pwc-archive/papers-with-abstracts huggingface dataset:
Biomarker Gene Identification for Breast Cancer Classification
Authors: Sheetal Rajpal, Ankit Rajpal, Manoj Agarwal, Naveen Kumar
Date: 2021-11-10 00:00:00
Tasks: Cancer Classification, Classification

BACKGROUND: Breast cancer has emerged as one of the most prevalent cancers among women leading to a high mortality rate. Due to the heterogeneous nature of breast cancer, there is a need to identify differentially expressed genes associated with breast cancer subtypes for its timely diagnosis and treatment. OBJECTIVE: To identify a small gene set for each of the four breast cancer subtypes that could act as its signature, the paper proposes a novel algorithm for gene signature identification. METHODS: The present work uses interpretable AI methods to investigate the predictions made by the deep neural network employed for subtype classification to identify biomarkers using the TCGA breast cancer RNA Sequence data. RESULTS: The proposed algorithm led to the discovery of a set of 43 differentially expressed gene signatures. We achieved a competitive average 10-fold accuracy of 0.91, using neural network classifier. Further, gene set analysis revealed several relevant pathways, such as GRB7 events in ERBB2 and p53 signaling pathway. Using the Pearson correlation matrix, we noted that the subtype-specific genes are correlated within each subtype. CONCLUSIONS: The proposed technique enables us to find a concise and clinically relevant gene signature set.
Deducing Optimal Classification Algorithm for Heterogeneous Fabric
Authors: Omar Alfarisi, Zeyar Aung, Mohamed Sassi
Date: 2021-11-10 00:00:00
Tasks: BIG-bench Machine Learning, Classification

For defining the optimal machine learning algorithm, the decision was not easy for which we shall choose. To help future researchers, we describe in this paper the optimal among the best of the algorithms. We built a synthetic data set and performed the supervised machine learning runs for five different algorithms. For heterogeneous rock fabric, we identified Random Forest, among others, to be the appropriate algorithm.
Topic-aware latent models for representation learning on networks
Authors: Abdulkadir Çelikkanat, Fragkiskos D. Malliaros
Date: 2021-11-10 00:00:00
Tasks: Community Detection, Link Prediction, Node Classification, Representation Learning, Word Embeddings

Network representation learning (NRL) methods have received significant attention over the last years thanks to their success in several graph analysis problems, including node classification, link prediction, and clustering. Such methods aim to map each vertex of the network into a low-dimensional space in a way that the structural information of the network is preserved. Of particular interest are methods based on random walks; such methods transform the network into a collection of node sequences, aiming to learn node representations by predicting the context of each node within the sequence. In this paper, we introduce TNE, a generic framework to enhance the embeddings of nodes acquired by means of random walk-based approaches with topic-based information. Similar to the concept of topical word embeddings in Natural Language Processing, the proposed model first assigns each node to a latent community with the favor of various statistical graph models and community detection methods and then learns the enhanced topic-aware representations. We evaluate our methodology in two downstream tasks: node classification and link prediction. The experimental results demonstrate that by incorporating node and community embeddings, we are able to outperform widely-known baseline NRL models.
Safe Real-Time Optimization using Multi-Fidelity Gaussian Processes
Authors: Panagiotis Petsagkourakis, Benoit Chachuat, Ehecatl Antonio del Rio-Chanona
Date: 2021-11-10 00:00:00
Tasks: Bayesian Optimization, Gaussian Processes, Uncertainty Quantification

This paper proposes a new class of real-time optimization schemes to overcome system-model mismatch of uncertain processes. This work's novelty lies in integrating derivative-free optimization schemes and multi-fidelity Gaussian processes within a Bayesian optimization framework. The proposed scheme uses two Gaussian processes for the stochastic system, one emulates the (known) process model, and another, the true system through measurements. In this way, low fidelity samples can be obtained via a model, while high fidelity samples are obtained through measurements of the system. This framework captures the system's behavior in a non-parametric fashion while driving exploration through acquisition functions. The benefit of using a Gaussian process to represent the system is the ability to perform uncertainty quantification in real-time and allow for chance constraints to be satisfied with high confidence. This results in a practical approach that is illustrated in numerical case studies, including a semi-batch photobioreactor optimization problem.
Graph Transplant: Node Saliency-Guided Graph Mixup with Local Structure Preservation
Authors: Joonhyung Park, Hajin Shim, Eunho Yang
Date: 2021-11-10 00:00:00
Tasks: Data Augmentation, Graph Classification

