On Robustness and Bias Analysis of BERT-based Relation Extraction

Fine-tuning pre-trained models have achieved impressive performance on standard natural language processing benchmarks. However, the resultant model generalizability remains poorly understood. We do not know, for example, how excellent performance can lead to the perfection of generalization models. In this study, we analyze a fine-tuned BERT model from different perspectives using relation extraction. We also characterize the differences in generalization techniques according to our proposed improvements. From empirical experimentation, we find that BERT suffers a bottleneck in terms of robustness by way of randomizations, adversarial and counterfactual tests, and biases (i.e., selection and semantic). These findings highlight opportunities for future improvements. Our open-sourced testbed DiagnoseRE is available in \url{https://github.com/zjunlp/DiagnoseRE}.Comment: work in progres

Structuring the Unstructured: Unlocking pharmacokinetic data from journals with Natural Language Processing

The development of a new drug is an increasingly expensive and inefficient process. Many drug candidates are discarded due to pharmacokinetic (PK) complications detected at clinical phases. It is critical to accurately estimate the PK parameters of new drugs before being tested in humans since they will determine their efficacy and safety outcomes. Preclinical predictions of PK parameters are largely based on prior knowledge from other compounds, but much of this potentially valuable data is currently locked in the format of scientific papers. With an ever-increasing amount of scientific literature, automated systems are essential to exploit this resource efficiently. Developing text mining systems that can structure PK literature is critical to improving the drug development pipeline. This thesis studied the development and application of text mining resources to accelerate the curation of PK databases. Specifically, the development of novel corpora and suitable natural language processing architectures in the PK domain were addressed. The work presented focused on machine learning approaches that can model the high diversity of PK studies, parameter mentions, numerical measurements, units, and contextual information reported across the literature. Additionally, architectures and training approaches that could efficiently deal with the scarcity of annotated examples were explored. The chapters of this thesis tackle the development of suitable models and corpora to (1) retrieve PK documents, (2) recognise PK parameter mentions, (3) link PK entities to a knowledge base and (4) extract relations between parameter mentions, estimated measurements, units and other contextual information. Finally, the last chapter of this thesis studied the feasibility of the whole extraction pipeline to accelerate tasks in drug development research. The results from this thesis exhibited the potential of text mining approaches to automatically generate PK databases that can aid researchers in the field and ultimately accelerate the drug development pipeline. Additionally, the thesis presented contributions to biomedical natural language processing by developing suitable architectures and corpora for multiple tasks, tackling novel entities and relations within the PK domain

A Survey of GPT-3 Family Large Language Models Including ChatGPT and GPT-4

Large language models (LLMs) are a special class of pretrained language models obtained by scaling model size, pretraining corpus and computation. LLMs, because of their large size and pretraining on large volumes of text data, exhibit special abilities which allow them to achieve remarkable performances without any task-specific training in many of the natural language processing tasks. The era of LLMs started with OpenAI GPT-3 model, and the popularity of LLMs is increasing exponentially after the introduction of models like ChatGPT and GPT4. We refer to GPT-3 and its successor OpenAI models, including ChatGPT and GPT4, as GPT-3 family large language models (GLLMs). With the ever-rising popularity of GLLMs, especially in the research community, there is a strong need for a comprehensive survey which summarizes the recent research progress in multiple dimensions and can guide the research community with insightful future research directions. We start the survey paper with foundation concepts like transformers, transfer learning, self-supervised learning, pretrained language models and large language models. We then present a brief overview of GLLMs and discuss the performances of GLLMs in various downstream tasks, specific domains and multiple languages. We also discuss the data labelling and data augmentation abilities of GLLMs, the robustness of GLLMs, the effectiveness of GLLMs as evaluators, and finally, conclude with multiple insightful future research directions. To summarize, this comprehensive survey paper will serve as a good resource for both academic and industry people to stay updated with the latest research related to GPT-3 family large language models.Comment: Preprint under review, 58 page

