings compared to standard blackbox classifiers and state-of-the-art time series classification techniques. We find that our embeddings encode important physical properties of the underlying data, including the stability of fixed points, conservation of energy, and the incompressibility of flows, with greater fidelity than competing methods. We finally apply our embeddings to the analysis of meteorological data, showing we can detect climatically meaningful features. Collectively, our results demonstrate the viability of embedding approaches for the discovery of dynamical features in physical systems.
Computing linear sections of varieties: quantum entanglement, tensor decompositions and beyond
Authors: Nathaniel Johnston, Benjamin Lovitz, Aravindan Vijayaraghavan
Date: 2022-12-07 00:00:00

We study the problem of finding elements in the intersection of an arbitrary conic variety in $\mathbb{F}^n$ with a given linear subspace (where $\mathbb{F}$ can be the real or complex field). This problem captures a rich family of algorithmic problems under different choices of the variety. The special case of the variety consisting of rank-1 matrices already has strong connections to central problems in different areas like quantum information theory and tensor decompositions. This problem is known to be NP-hard in the worst case, even for the variety of rank-1 matrices. Surprisingly, despite these hardness results we develop an algorithm that solves this problem efficiently for "typical" subspaces. Here, the subspace $U \subseteq \mathbb{F}^n$ is chosen generically of a certain dimension, potentially with some generic elements of the variety contained in it. Our main result is a guarantee that our algorithm recovers all the elements of $U$ that lie in the variety, under some mild non-degeneracy assumptions on the variety. As corollaries, we obtain the following new results: $\bullet$ Polynomial time algorithms for several entangled subspaces problems in quantum entanglement, including determining r-entanglement, complete entanglement, and genuine entanglement of a subspace. While all of these problems are NP-hard in the worst case, our algorithm solves them in polynomial time for generic subspaces of dimension up to a constant multiple of the maximum possible. $\bullet$ Uniqueness results and polynomial time algorithmic guarantees for generic instances of a broad class of low-rank decomposition problems that go beyond tensor decompositions. Here, we recover a decomposition of the form $\sum_{i=1}^R v_i \otimes w_i$, where the $v_i$ are elements of the variety $X$. This implies new uniqueness results and genericity guarantees even in the special case of tensor decompositions.
Fairness and Explainability: Bridging the Gap Towards Fair Model Explanations
Authors: Yuying Zhao, Yu Wang, Tyler Derr
Date: 2022-12-07 00:00:00
Tasks: Decision Making, Fairness

While machine learning models have achieved unprecedented success in real-world applications, they might make biased/unfair decisions for specific demographic groups and hence result in discriminative outcomes. Although research efforts have been devoted to measuring and mitigating bias, they mainly study bias from the result-oriented perspective while neglecting the bias encoded in the decision-making procedure. This results in their inability to capture procedure-oriented bias, which therefore limits the ability to have a fully debiasing method. Fortunately, with the rapid development of explainable machine learning, explanations for predictions are now available to gain insights into the procedure. In this work, we bridge the gap between fairness and explainability by presenting a novel perspective of procedure-oriented fairness based on explanations. We identify the procedure-based bias by measuring the gap of explanation quality between different groups with Ratio-based and Value-based Explanation Fairness. The new metrics further motivate us to design an optimization objective to mitigate the procedure-based bias where we observe that it will also mitigate bias from the prediction. Based on our designed optimization objective, we propose a Comprehensive Fairness Algorithm (CFA), which simultaneously fulfills multiple objectives - improving traditional fairness, satisfying explanation fairness, and maintaining the utility performance. Extensive experiments on real-world datasets demonstrate the effectiveness of our proposed CFA and highlight the importance of considering fairness from the explainability perspective. Our code is publicly available at https://github.com/YuyingZhao/FairExplanations-CFA .
A Frequency-Structure Approach for Link Stream Analysis
Authors: Esteban Bautista, Matthieu Latapy
Date: 2022-12-07 00:00:00
Tasks: Time Series Analysis

A link stream is a set of triplets $(t, u, v)$ indicating that $u$ and $v$ interacted at time $t$. Link streams model numerous datasets and their proper study is crucial in many applications. In practice, raw link streams are often aggregated or transformed into time series or graphs where decisions are made. Yet, it remains unclear how the dynamical and structural information of a raw link stream carries into the transformed object. This work shows that it is possible to shed light into this question by studying link streams via algebraically linear graph and signal operators, for which we introduce a novel linear matrix framework for the analysis of link streams. We show that, due to their linearity, most methods in signal processing can be easily adopted by our framework to analyze the time/frequency information of link streams. However, the availability of linear graph methods to analyze relational/structural information is limited. We address this limitation by developing (i) a new basis for graphs that allow us to decompose them into structures at different resolution levels; and (ii) filters for graphs that allow us to change their structural information in a controlled manner. By plugging-in these developments and their time-domain counterpart into our framework, we are able to (i) obtain a new basis for link streams that allow us to represent them in a frequency-structure domain; and (ii) show that many interesting transformations to link streams, like the aggregation of interactions or their embedding into a euclidean space, can be seen as simple filters in our frequency-structure domain.
Unsupervised spectral-band feature identification for optimal process discrimination
Authors: Akash Tiwari, Satish Bukkapatnam
Date: 2022-12-07 00:00:00
Tasks: global-optimization

