pwc-archive/papers-with-abstracts huggingface dataset:
Functional universality in slow-growing microbial communities arises from thermodynamic constraints
Authors: Ashish B. George, Tong Wang, Sergei Maslov
Date: 2022-03-11 00:00:00

The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform substrates to products. In many anoxic environments, these reactions are close to thermodynamic equilibrium and growth is slow. To understand the community structure in these energy-limited environments, we developed a microbial community consumer-resource model incorporating energetic and thermodynamic constraints on an interconnected metabolic network. The central ingredient of the model is product inhibition, meaning that microbial growth may be limited not only by depletion of metabolic substrates but also by accumulation of products. We demonstrate that these additional constraints on microbial growth cause a convergence in the structure and function of the community metabolic network -- independent of species composition and biochemical details -- providing a possible explanation for convergence of community function despite taxonomic variation observed in many natural and industrial environments. Furthermore, we discovered that the structure of community metabolic network is governed by the thermodynamic principle of maximum heat dissipation. Overall, the work demonstrates how universal thermodynamic principles may constrain community metabolism and explain observed functional convergence in microbial communities.
An Empirical Study of Graphormer on Large-Scale Molecular Modeling Datasets
Authors: Yu Shi, Shuxin Zheng, Guolin Ke, Yifei Shen, Jiacheng You, Jiyan He, Shengjie Luo, Chang Liu, Di He, Tie-Yan Liu
Date: 2022-02-28 00:00:00

This technical note describes the recent updates of Graphormer, including architecture design modifications, and the adaption to 3D molecular dynamics simulation. The "Graphormer-V2" could attain better results on large-scale molecular modeling datasets than the vanilla one, and the performance gain could be consistently obtained on downstream tasks. In addition, we show that with a global receptive field and an adaptive aggregation strategy, Graphormer is more powerful than classic message-passing-based GNNs. Graphormer-V2 achieves much less MAE than the vanilla Graphormer on the PCQM4M quantum chemistry dataset used in KDD Cup 2021, where the latter one won the first place in this competition. In the meanwhile, Graphormer-V2 greatly outperforms the competitors in the recent Open Catalyst Challenge, which is a competition track on NeurIPS 2021 workshop, and aims to model the catalyst-adsorbate reaction system with advanced AI models. All models could be found at \url{https://github.com/Microsoft/Graphormer}.
neos: End-to-End-Optimised Summary Statistics for High Energy Physics
Authors: Nathan Simpson, Lukas Heinrich
Date: 2022-03-10 00:00:00
Tasks: Deep Learning, Vocal Bursts Intensity Prediction

The advent of deep learning has yielded powerful tools to automatically compute gradients of computations. This is because training a neural network equates to iteratively updating its parameters using gradient descent to find the minimum of a loss function. Deep learning is then a subset of a broader paradigm; a workflow with free parameters that is end-to-end optimisable, provided one can keep track of the gradients all the way through. This work introduces neos: an example implementation following this paradigm of a fully differentiable high-energy physics workflow, capable of optimising a learnable summary statistic with respect to the expected sensitivity of an analysis. Doing this results in an optimisation process that is aware of the modelling and treatment of systematic uncertainties.
Deep AutoAugment
Authors: Yu Zheng, Zhi Zhang, Shen Yan, Mi Zhang
Date: 2022-03-11 00:00:00
Tasks: AutoML, Data Augmentation, Image Classification

While recent automated data augmentation methods lead to state-of-the-art results, their design spaces and the derived data augmentation strategies still incorporate strong human priors. In this work, instead of fixing a set of hand-picked default augmentations alongside the searched data augmentations, we propose a fully automated approach for data augmentation search named Deep AutoAugment (DeepAA). DeepAA progressively builds a multi-layer data augmentation pipeline from scratch by stacking augmentation layers one at a time until reaching convergence. For each augmentation layer, the policy is optimized to maximize the cosine similarity between the gradients of the original and augmented data along the direction with low variance. Our experiments show that even without default augmentations, we can learn an augmentation policy that achieves strong performance with that of previous works. Extensive ablation studies show that the regularized gradient matching is an effective search method for data augmentation policies. Our code is available at: https://github.com/MSU-MLSys-Lab/DeepAA .
LaPraDoR: Unsupervised Pretrained Dense Retriever for Zero-Shot Text Retrieval
Authors: Canwen Xu, Daya Guo, Nan Duan, Julian McAuley
Date: 2022-03-11 00:00:00
Proceeding: Findings (ACL) 2022 5
Tasks: Contrastive Learning, Re-Ranking, Retrieval, Text Retrieval, Zero-shot Text Retrieval

