pwc-archive/papers-with-abstracts huggingface dataset:
CLMB: deep contrastive learning for robust metagenomic binning
Authors: Pengfei Zhang, Zhengyuan Jiang, YiXuan Wang, Yu Li
Date: 2021-11-18 00:00:00
Tasks: Benchmarking, Contrastive Learning, Denoising

The reconstruction of microbial genomes from large metagenomic datasets is a critical procedure for finding uncultivated microbial populations and defining their microbial functional roles. To achieve that, we need to perform metagenomic binning, clustering the assembled contigs into draft genomes. Despite the existing computational tools, most of them neglect one important property of the metagenomic data, that is, the noise. To further improve the metagenomic binning step and reconstruct better metagenomes, we propose a deep Contrastive Learning framework for Metagenome Binning (CLMB), which can efficiently eliminate the disturbance of noise and produce more stable and robust results. Essentially, instead of denoising the data explicitly, we add simulated noise to the training data and force the deep learning model to produce similar and stable representations for both the noise-free data and the distorted data. Consequently, the trained model will be robust to noise and handle it implicitly during usage. CLMB outperforms the previous state-of-the-art binning methods significantly, recovering the most near-complete genomes on almost all the benchmarking datasets (up to 17\% more reconstructed genomes compared to the second-best method). It also improves the performance of bin refinement, reconstructing 8-22 more high-quality genomes and 15-32 more middle-quality genomes than the second-best result. Impressively, in addition to being compatible with the binning refiner, single CLMB even recovers on average 15 more HQ genomes than the refiner of VAMB and Maxbin on the benchmarking datasets. CLMB is open-source and available at https://github.com/zpf0117b/CLMB/.
To Augment or Not to Augment? A Comparative Study on Text Augmentation Techniques for Low-Resource NLP
Authors: Gözde Gül Şahin
Date: 2021-11-18 00:00:00
Proceeding: CL (ACL) 2022 3
Tasks: Dependency Parsing, Part-Of-Speech Tagging, Semantic Role Labeling, Text Augmentation

Data-hungry deep neural networks have established themselves as the standard for many NLP tasks including the traditional sequence tagging ones. Despite their state-of-the-art performance on high-resource languages, they still fall behind of their statistical counter-parts in low-resource scenarios. One methodology to counter attack this problem is text augmentation, i.e., generating new synthetic training data points from existing data. Although NLP has recently witnessed a load of textual augmentation techniques, the field still lacks a systematic performance analysis on a diverse set of languages and sequence tagging tasks. To fill this gap, we investigate three categories of text augmentation methodologies which perform changes on the syntax (e.g., cropping sub-sentences), token (e.g., random word insertion) and character (e.g., character swapping) levels. We systematically compare them on part-of-speech tagging, dependency parsing and semantic role labeling for a diverse set of language families using various models including the architectures that rely on pretrained multilingual contextualized language models such as mBERT. Augmentation most significantly improves dependency parsing, followed by part-of-speech tagging and semantic role labeling. We find the experimented techniques to be effective on morphologically rich languages in general rather than analytic languages such as Vietnamese. Our results suggest that the augmentation techniques can further improve over strong baselines based on mBERT. We identify the character-level methods as the most consistent performers, while synonym replacement and syntactic augmenters provide inconsistent improvements. Finally, we discuss that the results most heavily depend on the task, language pair, and the model type.
Improving Transferability of Representations via Augmentation-Aware Self-Supervision
Authors: Hankook Lee, Kibok Lee, Kimin Lee, Honglak Lee, Jinwoo Shin
Date: 2021-11-18 00:00:00
Proceeding: NeurIPS 2021 12
Tasks: Representation Learning, Transfer Learning