Changes in real-world dynamic processes are often described in terms of differences in energies $\textbf{E}(\underline{\alpha})$ of a set of spectral-bands $\underline{\alpha}$. Given continuous spectra of two classes $A$ and $B$, or in general, two stochastic processes $S^{(A)}(f)$ and $S^{(B)}(f)$, $f \in \mathbb{R}^+$, we address the ubiquitous problem of identifying a subset of intervals of $f$ called spectral-bands $\underline{\alpha} \subset \mathbb{R}^+$ such that the energies $\textbf{E}(\underline{\alpha})$ of these bands can optimally discriminate between the two classes. We introduce EGO-MDA, an unsupervised method to identify optimal spectral-bands $\underline{\alpha}^*$ for given samples of spectra from two classes. EGO-MDA employs a statistical approach that iteratively minimizes an adjusted multinomial log-likelihood (deviance) criterion $\mathcal{D}(\underline{\alpha},\mathcal{M})$. Here, Mixture Discriminant Analysis (MDA) aims to derive MLE of two GMM distribution parameters, i.e., $\mathcal{M}^* = \underset{\mathcal{M}}{\rm argmin}~\mathcal{D}(\underline{\alpha}, \mathcal{M})$ and identify a classifier that optimally discriminates between two classes for a given spectral representation. The Efficient Global Optimization (EGO) finds the spectral-bands $\underline{\alpha}^* = \underset{\underline{\alpha}}{\rm argmin}~\mathcal{D}(\underline{\alpha},\mathcal{M})$ for given GMM parameters $\mathcal{M}$. For pathological cases of low separation between mixtures and model misspecification, we discuss the effect of the sample size and the number of iterations on the estimates of parameters $\mathcal{M}$ and therefore the classifier performance. A case study on a synthetic data set is provided. In an engineering application of optimal spectral-banding for anomaly tracking, EGO-MDA achieved at least 70% improvement in the median deviance relative to other methods tested.
Stochastic Rising Bandits
Authors: Alberto Maria Metelli, Francesco Trovò, Matteo Pirola, Marcello Restelli
Date: 2022-12-07 00:00:00
Tasks: Model Selection, Multi-Armed Bandits

This paper is in the field of stochastic Multi-Armed Bandits (MABs), i.e., those sequential selection techniques able to learn online using only the feedback given by the chosen option (a.k.a. arm). We study a particular case of the rested and restless bandits in which the arms' expected payoff is monotonically non-decreasing. This characteristic allows designing specifically crafted algorithms that exploit the regularity of the payoffs to provide tight regret bounds. We design an algorithm for the rested case (R-ed-UCB) and one for the restless case (R-less-UCB), providing a regret bound depending on the properties of the instance and, under certain circumstances, of $\widetilde{\mathcal{O}}(T^{\frac{2}{3}})$. We empirically compare our algorithms with state-of-the-art methods for non-stationary MABs over several synthetically generated tasks and an online model selection problem for a real-world dataset. Finally, using synthetic and real-world data, we illustrate the effectiveness of the proposed approaches compared with state-of-the-art algorithms for the non-stationary bandits.
A Neural Network Approach for Selecting Track-like Events in Fluorescence Telescope Data
Authors: Mikhail Zotov, Denis Sokolinskii
Date: 2022-12-07 00:00:00

In 2016-2017, TUS, the world's first experiment for testing the possibility of registering ultra-high energy cosmic rays (UHECRs) by their fluorescent radiation in the night atmosphere of Earth was carried out. Since 2019, the Russian-Italian fluorescence telescope (FT) Mini-EUSO ("UV Atmosphere") has been operating on the ISS. The stratospheric experiment EUSO-SPB2, which will employ an FT for registering UHECRs, is planned for 2023. We show how a simple convolutional neural network can be effectively used to find track-like events in the variety of data obtained with such instruments.
Tight bounds for maximum $\ell_1$-margin classifiers
Authors: Stefan Stojanovic, Konstantin Donhauser, Fanny Yang
Date: 2022-12-07 00:00:00

Popular iterative algorithms such as boosting methods and coordinate descent on linear models converge to the maximum $\ell_1$-margin classifier, a.k.a. sparse hard-margin SVM, in high dimensional regimes where the data is linearly separable. Previous works consistently show that many estimators relying on the $\ell_1$-norm achieve improved statistical rates for hard sparse ground truths. We show that surprisingly, this adaptivity does not apply to the maximum $\ell_1$-margin classifier for a standard discriminative setting. In particular, for the noiseless setting, we prove tight upper and lower bounds for the prediction error that match existing rates of order $\frac{\|w^*\|_1^{2/3}}{n^{1/3}}$ for general ground truths. To complete the picture, we show that when interpolating noisy observations, the error vanishes at a rate of order $\frac{1}{\sqrt{\log(d/n)}}$. We are therefore first to show benign overfitting for the maximum $\ell_1$-margin classifier.