Inferring knowledge from clinical trials using knowledge graph embedding is an emerging area. However, customizing graph embeddings for different use cases remains a significant challenge. We propose custom2vec, an algorithmic framework to customize graph embeddings by incorporating user preferences in training the embeddings. It captures user preferences by adding custom nodes and links derived from manually vetted results of a separate information retrieval method. We propose a joint learning objective to preserve the original network structure while incorporating the user's custom annotations. We hypothesize that the custom training improves user-expected predictions, for example, in link prediction tasks. We demonstrate the effectiveness of custom2vec for clinical trials related to non-small cell lung cancer (NSCLC) with two customization scenarios: recommending immuno-oncology trials evaluating PD-1 inhibitors and exploring similar trials that compare new therapies with a standard of care. The results show that custom2vec training achieves better performance than the conventional training methods. Our approach is a novel way to customize knowledge graph embeddings and enable more accurate recommendations and predictions.

With an increasing amount of data in the art world, discovering artists and artworks suitable to collectors' tastes becomes a challenge. It is no longer enough to use visual information, as contextual information about the artist has become just as important in contemporary art. In this work, we present a generic Natural Language Processing framework (called ArtLM) to discover the connections among contemporary artists based on their biographies. In this approach, we first continue to pre-train the existing general English language models with a large amount of unlabelled art-related data. We then fine-tune this new pre-trained model with our biography pair dataset manually annotated by a team of professionals in the art industry. With extensive experiments, we demonstrate that our ArtLM achieves 85.6% accuracy and 84.0% F1 score and outperforms other baseline models. We also provide a visualisation and a qualitative analysis of the artist network built from ArtLM's outputs.

Long document retrieval aims to fetch query-relevant documents from a large-scale collection, where knowledge distillation has become de facto to improve a retriever by mimicking a heterogeneous yet powerful cross-encoder. However, in contrast to passages or sentences, retrieval on long documents suffers from the scope hypothesis that a long document may cover multiple topics. This maximizes their structure heterogeneity and poses a granular-mismatch issue, leading to an inferior distillation efficacy. In this work, we propose a new learning framework, fine-grained distillation (FGD), for long-document retrievers. While preserving the conventional dense retrieval paradigm, it first produces global-consistent representations crossing different fine granularity and then applies multi-granular aligned distillation merely during training. In experiments, we evaluate our framework on two long-document retrieval benchmarks, which show state-of-the-art performance.

A popular approach to creating a zero-shot cross-language retrieval model is to substitute a monolingual pretrained language model in the retrieval model with a multilingual pretrained language model such as Multilingual BERT. This multilingual model is fined-tuned to the retrieval task with monolingual data such as English MS MARCO using the same training recipe as the monolingual retrieval model used. However, such transferred models suffer from mismatches in the languages of the input text during training and inference. In this work, we propose transferring monolingual retrieval models using adapters, a parameter-efficient component for a transformer network. By adding adapters pretrained on language tasks for a specific language with task-specific adapters, prior work has shown that the adapter-enhanced models perform better than fine-tuning the entire model when transferring across languages in various NLP tasks. By constructing dense retrieval models with adapters, we show that models trained with monolingual data are more effective than fine-tuning the entire model when transferring to a Cross Language Information Retrieval (CLIR) setting. However, we found that the prior suggestion of replacing the language adapters to match the target language at inference time is suboptimal for dense retrieval models. We provide an in-depth analysis of this discrepancy between other cross-language NLP tasks and CLIR.

To improve the performance of the dual-encoder retriever, one effective approach is knowledge distillation from the cross-encoder ranker. Existing works construct the candidate passages following the supervised learning setting where a query is paired with a positive passage and a batch of negatives. However, through empirical observation, we find that even the hard negatives from advanced methods are still too trivial for the teacher to distinguish, preventing the teacher from transferring abundant dark knowledge to the student through its soft label. To alleviate this issue, we propose ADAM, a knowledge distillation framework that can better transfer the dark knowledge held in the teacher with Adaptive Dark exAMples. Different from previous works that only rely on one positive and hard negatives as candidate passages, we create dark examples that all have moderate relevance to the query through mixing-up and masking in discrete space. Furthermore, as the quality of knowledge held in different training instances varies as measured by the teacher's confidence score, we propose a self-paced distillation strategy that adaptively concentrates on a subset of high-quality instances to conduct our dark-example-based knowledge distillation to help the student learn better. We conduct experiments on two widely-used benchmarks and verify the effectiveness of our method.

