Chest X-rays have been widely used for COVID-19 screening; however, 3D computed tomography (CT) is a more effective modality. We present our findings on COVID-19 severity prediction from chest CT scans using the STOIC dataset. We developed an ensemble deep learning based model that incorporates multiple neural networks to improve predictions. To address data imbalance, we used slicing functions and data augmentation. We further improved performance using test time data augmentation. Our approach which employs a simple yet effective ensemble of deep learning-based models with strong test time augmentations, achieved results comparable to more complex methods and secured the fourth position in the STOIC2021 COVID-19 AI Challenge. Our code is available on online: at: //github.com/aleemsidra/stoic2021- baseline-finalphase-main.
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Given a limited labeling budget, active learning (AL) aims to sample the most informative instances from an unlabeled pool to acquire labels for subsequent model training. To achieve this, AL typically measures the informativeness of unlabeled instances based on uncertainty and diversity. However, it does not consider erroneous instances with their neighborhood error density, which have great potential to improve the model performance. To address this limitation, we propose $REAL$, a novel approach to select data instances with $\underline{R}$epresentative $\underline{E}$rrors for $\underline{A}$ctive $\underline{L}$earning. It identifies minority predictions as \emph{pseudo errors} within a cluster and allocates an adaptive sampling budget for the cluster based on estimated error density. Extensive experiments on five text classification datasets demonstrate that $REAL$ consistently outperforms all best-performing baselines regarding accuracy and F1-macro scores across a wide range of hyperparameter settings. Our analysis also shows that $REAL$ selects the most representative pseudo errors that match the distribution of ground-truth errors along the decision boundary. Our code is publicly available at //github.com/withchencheng/ECML_PKDD_23_Real.
Vision-language tasks, such as VQA, SNLI-VE, and VCR are challenging because they require the model's reasoning ability to understand the semantics of the visual world and natural language. Supervised methods working for vision-language tasks have been well-studied. However, solving these tasks in a zero-shot setting is less explored. Since Contrastive Language-Image Pre-training (CLIP) has shown remarkable zero-shot performance on image-text matching, previous works utilized its strong zero-shot ability by converting vision-language tasks into an image-text matching problem, and they mainly consider global-level matching (e.g., the whole image or sentence). However, we find visual and textual fine-grained information, e.g., keywords in the sentence and objects in the image, can be fairly informative for semantics understanding. Inspired by this, we propose a unified framework to take advantage of the fine-grained information for zero-shot vision-language learning, covering multiple tasks such as VQA, SNLI-VE, and VCR. Our experiments show that our framework outperforms former zero-shot methods on VQA and achieves substantial improvement on SNLI-VE and VCR. Furthermore, our ablation studies confirm the effectiveness and generalizability of our proposed method. Code will be available at //github.com/ThreeSR/UniFine
Reinforcement learning is a learning paradigm for solving sequential decision-making problems. Recent years have witnessed remarkable progress in reinforcement learning upon the fast development of deep neural networks. Along with the promising prospects of reinforcement learning in numerous domains such as robotics and game-playing, transfer learning has arisen to tackle various challenges faced by reinforcement learning, by transferring knowledge from external expertise to facilitate the efficiency and effectiveness of the learning process. In this survey, we systematically investigate the recent progress of transfer learning approaches in the context of deep reinforcement learning. Specifically, we provide a framework for categorizing the state-of-the-art transfer learning approaches, under which we analyze their goals, methodologies, compatible reinforcement learning backbones, and practical applications. We also draw connections between transfer learning and other relevant topics from the reinforcement learning perspective and explore their potential challenges that await future research progress.
Interatomic potentials learned using machine learning methods have been successfully applied to atomistic simulations. However, deep learning pipelines are notoriously data-hungry, while generating reference calculations is computationally demanding. To overcome this difficulty, we propose a transfer learning algorithm that leverages the ability of graph neural networks (GNNs) in describing chemical environments, together with kernel mean embeddings. We extract a feature map from GNNs pre-trained on the OC20 dataset and use it to learn the potential energy surface from system-specific datasets of catalytic processes. Our method is further enhanced by a flexible kernel function that incorporates chemical species information, resulting in improved performance and interpretability. We test our approach on a series of realistic datasets of increasing complexity, showing excellent generalization and transferability performance, and improving on methods that rely on GNNs or ridge regression alone, as well as similar fine-tuning approaches. We make the code available to the community at //github.com/IsakFalk/atomistic_transfer_mekrr.