In this paper, we propose LaPraDoR, a pretrained dual-tower dense retriever that does not require any supervised data for training. Specifically, we first present Iterative Contrastive Learning (ICoL) that iteratively trains the query and document encoders with a cache mechanism. ICoL not only enlarges the number of negative instances but also keeps representations of cached examples in the same hidden space. We then propose Lexicon-Enhanced Dense Retrieval (LEDR) as a simple yet effective way to enhance dense retrieval with lexical matching. We evaluate LaPraDoR on the recently proposed BEIR benchmark, including 18 datasets of 9 zero-shot text retrieval tasks. Experimental results show that LaPraDoR achieves state-of-the-art performance compared with supervised dense retrieval models, and further analysis reveals the effectiveness of our training strategy and objectives. Compared to re-ranking, our lexicon-enhanced approach can be run in milliseconds (22.5x faster) while achieving superior performance.
Symmetry Group Equivariant Architectures for Physics
Authors: Alexander Bogatskiy, Sanmay Ganguly, Thomas Kipf, Risi Kondor, David W. Miller, Daniel Murnane, Jan T. Offermann, Mariel Pettee, Phiala Shanahan, Chase Shimmin, Savannah Thais
Date: 2022-03-11 00:00:00
Tasks: BIG-bench Machine Learning

Physical theories grounded in mathematical symmetries are an essential component of our understanding of a wide range of properties of the universe. Similarly, in the domain of machine learning, an awareness of symmetries such as rotation or permutation invariance has driven impressive performance breakthroughs in computer vision, natural language processing, and other important applications. In this report, we argue that both the physics community and the broader machine learning community have much to understand and potentially to gain from a deeper investment in research concerning symmetry group equivariant machine learning architectures. For some applications, the introduction of symmetries into the fundamental structural design can yield models that are more economical (i.e. contain fewer, but more expressive, learned parameters), interpretable (i.e. more explainable or directly mappable to physical quantities), and/or trainable (i.e. more efficient in both data and computational requirements). We discuss various figures of merit for evaluating these models as well as some potential benefits and limitations of these methods for a variety of physics applications. Research and investment into these approaches will lay the foundation for future architectures that are potentially more robust under new computational paradigms and will provide a richer description of the physical systems to which they are applied.
Moral Dilemmas for Moral Machines
Authors: Travis LaCroix
Date: 2022-03-11 00:00:00
Tasks: Autonomous Vehicles, Decision Making, Ethics

Autonomous systems are being developed and deployed in situations that may require some degree of ethical decision-making ability. As a result, research in machine ethics has proliferated in recent years. This work has included using moral dilemmas as validation mechanisms for implementing decision-making algorithms in ethically-loaded situations. Using trolley-style problems in the context of autonomous vehicles as a case study, I argue (1) that this is a misapplication of philosophical thought experiments because (2) it fails to appreciate the purpose of moral dilemmas, and (3) this has potentially catastrophic consequences; however, (4) there are uses of moral dilemmas in machine ethics that are appropriate and the novel situations that arise in a machine-learning context can shed some light on philosophical work in ethics.
Detection of multiple retinal diseases in ultra-widefield fundus images using deep learning: data-driven identification of relevant regions
Authors: Justin Engelmann, Alice D. McTrusty, Ian J. C. MacCormick, Emma Pead, Amos Storkey, Miguel O. Bernabeu
Date: 2022-03-11 00:00:00