Recent advances in open-domain question answering (ODQA) have demonstrated impressive accuracy on standard Wikipedia style benchmarks. However, it is less clear how robust these models are and how well they perform when applied to real-world applications in drastically different domains. While there has been some work investigating how well ODQA models perform when tested for out-of-domain (OOD) generalization, these studies have been conducted only under conservative shifts in data distribution and typically focus on a single component (ie. retrieval) rather than an end-to-end system. In response, we propose a more realistic and challenging domain shift evaluation setting and, through extensive experiments, study end-to-end model performance. We find that not only do models fail to generalize, but high retrieval scores often still yield poor answer prediction accuracy. We then categorize different types of shifts and propose techniques that, when presented with a new dataset, predict if intervention methods are likely to be successful. Finally, using insights from this analysis, we propose and evaluate several intervention methods which improve end-to-end answer F1 score by up to 24 points.

Pre-trained language models have achieved promising success in code retrieval tasks, where a natural language documentation query is given to find the most relevant existing code snippet. However, existing models focus only on optimizing the documentation code pairs by embedding them into latent space, without the association of external knowledge. In this paper, we propose a generation-augmented query expansion framework. Inspired by the human retrieval process - sketching an answer before searching, in this work, we utilize the powerful code generation model to benefit the code retrieval task. Specifically, we demonstrate that rather than merely retrieving the target code snippet according to the documentation query, it would be helpful to augment the documentation query with its generation counterpart - generated code snippets from the code generation model. To the best of our knowledge, this is the first attempt that leverages the code generation model to enhance the code retrieval task. We achieve new state-of-the-art results on the CodeSearchNet benchmark and surpass the baselines significantly.

Automated summarization of clinical texts can reduce the burden of medical professionals. "Discharge summaries" are one promising application of the summarization, because they can be generated from daily inpatient records. Our preliminary experiment suggests that 20-31% of the descriptions in discharge summaries overlap with the content of the inpatient records. However, it remains unclear how the summaries should be generated from the unstructured source. To decompose the physician's summarization process, this study aimed to identify the optimal granularity in summarization. We first defined three types of summarization units with different granularities to compare the performance of the discharge summary generation: whole sentences, clinical segments, and clauses. We defined clinical segments in this study, aiming to express the smallest medically meaningful concepts. To obtain the clinical segments, it was necessary to automatically split the texts in the first stage of the pipeline. Accordingly, we compared rule-based methods and a machine learning method, and the latter outperformed the formers with an F1 score of 0.846 in the splitting task. Next, we experimentally measured the accuracy of extractive summarization using the three types of units, based on the ROUGE-1 metric, on a multi-institutional national archive of health records in Japan. The measured accuracies of extractive summarization using whole sentences, clinical segments, and clauses were 31.91, 36.15, and 25.18, respectively. We found that the clinical segments yielded higher accuracy than sentences and clauses. This result indicates that summarization of inpatient records demands finer granularity than sentence-oriented processing. Although we used only Japanese health records, it can be interpreted as follows: physicians extract "concepts of medical significance" from patient records and recombine them ...

In the past few decades, there has been an explosion in the amount of available data produced from various sources with different topics. The availability of this enormous data necessitates us to adopt effective computational tools to explore the data. This leads to an intense growing interest in the research community to develop computational methods focused on processing this text data. A line of study focused on condensing the text so that we are able to get a higher level of understanding in a shorter time. The two important tasks to do this are keyword extraction and text summarization. In keyword extraction, we are interested in finding the key important words from a text. This makes us familiar with the general topic of a text. In text summarization, we are interested in producing a short-length text which includes important information about the document. The TextRank algorithm, an unsupervised learning method that is an extension of the PageRank (algorithm which is the base algorithm of Google search engine for searching pages and ranking them) has shown its efficacy in large-scale text mining, especially for text summarization and keyword extraction. this algorithm can automatically extract the important parts of a text (keywords or sentences) and declare them as the result. However, this algorithm neglects the semantic similarity between the different parts. In this work, we improved the results of the TextRank algorithm by incorporating the semantic similarity between parts of the text. Aside from keyword extraction and text summarization, we develop a topic clustering algorithm based on our framework which can be used individually or as a part of generating the summary to overcome coverage problems.

Medical systematic reviews typically require assessing all the documents retrieved by a search. The reason is two-fold: the task aims for ``total recall''; and documents retrieved using Boolean search are an unordered set, and thus it is unclear how an assessor could examine only a subset. Screening prioritisation is the process of ranking the (unordered) set of retrieved documents, allowing assessors to begin the downstream processes of the systematic review creation earlier, leading to earlier completion of the review, or even avoiding screening documents ranked least relevant. Screening prioritisation requires highly effective ranking methods. Pre-trained language models are state-of-the-art on many IR tasks but have yet to be applied to systematic review screening prioritisation. In this paper, we apply several pre-trained language models to the systematic review document ranking task, both directly and fine-tuned. An empirical analysis compares how effective neural methods compare to traditional methods for this task. We also investigate different types of document representations for neural methods and their impact on ranking performance. Our results show that BERT-based rankers outperform the current state-of-the-art screening prioritisation methods. However, BERT rankers and existing methods can actually be complementary, and thus, further improvements may be achieved if used in conjunction.