Recent unsupervised representation learning methods have shown to be effective in a range of vision tasks by learning representations invariant to data augmentations such as random cropping and color jittering. However, such invariance could be harmful to downstream tasks if they rely on the characteristics of the data augmentations, e.g., location- or color-sensitive. This is not an issue just for unsupervised learning; we found that this occurs even in supervised learning because it also learns to predict the same label for all augmented samples of an instance. To avoid such failures and obtain more generalizable representations, we suggest to optimize an auxiliary self-supervised loss, coined AugSelf, that learns the difference of augmentation parameters (e.g., cropping positions, color adjustment intensities) between two randomly augmented samples. Our intuition is that AugSelf encourages to preserve augmentation-aware information in learned representations, which could be beneficial for their transferability. Furthermore, AugSelf can easily be incorporated into recent state-of-the-art representation learning methods with a negligible additional training cost. Extensive experiments demonstrate that our simple idea consistently improves the transferability of representations learned by supervised and unsupervised methods in various transfer learning scenarios. The code is available at https://github.com/hankook/AugSelf.
The Prominence of Artificial Intelligence in COVID-19
Authors: MD Abdullah Al Nasim, Aditi Dhali, Faria Afrin, Noshin Tasnim Zaman, Nazmul Karimm, Md Mahim Anjum Haque
Date: 2021-11-18 00:00:00

In December 2019, a novel virus called COVID-19 had caused an enormous number of causalities to date. The battle with the novel Coronavirus is baffling and horrifying after the Spanish Flu 2019. While the front-line doctors and medical researchers have made significant progress in controlling the spread of the highly contiguous virus, technology has also proved its significance in the battle. Moreover, Artificial Intelligence has been adopted in many medical applications to diagnose many diseases, even baffling experienced doctors. Therefore, this survey paper explores the methodologies proposed that can aid doctors and researchers in early and inexpensive methods of diagnosis of the disease. Most developing countries have difficulties carrying out tests using the conventional manner, but a significant way can be adopted with Machine and Deep Learning. On the other hand, the access to different types of medical images has motivated the researchers. As a result, a mammoth number of techniques are proposed. This paper first details the background knowledge of the conventional methods in the Artificial Intelligence domain. Following that, we gather the commonly used datasets and their use cases to date. In addition, we also show the percentage of researchers adopting Machine Learning over Deep Learning. Thus we provide a thorough analysis of this scenario. Lastly, in the research challenges, we elaborate on the problems faced in COVID-19 research, and we address the issues with our understanding to build a bright and healthy environment.
DeepGuard: A Framework for Safeguarding Autonomous Driving Systems from Inconsistent Behavior
Authors: Manzoor Hussain, Nazakat Ali, Jang-Eui Hong
Date: 2021-11-18 00:00:00
Tasks: Anomaly Detection, Autonomous Driving, Autonomous Vehicles, Time Series, Time Series Analysis

The deep neural networks (DNNs)based autonomous driving systems (ADSs) are expected to reduce road accidents and improve safety in the transportation domain as it removes the factor of human error from driving tasks. The DNN based ADS sometimes may exhibit erroneous or unexpected behaviors due to unexpected driving conditions which may cause accidents. It is not possible to generalize the DNN model performance for all driving conditions. Therefore, the driving conditions that were not considered during the training of the ADS may lead to unpredictable consequences for the safety of autonomous vehicles. This study proposes an autoencoder and time series analysis based anomaly detection system to prevent the safety critical inconsistent behavior of autonomous vehicles at runtime. Our approach called DeepGuard consists of two components. The first component, the inconsistent behavior predictor, is based on an autoencoder and time series analysis to reconstruct the driving scenarios. Based on reconstruction error and threshold it determines the normal and unexpected driving scenarios and predicts potential inconsistent behavior. The second component provides on the fly safety guards, that is, it automatically activates healing strategies to prevent inconsistencies in the behavior. We evaluated the performance of DeepGuard in predicting the injected anomalous driving scenarios using already available open sourced DNN based ADSs in the Udacity simulator. Our simulation results show that the best variant of DeepGuard can predict up to 93 percent on the CHAUFFEUR ADS, 83 percent on DAVE2 ADS, and 80 percent of inconsistent behavior on the EPOCH ADS model, outperforming SELFORACLE and DeepRoad. Overall, DeepGuard can prevent up to 89 percent of all predicted inconsistent behaviors of ADS by executing predefined safety guards.
Docking-based Virtual Screening with Multi-Task Learning
Authors: Zijing Liu, Xianbin Ye, Xiaomin Fang, Fan Wang, Hua Wu, Haifeng Wang
Date: 2021-11-18 00:00:00
Tasks: BIG-bench Machine Learning, Drug Discovery, Multi-Task Learning