Graph-structured datasets usually have irregular graph sizes and connectivities, rendering the use of recent data augmentation techniques, such as Mixup, difficult. To tackle this challenge, we present the first Mixup-like graph augmentation method at the graph-level called Graph Transplant, which mixes irregular graphs in data space. To be well defined on various scales of the graph, our method identifies the sub-structure as a mix unit that can preserve the local information. Since the mixup-based methods without special consideration of the context are prone to generate noisy samples, our method explicitly employs the node saliency information to select meaningful subgraphs and adaptively determine the labels. We extensively validate our method with diverse GNN architectures on multiple graph classification benchmark datasets from a wide range of graph domains of different sizes. Experimental results show the consistent superiority of our method over other basic data augmentation baselines. We also demonstrate that Graph Transplant enhances the performance in terms of robustness and model calibration.
Parallel Physics-Informed Neural Networks with Bidirectional Balance
Authors: Yuhao Huang
Date: 2021-11-10 00:00:00

As an emerging technology in deep learning, physics-informed neural networks (PINNs) have been widely used to solve various partial differential equations (PDEs) in engineering. However, PDEs based on practical considerations contain multiple physical quantities and complex initial boundary conditions, thus PINNs often returns incorrect results. Here we take heat transfer problem in multilayer fabrics as a typical example. It is coupled by multiple temperature fields with strong correlation, and the values of variables are extremely unbalanced among different dimensions. We clarify the potential difficulties of solving such problems by classic PINNs, and propose a parallel physics-informed neural networks with bidirectional balance. In detail, our parallel solving framework synchronously fits coupled equations through several multilayer perceptions. Moreover, we design two modules to balance forward process of data and back-propagation process of loss gradient. This bidirectional balance not only enables the whole network to converge stably, but also helps to fully learn various physical conditions in PDEs. We provide a series of ablation experiments to verify the effectiveness of the proposed methods. The results show that our approach makes the PINNs unsolvable problem solvable, and achieves excellent solving accuracy.
Conditional Alignment and Uniformity for Contrastive Learning with Continuous Proxy Labels
Authors: Benoit Dufumier, Pietro Gori, Julie Victor, Antoine Grigis, Edouard Duchesnay
Date: 2021-11-10 00:00:00
Tasks: Contrastive Learning, Linear evaluation

Contrastive Learning has shown impressive results on natural and medical images, without requiring annotated data. However, a particularity of medical images is the availability of meta-data (such as age or sex) that can be exploited for learning representations. Here, we show that the recently proposed contrastive y-Aware InfoNCE loss, that integrates multi-dimensional meta-data, asymptotically optimizes two properties: conditional alignment and global uniformity. Similarly to [Wang, 2020], conditional alignment means that similar samples should have similar features, but conditionally on the meta-data. Instead, global uniformity means that the (normalized) features should be uniformly distributed on the unit hyper-sphere, independently of the meta-data. Here, we propose to define conditional uniformity, relying on the meta-data, that repel only samples with dissimilar meta-data. We show that direct optimization of both conditional alignment and uniformity improves the representations, in terms of linear evaluation, on both CIFAR-100 and a brain MRI dataset.
DeCOM: Decomposed Policy for Constrained Cooperative Multi-Agent Reinforcement Learning
Authors: Zhaoxing Yang, Rong Ding, Haiming Jin, Yifei Wei, Haoyi You, Guiyun Fan, Xiaoying Gan, Xinbing Wang
Date: 2021-11-10 00:00:00
Tasks: Multi-agent Reinforcement Learning, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL)