Ultra-widefield (UWF) imaging is a promising modality that captures a larger retinal field of view compared to traditional fundus photography. Previous studies showed that deep learning (DL) models are effective for detecting retinal disease in UWF images, but primarily considered individual diseases under less-than-realistic conditions (excluding images with other diseases, artefacts, comorbidities, or borderline cases; and balancing healthy and diseased images) and did not systematically investigate which regions of the UWF images are relevant for disease detection. We first improve on the state of the field by proposing a DL model that can recognise multiple retinal diseases under more realistic conditions. We then use global explainability methods to identify which regions of the UWF images the model generally attends to. Our model performs very well, separating between healthy and diseased retinas with an area under the curve (AUC) of 0.9206 on an internal test set, and an AUC of 0.9841 on a challenging, external test set. When diagnosing specific diseases, the model attends to regions where we would expect those diseases to occur. We further identify the posterior pole as the most important region in a purely data-driven fashion. Surprisingly, 10% of the image around the posterior pole is sufficient for achieving comparable performance to having the full images available.
Active Evaluation: Efficient NLG Evaluation with Few Pairwise Comparisons
Authors: Akash Kumar Mohankumar, Mitesh M. Khapra
Date: 2022-03-11 00:00:00
Proceeding: ACL 2022 5
Tasks: nlg evaluation

Recent studies have shown the advantages of evaluating NLG systems using pairwise comparisons as opposed to direct assessment. Given $k$ systems, a naive approach for identifying the top-ranked system would be to uniformly obtain pairwise comparisons from all ${k \choose 2}$ pairs of systems. However, this can be very expensive as the number of human annotations required would grow quadratically with $k$. In this work, we introduce Active Evaluation, a framework to efficiently identify the top-ranked system by actively choosing system pairs for comparison using dueling bandit algorithms. We perform extensive experiments with 13 dueling bandits algorithms on 13 NLG evaluation datasets spanning 5 tasks and show that the number of human annotations can be reduced by 80%. To further reduce the number of human annotations, we propose model-based dueling bandit algorithms which combine automatic evaluation metrics with human evaluations. Specifically, we eliminate sub-optimal systems even before the human annotation process and perform human evaluations only on test examples where the automatic metric is highly uncertain. This reduces the number of human annotations required further by 89%. In effect, we show that identifying the top-ranked system requires only a few hundred human annotations, which grow linearly with $k$. Lastly, we provide practical recommendations and best practices to identify the top-ranked system efficiently. Our code has been made publicly available at https://github.com/akashkm99/duelnlg
A Machine Learning Approach for Prosumer Management in Intraday Electricity Markets
Authors: Saeed Mohammadi, Mohammad Reza Hesamzadeh
Date: 2022-03-11 00:00:00
Tasks: BIG-bench Machine Learning, Management, Q-Learning, Reinforcement Learning (RL), Stochastic Optimization

Prosumer operators are dealing with extensive challenges to participate in short-term electricity markets while taking uncertainties into account. Challenges such as variation in demand, solar energy, wind power, and electricity prices as well as faster response time in intraday electricity markets. Machine learning approaches could resolve these challenges due to their ability to continuous learning of complex relations and providing a real-time response. Such approaches are applicable with presence of the high performance computing and big data. To tackle these challenges, a Markov decision process is proposed and solved with a reinforcement learning algorithm with proper observations and actions employing tabular Q-learning. Trained agent converges to a policy which is similar to the global optimal solution. It increases the prosumer's profit by 13.39% compared to the well-known stochastic optimization approach.
Sparse Subspace Clustering for Concept Discovery (SSCCD)
Authors: Johanna Vielhaben, Stefan Blücher, Nils Strodthoff
Date: 2022-03-11 00:00:00
Tasks: Clustering, Explainable Artificial Intelligence (XAI), image-classification, Image Classification