Machine learning shows great potential in virtual screening for drug discovery. Current efforts on accelerating docking-based virtual screening do not consider using existing data of other previously developed targets. To make use of the knowledge of the other targets and take advantage of the existing data, in this work, we apply multi-task learning to the problem of docking-based virtual screening. With two large docking datasets, the results of extensive experiments show that multi-task learning can achieve better performances on docking score prediction. By learning knowledge across multiple targets, the model trained by multi-task learning shows a better ability to adapt to a new target. Additional empirical study shows that other problems in drug discovery, such as the experimental drug-target affinity prediction, may also benefit from multi-task learning. Our results demonstrate that multi-task learning is a promising machine learning approach for docking-based virtual screening and accelerating the process of drug discovery.
Software Engineering for Responsible AI: An Empirical Study and Operationalised Patterns
Authors: Qinghua Lu, Liming Zhu, Xiwei Xu, Jon Whittle, David Douglas, Conrad Sanderson
Date: 2021-11-18 00:00:00
Tasks: Ethics

Although artificial intelligence (AI) is solving real-world challenges and transforming industries, there are serious concerns about its ability to behave and make decisions in a responsible way. Many AI ethics principles and guidelines for responsible AI have been recently issued by governments, organisations, and enterprises. However, these AI ethics principles and guidelines are typically high-level and do not provide concrete guidance on how to design and develop responsible AI systems. To address this shortcoming, we first present an empirical study where we interviewed 21 scientists and engineers to understand the practitioners' perceptions on AI ethics principles and their implementation. We then propose a template that enables AI ethics principles to be operationalised in the form of concrete patterns and suggest a list of patterns using the newly created template. These patterns provide concrete, operationalised guidance that facilitate the development of responsible AI systems.
Lifelong Reinforcement Learning with Temporal Logic Formulas and Reward Machines
Authors: Xuejing Zheng, Chao Yu, Chen Chen, Jianye Hao, Hankz Hankui Zhuo
Date: 2021-11-18 00:00:00
Tasks: Lifelong learning, reinforcement-learning, Reinforcement Learning, Reinforcement Learning (RL), Transfer Learning

Continuously learning new tasks using high-level ideas or knowledge is a key capability of humans. In this paper, we propose Lifelong reinforcement learning with Sequential linear temporal logic formulas and Reward Machines (LSRM), which enables an agent to leverage previously learned knowledge to fasten learning of logically specified tasks. For the sake of more flexible specification of tasks, we first introduce Sequential Linear Temporal Logic (SLTL), which is a supplement to the existing Linear Temporal Logic (LTL) formal language. We then utilize Reward Machines (RM) to exploit structural reward functions for tasks encoded with high-level events, and propose automatic extension of RM and efficient knowledge transfer over tasks for continuous learning in lifetime. Experimental results show that LSRM outperforms the methods that learn the target tasks from scratch by taking advantage of the task decomposition using SLTL and knowledge transfer over RM during the lifelong learning process.
Sustainable Artificial Intelligence through Continual Learning
Authors: Andrea Cossu, Marta Ziosi, Vincenzo Lomonaco
Date: 2021-11-17 00:00:00
Tasks: Continual Learning

The increasing attention on Artificial Intelligence (AI) regulation has led to the definition of a set of ethical principles grouped into the Sustainable AI framework. In this article, we identify Continual Learning, an active area of AI research, as a promising approach towards the design of systems compliant with the Sustainable AI principles. While Sustainable AI outlines general desiderata for ethical applications, Continual Learning provides means to put such desiderata into practice.
High Quality Rather than High Model Probability: Minimum Bayes Risk Decoding with Neural Metrics
Authors: Markus Freitag, David Grangier, Qijun Tan, Bowen Liang
Date: 2021-11-17 00:00:00
Tasks: Machine Translation, Sentence, Translation, Vocal Bursts Intensity Prediction

