Multi-modal data abounds in biomedicine, such as radiology images and reports. Interpreting this data at scale is essential for improving clinical care and accelerating clinical research. Biomedical text with its complex semantics poses additional challenges in vision--language modelling compared to the general domain, and previous work has used insufficiently adapted models that lack domain-specific language understanding. In this paper, we show that principled textual semantic modelling can substantially improve contrastive learning in self-supervised vision--language processing. We release a language model that achieves state-of-the-art results in radiology natural language inference through its improved vocabulary and novel language pretraining objective leveraging semantics and discourse characteristics in radiology reports. Further, we propose a self-supervised joint vision--language approach with a focus on better text modelling. It establishes new state of the art results on a wide range of publicly available benchmarks, in part by leveraging our new domain-specific language model. We release a new dataset with locally-aligned phrase grounding annotations by radiologists to facilitate the study of complex semantic modelling in biomedical vision--language processing. A broad evaluation, including on this new dataset, shows that our contrastive learning approach, aided by textual-semantic modelling, outperforms prior methods in segmentation tasks, despite only using a global-alignment objective.
In this research note, I derive explicit dynamical systems for language within an acquisition-driven framework (Niyogi \& Berwick, 1997; Niyogi, 2006) assuming that children/learners follow the Tolerance Principle (Yang, 2016) to determine whether a rule is productive during the process of language acquisition. I consider different theoretical parameters such as population size (finite vs. infinite) and the number of previous generations that provide learners with data. Multiple simulations of the dynamics obtained here and applications to diacrhonic language data are in preparation, so they are not included in this first note.
Post-processing of static embedding has beenshown to improve their performance on both lexical and sequence-level tasks. However, post-processing for contextualized embeddings is an under-studied problem. In this work, we question the usefulness of post-processing for contextualized embeddings obtained from different layers of pre-trained language models. More specifically, we standardize individual neuron activations using z-score, min-max normalization, and by removing top principle components using the all-but-the-top method. Additionally, we apply unit length normalization to word representations. On a diverse set of pre-trained models, we show that post-processing unwraps vital information present in the representations for both lexical tasks (such as word similarity and analogy)and sequence classification tasks. Our findings raise interesting points in relation to theresearch studies that use contextualized representations, and suggest z-score normalization as an essential step to consider when using them in an application.
Semantic localization (SeLo) refers to the task of obtaining the most relevant locations in large-scale remote sensing (RS) images using semantic information such as text. As an emerging task based on cross-modal retrieval, SeLo achieves semantic-level retrieval with only caption-level annotation, which demonstrates its great potential in unifying downstream tasks. Although SeLo has been carried out successively, but there is currently no work has systematically explores and analyzes this urgent direction. In this paper, we thoroughly study this field and provide a complete benchmark in terms of metrics and testdata to advance the SeLo task. Firstly, based on the characteristics of this task, we propose multiple discriminative evaluation metrics to quantify the performance of the SeLo task. The devised significant area proportion, attention shift distance, and discrete attention distance are utilized to evaluate the generated SeLo map from pixel-level and region-level. Next, to provide standard evaluation data for the SeLo task, we contribute a diverse, multi-semantic, multi-objective Semantic Localization Testset (AIR-SLT). AIR-SLT consists of 22 large-scale RS images and 59 test cases with different semantics, which aims to provide a comprehensive evaluations for retrieval models. Finally, we analyze the SeLo performance of RS cross-modal retrieval models in detail, explore the impact of different variables on this task, and provide a complete benchmark for the SeLo task. We have also established a new paradigm for RS referring expression comprehension, and demonstrated the great advantage of SeLo in semantics through combining it with tasks such as detection and road extraction. The proposed evaluation metrics, semantic localization testsets, and corresponding scripts have been open to access at github.com/xiaoyuan1996/SemanticLocalizationMetrics .
Disease risk models can identify high-risk patients and help clinicians provide more personalized care. However, risk models developed on one dataset may not generalize across diverse subpopulations of patients in different datasets and may have unexpected performance. It is challenging for clinical researchers to inspect risk models across different subgroups without any tools. Therefore, we developed an interactive visualization system called RMExplorer (Risk Model Explorer) to enable interactive risk model assessment. Specifically, the system allows users to define subgroups of patients by selecting clinical, demographic, or other characteristics, to explore the performance and fairness of risk models on the subgroups, and to understand the feature contributions to risk scores. To demonstrate the usefulness of the tool, we conduct a case study, where we use RMExplorer to explore three atrial fibrillation risk models by applying them to the UK Biobank dataset of 445,329 individuals. RMExplorer can help researchers to evaluate the performance and biases of risk models on subpopulations of interest in their data.
Transformer, an attention-based encoder-decoder architecture, has revolutionized the field of natural language processing. Inspired by this significant achievement, some pioneering works have recently been done on adapting Transformerliked architectures to Computer Vision (CV) fields, which have demonstrated their effectiveness on various CV tasks. Relying on competitive modeling capability, visual Transformers have achieved impressive performance on multiple benchmarks such as ImageNet, COCO, and ADE20k as compared with modern Convolution Neural Networks (CNN). In this paper, we have provided a comprehensive review of over one hundred different visual Transformers for three fundamental CV tasks (classification, detection, and segmentation), where a taxonomy is proposed to organize these methods according to their motivations, structures, and usage scenarios. Because of the differences in training settings and oriented tasks, we have also evaluated these methods on different configurations for easy and intuitive comparison instead of only various benchmarks. Furthermore, we have revealed a series of essential but unexploited aspects that may empower Transformer to stand out from numerous architectures, e.g., slack high-level semantic embeddings to bridge the gap between visual and sequential Transformers. Finally, three promising future research directions are suggested for further investment.