In recent years, multi-agent reinforcement learning (MARL) has presented impressive performance in various applications. However, physical limitations, budget restrictions, and many other factors usually impose \textit{constraints} on a multi-agent system (MAS), which cannot be handled by traditional MARL frameworks. Specifically, this paper focuses on constrained MASes where agents work \textit{cooperatively} to maximize the expected team-average return under various constraints on expected team-average costs, and develops a \textit{constrained cooperative MARL} framework, named DeCOM, for such MASes. In particular, DeCOM decomposes the policy of each agent into two modules, which empowers information sharing among agents to achieve better cooperation. In addition, with such modularization, the training algorithm of DeCOM separates the original constrained optimization into an unconstrained optimization on reward and a constraints satisfaction problem on costs. DeCOM then iteratively solves these problems in a computationally efficient manner, which makes DeCOM highly scalable. We also provide theoretical guarantees on the convergence of DeCOM's policy update algorithm. Finally, we validate the effectiveness of DeCOM with various types of costs in both toy and large-scale (with 500 agents) environments.
Automatically detecting data drift in machine learning classifiers
Authors: Samuel Ackerman, Orna Raz, Marcel Zalmanovici, Aviad Zlotnick
Date: 2021-11-10 00:00:00
Tasks: BIG-bench Machine Learning

Classifiers and other statistics-based machine learning (ML) techniques generalize, or learn, based on various statistical properties of the training data. The assumption underlying statistical ML resulting in theoretical or empirical performance guarantees is that the distribution of the training data is representative of the production data distribution. This assumption often breaks; for instance, statistical distributions of the data may change. We term changes that affect ML performance `data drift' or `drift'. Many classification techniques compute a measure of confidence in their results. This measure might not reflect the actual ML performance. A famous example is the Panda picture that is correctly classified as such with a confidence of about 60\%, but when noise is added it is incorrectly classified as a Gibbon with a confidence of above 99\%. However, the work we report on here suggests that a classifier's measure of confidence can be used for the purpose of detecting data drift. We propose an approach based solely on classifier suggested labels and its confidence in them, for alerting on data distribution or feature space changes that are likely to cause data drift. Our approach identities degradation in model performance and does not require labeling of data in production which is often lacking or delayed. Our experiments with three different data sets and classifiers demonstrate the effectiveness of this approach in detecting data drift. This is especially encouraging as the classification itself may or may not be correct and no model input data is required. We further explore the statistical approach of sequential change-point tests to automatically determine the amount of data needed in order to identify drift while controlling the false positive rate (Type-1 error).
HARPO: Learning to Subvert Online Behavioral Advertising
Authors: Jiang Zhang, Konstantinos Psounis, Muhammad Haroon, Zubair Shafiq
Date: 2021-11-09 00:00:00
Tasks: Reinforcement Learning (RL)

Online behavioral advertising, and the associated tracking paraphernalia, poses a real privacy threat. Unfortunately, existing privacy-enhancing tools are not always effective against online advertising and tracking. We propose Harpo, a principled learning-based approach to subvert online behavioral advertising through obfuscation. Harpo uses reinforcement learning to adaptively interleave real page visits with fake pages to distort a tracker's view of a user's browsing profile. We evaluate Harpo against real-world user profiling and ad targeting models used for online behavioral advertising. The results show that Harpo improves privacy by triggering more than 40% incorrect interest segments and 6x higher bid values. Harpo outperforms existing obfuscation tools by as much as 16x for the same overhead. Harpo is also able to achieve better stealthiness to adversarial detection than existing obfuscation tools. Harpo meaningfully advances the state-of-the-art in leveraging obfuscation to subvert online behavioral advertising
SwAMP: Swapped Assignment of Multi-Modal Pairs for Cross-Modal Retrieval
Authors: Minyoung Kim
Date: 2021-11-10 00:00:00
Tasks: Contrastive Learning, Cross-Modal Retrieval, Image Retrieval, Image-text Retrieval, Retrieval, Sketch-Based Image Retrieval, Text Retrieval, Video Retrieval