In Neural Machine Translation, it is typically assumed that the sentence with the highest estimated probability should also be the translation with the highest quality as measured by humans. In this work, we question this assumption and show that model estimates and translation quality only vaguely correlate. We apply Minimum Bayes Risk (MBR) decoding on unbiased samples to optimize diverse automated metrics of translation quality as an alternative inference strategy to beam search. Instead of targeting the hypotheses with the highest model probability, MBR decoding extracts the hypotheses with the highest estimated quality. Our experiments show that the combination of a neural translation model with a neural reference-based metric, BLEURT, results in significant improvement in human evaluations. This improvement is obtained with translations different from classical beam-search output: these translations have much lower model likelihood and are less favored by surface metrics like BLEU.
MEDCOD: A Medically-Accurate, Emotive, Diverse, and Controllable Dialog System
Authors: Rhys Compton, Ilya Valmianski, Li Deng, Costa Huang, Namit Katariya, Xavier Amatriain, Anitha Kannan
Date: 2021-11-17 00:00:00
Tasks: Sentence

We present MEDCOD, a Medically-Accurate, Emotive, Diverse, and Controllable Dialog system with a unique approach to the natural language generator module. MEDCOD has been developed and evaluated specifically for the history taking task. It integrates the advantage of a traditional modular approach to incorporate (medical) domain knowledge with modern deep learning techniques to generate flexible, human-like natural language expressions. Two key aspects of MEDCOD's natural language output are described in detail. First, the generated sentences are emotive and empathetic, similar to how a doctor would communicate to the patient. Second, the generated sentence structures and phrasings are varied and diverse while maintaining medical consistency with the desired medical concept (provided by the dialogue manager module of MEDCOD). Experimental results demonstrate the effectiveness of our approach in creating a human-like medical dialogue system. Relevant code is available at https://github.com/curai/curai-research/tree/main/MEDCOD
Simple but Effective: CLIP Embeddings for Embodied AI
Authors: Apoorv Khandelwal, Luca Weihs, Roozbeh Mottaghi, Aniruddha Kembhavi
Date: 2021-11-18 00:00:00
Proceeding: CVPR 2022 1
Tasks: Image Manipulation, Navigate

Contrastive language image pretraining (CLIP) encoders have been shown to be beneficial for a range of visual tasks from classification and detection to captioning and image manipulation. We investigate the effectiveness of CLIP visual backbones for Embodied AI tasks. We build incredibly simple baselines, named EmbCLIP, with no task specific architectures, inductive biases (such as the use of semantic maps), auxiliary tasks during training, or depth maps -- yet we find that our improved baselines perform very well across a range of tasks and simulators. EmbCLIP tops the RoboTHOR ObjectNav leaderboard by a huge margin of 20 pts (Success Rate). It tops the iTHOR 1-Phase Rearrangement leaderboard, beating the next best submission, which employs Active Neural Mapping, and more than doubling the % Fixed Strict metric (0.08 to 0.17). It also beats the winners of the 2021 Habitat ObjectNav Challenge, which employ auxiliary tasks, depth maps, and human demonstrations, and those of the 2019 Habitat PointNav Challenge. We evaluate the ability of CLIP's visual representations at capturing semantic information about input observations -- primitives that are useful for navigation-heavy embodied tasks -- and find that CLIP's representations encode these primitives more effectively than ImageNet-pretrained backbones. Finally, we extend one of our baselines, producing an agent capable of zero-shot object navigation that can navigate to objects that were not used as targets during training. Our code and models are available at https://github.com/allenai/embodied-clip
PyTorchVideo: A Deep Learning Library for Video Understanding
Authors: Haoqi Fan, Tullie Murrell, Heng Wang, Kalyan Vasudev Alwala, Yanghao Li, Yilei Li, Bo Xiong, Nikhila Ravi, Meng Li, Haichuan Yang, Jitendra Malik, Ross Girshick, Matt Feiszli, Aaron Adcock, Wan-Yen Lo, Christoph Feichtenhofer
Date: 2021-11-18 00:00:00
Tasks: Deep Learning, Self-Supervised Learning, Video Understanding