A Survey on Knowledge Graphs: Representation, Acquisition and Applications

Human knowledge provides a formal understanding of the world. Knowledge graphs that represent structural relations between entities have become an increasingly popular research direction towards cognition and human-level intelligence. In this survey, we provide a comprehensive review of knowledge graph covering overall research topics about 1) knowledge graph representation learning, 2) knowledge acquisition and completion, 3) temporal knowledge graph, and 4) knowledge-aware applications, and summarize recent breakthroughs and perspective directions to facilitate future research. We propose a full-view categorization and new taxonomies on these topics. Knowledge graph embedding is organized from four aspects of representation space, scoring function, encoding models, and auxiliary information. For knowledge acquisition, especially knowledge graph completion, embedding methods, path inference, and logical rule reasoning, are reviewed. We further explore several emerging topics, including meta relational learning, commonsense reasoning, and temporal knowledge graphs. To facilitate future research on knowledge graphs, we also provide a curated collection of datasets and open-source libraries on different tasks. In the end, we have a thorough outlook on several promising research directions

RLSbench: Domain Adaptation Under Relaxed Label Shift

Despite the emergence of principled methods for domain adaptation under label shift, their sensitivity to shifts in class conditional distributions is precariously under explored. Meanwhile, popular deep domain adaptation heuristics tend to falter when faced with label proportions shifts. While several papers modify these heuristics in attempts to handle label proportions shifts, inconsistencies in evaluation standards, datasets, and baselines make it difficult to gauge the current best practices. In this paper, we introduce RLSbench, a large-scale benchmark for relaxed label shift, consisting of $>$500 distribution shift pairs spanning vision, tabular, and language modalities, with varying label proportions. Unlike existing benchmarks, which primarily focus on shifts in class-conditional $p(x|y)$, our benchmark also focuses on label marginal shifts. First, we assess 13 popular domain adaptation methods, demonstrating more widespread failures under label proportion shifts than were previously known. Next, we develop an effective two-step meta-algorithm that is compatible with most domain adaptation heuristics: (i) pseudo-balance the data at each epoch; and (ii) adjust the final classifier with target label distribution estimate. The meta-algorithm improves existing domain adaptation heuristics under large label proportion shifts, often by 2--10\% accuracy points, while conferring minimal effect ($<$0.5\%) when label proportions do not shift. We hope that these findings and the availability of RLSbench will encourage researchers to rigorously evaluate proposed methods in relaxed label shift settings. Code is publicly available at https://github.com/acmi-lab/RLSbench.Comment: Accepted at ICML 2023. Paper website: https://sites.google.com/view/rlsbench

Obsessive-compulsive disorder and related disorders: a comprehensive survey

Our aim was to present a comprehensive, updated survey on obsessive-compulsive disorder (OCD) and obsessive-compulsive related disorders (OCRDs) and their clinical management via literature review, critical analysis and synthesis

Deep Active Learning for Computer Vision: Past and Future

As an important data selection schema, active learning emerges as the essential component when iterating an Artificial Intelligence (AI) model. It becomes even more critical given the dominance of deep neural network based models, which are composed of a large number of parameters and data hungry, in application. Despite its indispensable role for developing AI models, research on active learning is not as intensive as other research directions. In this paper, we present a review of active learning through deep active learning approaches from the following perspectives: 1) technical advancements in active learning, 2) applications of active learning in computer vision, 3) industrial systems leveraging or with potential to leverage active learning for data iteration, 4) current limitations and future research directions. We expect this paper to clarify the significance of active learning in a modern AI model manufacturing process and to bring additional research attention to active learning. By addressing data automation challenges and coping with automated machine learning systems, active learning will facilitate democratization of AI technologies by boosting model production at scale.Comment: Accepted by APSIPA Transactions on Signal and Information Processin

A Comprehensive Survey on Test-Time Adaptation under Distribution Shifts

Machine learning methods strive to acquire a robust model during training that can generalize well to test samples, even under distribution shifts. However, these methods often suffer from a performance drop due to unknown test distributions. Test-time adaptation (TTA), an emerging paradigm, has the potential to adapt a pre-trained model to unlabeled data during testing, before making predictions. Recent progress in this paradigm highlights the significant benefits of utilizing unlabeled data for training self-adapted models prior to inference. In this survey, we divide TTA into several distinct categories, namely, test-time (source-free) domain adaptation, test-time batch adaptation, online test-time adaptation, and test-time prior adaptation. For each category, we provide a comprehensive taxonomy of advanced algorithms, followed by a discussion of different learning scenarios. Furthermore, we analyze relevant applications of TTA and discuss open challenges and promising areas for future research. A comprehensive list of TTA methods can be found at \url{https://github.com/tim-learn/awesome-test-time-adaptation}.Comment: Discussions, comments, and questions are all welcomed in \url{https://github.com/tim-learn/awesome-test-time-adaptation