We tackle the cross-modal retrieval problem, where learning is only supervised by relevant multi-modal pairs in the data. Although the contrastive learning is the most popular approach for this task, it makes potentially wrong assumption that the instances in different pairs are automatically irrelevant. To address the issue, we propose a novel loss function that is based on self-labeling of the unknown semantic classes. Specifically, we aim to predict class labels of the data instances in each modality, and assign those labels to the corresponding instances in the other modality (i.e., swapping the pseudo labels). With these swapped labels, we learn the data embedding for each modality using the supervised cross-entropy loss. This way, cross-modal instances from different pairs that are semantically related can be aligned to each other by the class predictor. We tested our approach on several real-world cross-modal retrieval problems, including text-based video retrieval, sketch-based image retrieval, and image-text retrieval. For all these tasks our method achieves significant performance improvement over the contrastive learning.
Multi-Task Neural Processes
Authors: Jiayi Shen, XianTong Zhen, Marcel Worring, Ling Shao
Date: 2021-11-10 00:00:00
Tasks: Bayesian Inference, Brain Image Segmentation, Image Segmentation, Inductive Bias, Multi-Task Learning, Semantic Segmentation

Neural processes have recently emerged as a class of powerful neural latent variable models that combine the strengths of neural networks and stochastic processes. As they can encode contextual data in the network's function space, they offer a new way to model task relatedness in multi-task learning. To study its potential, we develop multi-task neural processes, a new variant of neural processes for multi-task learning. In particular, we propose to explore transferable knowledge from related tasks in the function space to provide inductive bias for improving each individual task. To do so, we derive the function priors in a hierarchical Bayesian inference framework, which enables each task to incorporate the shared knowledge provided by related tasks into its context of the prediction function. Our multi-task neural processes methodologically expand the scope of vanilla neural processes and provide a new way of exploring task relatedness in function spaces for multi-task learning. The proposed multi-task neural processes are capable of learning multiple tasks with limited labeled data and in the presence of domain shift. We perform extensive experimental evaluations on several benchmarks for the multi-task regression and classification tasks. The results demonstrate the effectiveness of multi-task neural processes in transferring useful knowledge among tasks for multi-task learning and superior performance in multi-task classification and brain image segmentation.
Physics-enhanced deep surrogates for partial differential equations
Authors: Raphaël Pestourie, Youssef Mroueh, Chris Rackauckas, Payel Das, Steven G. Johnson
Date: 2021-11-10 00:00:00
Tasks: Active Learning

Many physics and engineering applications demand Partial Differential Equations (PDE) property evaluations that are traditionally computed with resource-intensive high-fidelity numerical solvers. Data-driven surrogate models provide an efficient alternative but come with a significant cost of training. Emerging applications would benefit from surrogates with an improved accuracy-cost tradeoff, while studied at scale. Here we present a "physics-enhanced deep-surrogate" ("PEDS") approach towards developing fast surrogate models for complex physical systems, which is described by PDEs. Specifically, a combination of a low-fidelity, explainable physics simulator and a neural network generator is proposed, which is trained end-to-end to globally match the output of an expensive high-fidelity numerical solver. Experiments on three exemplar testcases, diffusion, reaction-diffusion, and electromagnetic scattering models, show that a PEDS surrogate can be up to 3$\times$ more accurate than an ensemble of feedforward neural networks with limited data ($\approx 10^3$ training points), and reduces the training data need by at least a factor of 100 to achieve a target error of 5%. Experiments reveal that PEDS provides a general, data-driven strategy to bridge the gap between a vast array of simplified physical models with corresponding brute-force numerical solvers modeling complex systems, offering accuracy, speed, data efficiency, as well as physical insights into the process.
Towards Green Automated Machine Learning: Status Quo and Future Directions
Authors: Tanja Tornede, Alexander Tornede, Jonas Hanselle, Marcel Wever, Felix Mohr, Eyke Hüllermeier
Date: 2021-11-10 00:00:00
Tasks: AutoML, BIG-bench Machine Learning