We introduce PyTorchVideo, an open-source deep-learning library that provides a rich set of modular, efficient, and reproducible components for a variety of video understanding tasks, including classification, detection, self-supervised learning, and low-level processing. The library covers a full stack of video understanding tools including multimodal data loading, transformations, and models that reproduce state-of-the-art performance. PyTorchVideo further supports hardware acceleration that enables real-time inference on mobile devices. The library is based on PyTorch and can be used by any training framework; for example, PyTorchLightning, PySlowFast, or Classy Vision. PyTorchVideo is available at https://pytorchvideo.org/
SimMIM: A Simple Framework for Masked Image Modeling
Authors: Zhenda Xie, Zheng Zhang, Yue Cao, Yutong Lin, Jianmin Bao, Zhuliang Yao, Qi Dai, Han Hu
Date: 2021-11-18 00:00:00
Proceeding: CVPR 2022 1
Tasks: Representation Learning, Self-Supervised Image Classification, Task 2

This paper presents SimMIM, a simple framework for masked image modeling. We simplify recently proposed related approaches without special designs such as block-wise masking and tokenization via discrete VAE or clustering. To study what let the masked image modeling task learn good representations, we systematically study the major components in our framework, and find that simple designs of each component have revealed very strong representation learning performance: 1) random masking of the input image with a moderately large masked patch size (e.g., 32) makes a strong pre-text task; 2) predicting raw pixels of RGB values by direct regression performs no worse than the patch classification approaches with complex designs; 3) the prediction head can be as light as a linear layer, with no worse performance than heavier ones. Using ViT-B, our approach achieves 83.8% top-1 fine-tuning accuracy on ImageNet-1K by pre-training also on this dataset, surpassing previous best approach by +0.6%. When applied on a larger model of about 650 million parameters, SwinV2-H, it achieves 87.1% top-1 accuracy on ImageNet-1K using only ImageNet-1K data. We also leverage this approach to facilitate the training of a 3B model (SwinV2-G), that by $40\times$ less data than that in previous practice, we achieve the state-of-the-art on four representative vision benchmarks. The code and models will be publicly available at https://github.com/microsoft/SimMIM.
Swin Transformer V2: Scaling Up Capacity and Resolution
Authors: Ze Liu, Han Hu, Yutong Lin, Zhuliang Yao, Zhenda Xie, Yixuan Wei, Jia Ning, Yue Cao, Zheng Zhang, Li Dong, Furu Wei, Baining Guo
Date: 2021-11-18 00:00:00
Proceeding: CVPR 2022 1
Tasks: Action Classification, image-classification, Image Classification, Instance Segmentation, Object Detection, Semantic Segmentation

Large-scale NLP models have been shown to significantly improve the performance on language tasks with no signs of saturation. They also demonstrate amazing few-shot capabilities like that of human beings. This paper aims to explore large-scale models in computer vision. We tackle three major issues in training and application of large vision models, including training instability, resolution gaps between pre-training and fine-tuning, and hunger on labelled data. Three main techniques are proposed: 1) a residual-post-norm method combined with cosine attention to improve training stability; 2) A log-spaced continuous position bias method to effectively transfer models pre-trained using low-resolution images to downstream tasks with high-resolution inputs; 3) A self-supervised pre-training method, SimMIM, to reduce the needs of vast labeled images. Through these techniques, this paper successfully trained a 3 billion-parameter Swin Transformer V2 model, which is the largest dense vision model to date, and makes it capable of training with images of up to 1,536$\times$1,536 resolution. It set new performance records on 4 representative vision tasks, including ImageNet-V2 image classification, COCO object detection, ADE20K semantic segmentation, and Kinetics-400 video action classification. Also note our training is much more efficient than that in Google's billion-level visual models, which consumes 40 times less labelled data and 40 times less training time. Code is available at \url{https://github.com/microsoft/Swin-Transformer}.