The coronavirus disease 2019 (COVID-19) has led to a global pandemic of significant severity. In addition to its high level of contagiousness, COVID-19 can have a heterogeneous clinical course, ranging from asymptomatic carriers to severe and potentially life-threatening health complications. Many patients have to revisit the emergency room (ER) within a short time after discharge, which significantly increases the workload for medical staff. Early identification of such patients is crucial for helping physicians focus on treating life-threatening cases. In this study, we obtained Electronic Health Records (EHRs) of 3,210 encounters from 13 affiliated ERs within the University of Pittsburgh Medical Center between March 2020 and January 2021. We leveraged a Natural Language Processing technique, ScispaCy, to extract clinical concepts and used the 1001 most frequent concepts to develop 7-day revisit models for COVID-19 patients in ERs. The research data we collected from 13 ERs may have distributional differences that could affect the model development. To address this issue, we employed a classic deep transfer learning method called the Domain Adversarial Neural Network (DANN) and evaluated different modeling strategies, including the Multi-DANN algorithm, the Single-DANN algorithm, and three baseline methods. Results showed that the Multi-DANN models outperformed the Single-DANN models and baseline models in predicting revisits of COVID-19 patients to the ER within 7 days after discharge. Notably, the Multi-DANN strategy effectively addressed the heterogeneity among multiple source domains and improved the adaptation of source data to the target domain. Moreover, the high performance of Multi-DANN models indicates that EHRs are informative for developing a prediction model to identify COVID-19 patients who are very likely to revisit an ER within 7 days after discharge.
Graph machine learning has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To tackle the challenge, automated graph machine learning, which aims at discovering the best hyper-parameter and neural architecture configuration for different graph tasks/data without manual design, is gaining an increasing number of attentions from the research community. In this paper, we extensively discuss automated graph machine approaches, covering hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We briefly overview existing libraries designed for either graph machine learning or automated machine learning respectively, and further in depth introduce AutoGL, our dedicated and the world's first open-source library for automated graph machine learning. Last but not least, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive discussion of approaches, libraries as well as directions for automated graph machine learning.
Unsupervised domain adaptation has recently emerged as an effective paradigm for generalizing deep neural networks to new target domains. However, there is still enormous potential to be tapped to reach the fully supervised performance. In this paper, we present a novel active learning strategy to assist knowledge transfer in the target domain, dubbed active domain adaptation. We start from an observation that energy-based models exhibit free energy biases when training (source) and test (target) data come from different distributions. Inspired by this inherent mechanism, we empirically reveal that a simple yet efficient energy-based sampling strategy sheds light on selecting the most valuable target samples than existing approaches requiring particular architectures or computation of the distances. Our algorithm, Energy-based Active Domain Adaptation (EADA), queries groups of targe data that incorporate both domain characteristic and instance uncertainty into every selection round. Meanwhile, by aligning the free energy of target data compact around the source domain via a regularization term, domain gap can be implicitly diminished. Through extensive experiments, we show that EADA surpasses state-of-the-art methods on well-known challenging benchmarks with substantial improvements, making it a useful option in the open world. Code is available at //github.com/BIT-DA/EADA.
As an effective strategy, data augmentation (DA) alleviates data scarcity scenarios where deep learning techniques may fail. It is widely applied in computer vision then introduced to natural language processing and achieves improvements in many tasks. One of the main focuses of the DA methods is to improve the diversity of training data, thereby helping the model to better generalize to unseen testing data. In this survey, we frame DA methods into three categories based on the diversity of augmented data, including paraphrasing, noising, and sampling. Our paper sets out to analyze DA methods in detail according to the above categories. Further, we also introduce their applications in NLP tasks as well as the challenges.
Graph neural networks (GNNs) is widely used to learn a powerful representation of graph-structured data. Recent work demonstrates that transferring knowledge from self-supervised tasks to downstream tasks could further improve graph representation. However, there is an inherent gap between self-supervised tasks and downstream tasks in terms of optimization objective and training data. Conventional pre-training methods may be not effective enough on knowledge transfer since they do not make any adaptation for downstream tasks. To solve such problems, we propose a new transfer learning paradigm on GNNs which could effectively leverage self-supervised tasks as auxiliary tasks to help the target task. Our methods would adaptively select and combine different auxiliary tasks with the target task in the fine-tuning stage. We design an adaptive auxiliary loss weighting model to learn the weights of auxiliary tasks by quantifying the consistency between auxiliary tasks and the target task. In addition, we learn the weighting model through meta-learning. Our methods can be applied to various transfer learning approaches, it performs well not only in multi-task learning but also in pre-training and fine-tuning. Comprehensive experiments on multiple downstream tasks demonstrate that the proposed methods can effectively combine auxiliary tasks with the target task and significantly improve the performance compared to state-of-the-art methods.
Most previous event extraction studies have relied heavily on features derived from annotated event mentions, thus cannot be applied to new event types without annotation effort. In this work, we take a fresh look at event extraction and model it as a grounding problem. We design a transferable neural architecture, mapping event mentions and types jointly into a shared semantic space using structural and compositional neural networks, where the type of each event mention can be determined by the closest of all candidate types . By leveraging (1)~available manual annotations for a small set of existing event types and (2)~existing event ontologies, our framework applies to new event types without requiring additional annotation. Experiments on both existing event types (e.g., ACE, ERE) and new event types (e.g., FrameNet) demonstrate the effectiveness of our approach. \textit{Without any manual annotations} for 23 new event types, our zero-shot framework achieved performance comparable to a state-of-the-art supervised model which is trained from the annotations of 500 event mentions.
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