Concepts are key building blocks of higher level human understanding. Explainable AI (XAI) methods have shown tremendous progress in recent years, however, local attribution methods do not allow to identify coherent model behavior across samples and therefore miss this essential component. In this work, we study concept-based explanations and put forward a new definition of concepts as low-dimensional subspaces of hidden feature layers. We novelly apply sparse subspace clustering to discover these concept subspaces. Moving forward, we derive insights from concept subspaces in terms of localized input (concept) maps, show how to quantify concept relevances and lastly, evaluate similarities and transferability between concepts. We empirically demonstrate the soundness of the proposed Sparse Subspace Clustering for Concept Discovery (SSCCD) method for a variety of different image classification tasks. This approach allows for deeper insights into the actual model behavior that would remain hidden from conventional input-level heatmaps.
Exploiting Low-Rank Tensor-Train Deep Neural Networks Based on Riemannian Gradient Descent With Illustrations of Speech Processing
Authors: Jun Qi, Chao-Han Huck Yang, Pin-Yu Chen, Javier Tejedor
Date: 2022-03-11 00:00:00
Tasks: Speech Enhancement, Spoken Command Recognition, Tensor Networks

This work focuses on designing low complexity hybrid tensor networks by considering trade-offs between the model complexity and practical performance. Firstly, we exploit a low-rank tensor-train deep neural network (TT-DNN) to build an end-to-end deep learning pipeline, namely LR-TT-DNN. Secondly, a hybrid model combining LR-TT-DNN with a convolutional neural network (CNN), which is denoted as CNN+(LR-TT-DNN), is set up to boost the performance. Instead of randomly assigning large TT-ranks for TT-DNN, we leverage Riemannian gradient descent to determine a TT-DNN associated with small TT-ranks. Furthermore, CNN+(LR-TT-DNN) consists of convolutional layers at the bottom for feature extraction and several TT layers at the top to solve regression and classification problems. We separately assess the LR-TT-DNN and CNN+(LR-TT-DNN) models on speech enhancement and spoken command recognition tasks. Our empirical evidence demonstrates that the LR-TT-DNN and CNN+(LR-TT-DNN) models with fewer model parameters can outperform the TT-DNN and CNN+(TT-DNN) counterparts.
The Role of ImageNet Classes in Fréchet Inception Distance
Authors: Tuomas Kynkäänniemi, Tero Karras, Miika Aittala, Timo Aila, Jaakko Lehtinen
Date: 2022-03-11 00:00:00

Fr\'echet Inception Distance (FID) is the primary metric for ranking models in data-driven generative modeling. While remarkably successful, the metric is known to sometimes disagree with human judgement. We investigate a root cause of these discrepancies, and visualize what FID "looks at" in generated images. We show that the feature space that FID is (typically) computed in is so close to the ImageNet classifications that aligning the histograms of Top-$N$ classifications between sets of generated and real images can reduce FID substantially -- without actually improving the quality of results. Thus, we conclude that FID is prone to intentional or accidental distortions. As a practical example of an accidental distortion, we discuss a case where an ImageNet pre-trained FastGAN achieves a FID comparable to StyleGAN2, while being worse in terms of human evaluation.
Multi-modal Graph Learning for Disease Prediction
Authors: Shuai Zheng, Zhenfeng Zhu, Zhizhe Liu, Zhenyu Guo, Yang Liu, Yuchen Yang, Yao Zhao
Date: 2022-03-11 00:00:00
Tasks: Disease Prediction, Graph Learning, Graph Representation Learning, Inductive Learning, Prediction, Representation Learning

Benefiting from the powerful expressive capability of graphs, graph-based approaches have been popularly applied to handle multi-modal medical data and achieved impressive performance in various biomedical applications. For disease prediction tasks, most existing graph-based methods tend to define the graph manually based on specified modality (e.g., demographic information), and then integrated other modalities to obtain the patient representation by Graph Representation Learning (GRL). However, constructing an appropriate graph in advance is not a simple matter for these methods. Meanwhile, the complex correlation between modalities is ignored. These factors inevitably yield the inadequacy of providing sufficient information about the patient's condition for a reliable diagnosis. To this end, we propose an end-to-end Multi-modal Graph Learning framework (MMGL) for disease prediction with multi-modality. To effectively exploit the rich information across multi-modality associated with the disease, modality-aware representation learning is proposed to aggregate the features of each modality by leveraging the correlation and complementarity between the modalities. Furthermore, instead of defining the graph manually, the latent graph structure is captured through an effective way of adaptive graph learning. It could be jointly optimized with the prediction model, thus revealing the intrinsic connections among samples. Our model is also applicable to the scenario of inductive learning for those unseen data. An extensive group of experiments on two disease prediction tasks demonstrates that the proposed MMGL achieves more favorable performance. The code of MMGL is available at \url{https://github.com/SsGood/MMGL}.
Human Silhouette and Skeleton Video Synthesis through Wi-Fi signals
Authors: Danilo Avola, Marco Cascio, Luigi Cinque, Alessio Fagioli, Gian Luca Foresti
Date: 2022-03-11 00:00:00
Tasks: Image Generation