This paper surveys and organizes research works in a new paradigm in natural language processing, which we dub "prompt-based learning". Unlike traditional supervised learning, which trains a model to take in an input x and predict an output y as P(y|x), prompt-based learning is based on language models that model the probability of text directly. To use these models to perform prediction tasks, the original input x is modified using a template into a textual string prompt x' that has some unfilled slots, and then the language model is used to probabilistically fill the unfilled information to obtain a final string x, from which the final output y can be derived. This framework is powerful and attractive for a number of reasons: it allows the language model to be pre-trained on massive amounts of raw text, and by defining a new prompting function the model is able to perform few-shot or even zero-shot learning, adapting to new scenarios with few or no labeled data. In this paper we introduce the basics of this promising paradigm, describe a unified set of mathematical notations that can cover a wide variety of existing work, and organize existing work along several dimensions, e.g.the choice of pre-trained models, prompts, and tuning strategies. To make the field more accessible to interested beginners, we not only make a systematic review of existing works and a highly structured typology of prompt-based concepts, but also release other resources, e.g., a website //pretrain.nlpedia.ai/ including constantly-updated survey, and paperlist.
Link prediction on knowledge graphs (KGs) is a key research topic. Previous work mainly focused on binary relations, paying less attention to higher-arity relations although they are ubiquitous in real-world KGs. This paper considers link prediction upon n-ary relational facts and proposes a graph-based approach to this task. The key to our approach is to represent the n-ary structure of a fact as a small heterogeneous graph, and model this graph with edge-biased fully-connected attention. The fully-connected attention captures universal inter-vertex interactions, while with edge-aware attentive biases to particularly encode the graph structure and its heterogeneity. In this fashion, our approach fully models global and local dependencies in each n-ary fact, and hence can more effectively capture associations therein. Extensive evaluation verifies the effectiveness and superiority of our approach. It performs substantially and consistently better than current state-of-the-art across a variety of n-ary relational benchmarks. Our code is publicly available.
Detection and recognition of text in natural images are two main problems in the field of computer vision that have a wide variety of applications in analysis of sports videos, autonomous driving, industrial automation, to name a few. They face common challenging problems that are factors in how text is represented and affected by several environmental conditions. The current state-of-the-art scene text detection and/or recognition methods have exploited the witnessed advancement in deep learning architectures and reported a superior accuracy on benchmark datasets when tackling multi-resolution and multi-oriented text. However, there are still several remaining challenges affecting text in the wild images that cause existing methods to underperform due to there models are not able to generalize to unseen data and the insufficient labeled data. Thus, unlike previous surveys in this field, the objectives of this survey are as follows: first, offering the reader not only a review on the recent advancement in scene text detection and recognition, but also presenting the results of conducting extensive experiments using a unified evaluation framework that assesses pre-trained models of the selected methods on challenging cases, and applies the same evaluation criteria on these techniques. Second, identifying several existing challenges for detecting or recognizing text in the wild images, namely, in-plane-rotation, multi-oriented and multi-resolution text, perspective distortion, illumination reflection, partial occlusion, complex fonts, and special characters. Finally, the paper also presents insight into the potential research directions in this field to address some of the mentioned challenges that are still encountering scene text detection and recognition techniques.
Breast cancer remains a global challenge, causing over 1 million deaths globally in 2018. To achieve earlier breast cancer detection, screening x-ray mammography is recommended by health organizations worldwide and has been estimated to decrease breast cancer mortality by 20-40%. Nevertheless, significant false positive and false negative rates, as well as high interpretation costs, leave opportunities for improving quality and access. To address these limitations, there has been much recent interest in applying deep learning to mammography; however, obtaining large amounts of annotated data poses a challenge for training deep learning models for this purpose, as does ensuring generalization beyond the populations represented in the training dataset. Here, we present an annotation-efficient deep learning approach that 1) achieves state-of-the-art performance in mammogram classification, 2) successfully extends to digital breast tomosynthesis (DBT; "3D mammography"), 3) detects cancers in clinically-negative prior mammograms of cancer patients, 4) generalizes well to a population with low screening rates, and 5) outperforms five-out-of-five full-time breast imaging specialists by improving absolute sensitivity by an average of 14%. Our results demonstrate promise towards software that can improve the accuracy of and access to screening mammography worldwide.
Language model pre-training has proven to be useful in learning universal language representations. As a state-of-the-art language model pre-training model, BERT (Bidirectional Encoder Representations from Transformers) has achieved amazing results in many language understanding tasks. In this paper, we conduct exhaustive experiments to investigate different fine-tuning methods of BERT on text classification task and provide a general solution for BERT fine-tuning. Finally, the proposed solution obtains new state-of-the-art results on eight widely-studied text classification datasets.