Automated machine learning (AutoML) strives for the automatic configuration of machine learning algorithms and their composition into an overall (software) solution - a machine learning pipeline - tailored to the learning task (dataset) at hand. Over the last decade, AutoML has developed into an independent research field with hundreds of contributions. At the same time, AutoML is being criticised for its high resource consumption as many approaches rely on the (costly) evaluation of many machine learning pipelines, as well as the expensive large scale experiments across many datasets and approaches. In the spirit of recent work on Green AI, this paper proposes Green AutoML, a paradigm to make the whole AutoML process more environmentally friendly. Therefore, we first elaborate on how to quantify the environmental footprint of an AutoML tool. Afterward, different strategies on how to design and benchmark an AutoML tool wrt. their "greenness", i.e. sustainability, are summarized. Finally, we elaborate on how to be transparent about the environmental footprint and what kind of research incentives could direct the community into a more sustainable AutoML research direction. Additionally, we propose a sustainability checklist to be attached to every AutoML paper featuring all core aspects of Green AutoML.
Self-Supervised Audio-Visual Representation Learning with Relaxed Cross-Modal Synchronicity
Authors: Pritam Sarkar, Ali Etemad
Date: 2021-11-09 00:00:00
Tasks: Audio Classification, Retrieval, Self-Supervised Action Recognition, Self-Supervised Audio Classification, Self-Supervised Learning, Self-Supervised Sound Classification, Self-supervised Video Retrieval, Sound Classification

We present CrissCross, a self-supervised framework for learning audio-visual representations. A novel notion is introduced in our framework whereby in addition to learning the intra-modal and standard 'synchronous' cross-modal relations, CrissCross also learns 'asynchronous' cross-modal relationships. We perform in-depth studies showing that by relaxing the temporal synchronicity between the audio and visual modalities, the network learns strong generalized representations useful for a variety of downstream tasks. To pretrain our proposed solution, we use 3 different datasets with varying sizes, Kinetics-Sound, Kinetics400, and AudioSet. The learned representations are evaluated on a number of downstream tasks namely action recognition, sound classification, and action retrieval. Our experiments show that CrissCross either outperforms or achieves performances on par with the current state-of-the-art self-supervised methods on action recognition and action retrieval with UCF101 and HMDB51, as well as sound classification with ESC50 and DCASE. Moreover, CrissCross outperforms fully-supervised pretraining while pretrained on Kinetics-Sound. The codes and pretrained models are available on the project website.
Robust deep learning-based semantic organ segmentation in hyperspectral images
Authors: Silvia Seidlitz, Jan Sellner, Jan Odenthal, Berkin Özdemir, Alexander Studier-Fischer, Samuel Knödler, Leonardo Ayala, Tim J. Adler, Hannes G. Kenngott, Minu Tizabi, Martin Wagner, Felix Nickel, Beat P. Müller-Stich, Lena Maier-Hein
Date: 2021-11-09 00:00:00
Tasks: Deep Learning, Image Segmentation, Organ Segmentation, Scene Understanding, Segmentation, Semantic Segmentation, Superpixels

Semantic image segmentation is an important prerequisite for context-awareness and autonomous robotics in surgery. The state of the art has focused on conventional RGB video data acquired during minimally invasive surgery, but full-scene semantic segmentation based on spectral imaging data and obtained during open surgery has received almost no attention to date. To address this gap in the literature, we are investigating the following research questions based on hyperspectral imaging (HSI) data of pigs acquired in an open surgery setting: (1) What is an adequate representation of HSI data for neural network-based fully automated organ segmentation, especially with respect to the spatial granularity of the data (pixels vs. superpixels vs. patches vs. full images)? (2) Is there a benefit of using HSI data compared to other modalities, namely RGB data and processed HSI data (e.g. tissue parameters like oxygenation), when performing semantic organ segmentation? According to a comprehensive validation study based on 506 HSI images from 20 pigs, annotated with a total of 19 classes, deep learning-based segmentation performance increases, consistently across modalities, with the spatial context of the input data. Unprocessed HSI data offers an advantage over RGB data or processed data from the camera provider, with the advantage increasing with decreasing size of the input to the neural network. Maximum performance (HSI applied to whole images) yielded a mean DSC of 0.90 ((standard deviation (SD)) 0.04), which is in the range of the inter-rater variability (DSC of 0.89 ((standard deviation (SD)) 0.07)). We conclude that HSI could become a powerful image modality for fully-automatic surgical scene understanding with many advantages over traditional imaging, including the ability to recover additional functional tissue information. Code and pre-trained models: https://github.com/IMSY-DKFZ/htc.