The increasing availability of wireless access points (APs) is leading towards human sensing applications based on Wi-Fi signals as support or alternative tools to the widespread visual sensors, where the signals enable to address well-known vision-related problems such as illumination changes or occlusions. Indeed, using image synthesis techniques to translate radio frequencies to the visible spectrum can become essential to obtain otherwise unavailable visual data. This domain-to-domain translation is feasible because both objects and people affect electromagnetic waves, causing radio and optical frequencies variations. In literature, models capable of inferring radio-to-visual features mappings have gained momentum in the last few years since frequency changes can be observed in the radio domain through the channel state information (CSI) of Wi-Fi APs, enabling signal-based feature extraction, e.g., amplitude. On this account, this paper presents a novel two-branch generative neural network that effectively maps radio data into visual features, following a teacher-student design that exploits a cross-modality supervision strategy. The latter conditions signal-based features in the visual domain to completely replace visual data. Once trained, the proposed method synthesizes human silhouette and skeleton videos using exclusively Wi-Fi signals. The approach is evaluated on publicly available data, where it obtains remarkable results for both silhouette and skeleton videos generation, demonstrating the effectiveness of the proposed cross-modality supervision strategy.
Automatic Fine-grained Glomerular Lesion Recognition in Kidney Pathology
Authors: Yang Nan, Fengyi Li, Peng Tang, Guyue Zhang, Caihong Zeng, Guotong Xie, Zhihong Liu, Guang Yang
Date: 2022-03-11 00:00:00
Tasks: Fine-Grained Image Classification, whole slide images

Recognition of glomeruli lesions is the key for diagnosis and treatment planning in kidney pathology; however, the coexisting glomerular structures such as mesangial regions exacerbate the difficulties of this task. In this paper, we introduce a scheme to recognize fine-grained glomeruli lesions from whole slide images. First, a focal instance structural similarity loss is proposed to drive the model to locate all types of glomeruli precisely. Then an Uncertainty Aided Apportionment Network is designed to carry out the fine-grained visual classification without bounding-box annotations. This double branch-shaped structure extracts common features of the child class from the parent class and produces the uncertainty factor for reconstituting the training dataset. Results of slide-wise evaluation illustrate the effectiveness of the entire scheme, with an 8-22% improvement of the mean Average Precision compared with remarkable detection methods. The comprehensive results clearly demonstrate the effectiveness of the proposed method.
ZIN: When and How to Learn Invariance Without Environment Partition?
Authors: Yong Lin, Shengyu Zhu, Lu Tan, Peng Cui
Date: 2022-03-11 00:00:00

It is commonplace to encounter heterogeneous data, of which some aspects of the data distribution may vary but the underlying causal mechanisms remain constant. When data are divided into distinct environments according to the heterogeneity, recent invariant learning methods have proposed to learn robust and invariant models based on this environment partition. It is hence tempting to utilize the inherent heterogeneity even when environment partition is not provided. Unfortunately, in this work, we show that learning invariant features under this circumstance is fundamentally impossible without further inductive biases or additional information. Then, we propose a framework to jointly learn environment partition and invariant representation, assisted by additional auxiliary information. We derive sufficient and necessary conditions for our framework to provably identify invariant features under a fairly general setting. Experimental results on both synthetic and real world datasets validate our analysis and demonstrate an improved performance of the proposed framework over existing methods. Finally, our results also raise the need of making the role of inductive biases more explicit in future works, when considering learning invariant models without environment partition. Codes are available at https://github.com/linyongver/ZIN_official .