A Medical Literature Search System for Identifying Effective Treatments in Precision Medicine

The Precision Medicine Initiative states that treatments for a patient should take into account not only the patient's disease, but his/her specific genetic variation as well. The vast biomedical literature holds the potential for physicians to identify effective treatment options for a cancer patient. However, the complexity and ambiguity of medical terms can result in vocabulary mismatch between the physician's query and the literature. The physician's search intent (finding treatments instead of other types of studies) is difficult to explicitly formulate in a query. Therefore, simple ad hot retrieval approach will suffer from low recall and precision. In this paper, we propose a new retrieval system that helps physicians identify effective treatments in precision medicine. Given a cancer patient with a specific disease, genetic variation, and demographic information, the system aims to identify biomedical publications that report effective treatments. We approach this goal from two directions. First, we expand the original disease and gene terms using biomedical knowledge bases to improve recall of the initial retrieval. We then improve precision by promoting treatment-related publications to the top using a machine learning reranker trained on 2017 Text Retrieval Conference Precision Medicine (PM) track corpus. Batch evaluation results on 2018 PM track corpus show that the proposed approach effectively improves both recall and precision, achieving performance comparable to the top entries on the leaderboard of 2018 PM track.Comment: 32 page

A Fast Deep Learning Model for Textual Relevance in Biomedical Information Retrieval

Publications in the life sciences are characterized by a large technical vocabulary, with many lexical and semantic variations for expressing the same concept. Towards addressing the problem of relevance in biomedical literature search, we introduce a deep learning model for the relevance of a document's text to a keyword style query. Limited by a relatively small amount of training data, the model uses pre-trained word embeddings. With these, the model first computes a variable-length Delta matrix between the query and document, representing a difference between the two texts, which is then passed through a deep convolution stage followed by a deep feed-forward network to compute a relevance score. This results in a fast model suitable for use in an online search engine. The model is robust and outperforms comparable state-of-the-art deep learning approaches.Comment: To appear in proceeding of WWW 201

Complementing Lexical Retrieval with Semantic Residual Embedding

This paper presents CLEAR, a retrieval model that seeks to complement classical lexical exact-match models such as BM25 with semantic matching signals from a neural embedding matching model. CLEAR explicitly trains the neural embedding to encode language structures and semantics that lexical retrieval fails to capture with a novel residual-based embedding learning method. Empirical evaluations demonstrate the advantages of CLEAR over state-of-the-art retrieval models, and that it can substantially improve the end-to-end accuracy and efficiency of reranking pipelines.Comment: ECIR 202

Twitter100k: A Real-world Dataset for Weakly Supervised Cross-Media Retrieval

This paper contributes a new large-scale dataset for weakly supervised cross-media retrieval, named Twitter100k. Current datasets, such as Wikipedia, NUS Wide and Flickr30k, have two major limitations. First, these datasets are lacking in content diversity, i.e., only some pre-defined classes are covered. Second, texts in these datasets are written in well-organized language, leading to inconsistency with realistic applications. To overcome these drawbacks, the proposed Twitter100k dataset is characterized by two aspects: 1) it has 100,000 image-text pairs randomly crawled from Twitter and thus has no constraint in the image categories; 2) text in Twitter100k is written in informal language by the users. Since strongly supervised methods leverage the class labels that may be missing in practice, this paper focuses on weakly supervised learning for cross-media retrieval, in which only text-image pairs are exploited during training. We extensively benchmark the performance of four subspace learning methods and three variants of the Correspondence AutoEncoder, along with various text features on Wikipedia, Flickr30k and Twitter100k. Novel insights are provided. As a minor contribution, inspired by the characteristic of Twitter100k, we propose an OCR-based cross-media retrieval method. In experiment, we show that the proposed OCR-based method improves the baseline performance

Assessing Efficiency-Effectiveness Tradeoffs in Multi-Stage Retrieval Systems Without Using Relevance Judgments

Large-scale retrieval systems are often implemented as a cascading sequence of phases -- a first filtering step, in which a large set of candidate documents are extracted using a simple technique such as Boolean matching and/or static document scores; and then one or more ranking steps, in which the pool of documents retrieved by the filter is scored more precisely using dozens or perhaps hundreds of different features. The documents returned to the user are then taken from the head of the final ranked list. Here we examine methods for measuring the quality of filtering and preliminary ranking stages, and show how to use these measurements to tune the overall performance of the system. Standard top-weighted metrics used for overall system evaluation are not appropriate for assessing filtering stages, since the output is a set of documents, rather than an ordered sequence of documents. Instead, we use an approach in which a quality score is computed based on the discrepancy between filtered and full evaluation. Unlike previous approaches, our methods do not require relevance judgments, and thus can be used with virtually any query set. We show that this quality score directly correlates with actual differences in measured effectiveness when relevance judgments are available. Since the quality score does not require relevance judgments, it can be used to identify queries that perform particularly poorly for a given filter. Using these methods, we explore a wide range of filtering options using thousands of queries, categorize the relative merits of the different approaches, and identify useful parameter combinations

Effective Image Retrieval via Multilinear Multi-index Fusion

Multi-index fusion has demonstrated impressive performances in retrieval task by integrating different visual representations in a unified framework. However, previous works mainly consider propagating similarities via neighbor structure, ignoring the high order information among different visual representations. In this paper, we propose a new multi-index fusion scheme for image retrieval. By formulating this procedure as a multilinear based optimization problem, the complementary information hidden in different indexes can be explored more thoroughly. Specially, we first build our multiple indexes from various visual representations. Then a so-called index-specific functional matrix, which aims to propagate similarities, is introduced for updating the original index. The functional matrices are then optimized in a unified tensor space to achieve a refinement, such that the relevant images can be pushed more closer. The optimization problem can be efficiently solved by the augmented Lagrangian method with theoretical convergence guarantee. Unlike the traditional multi-index fusion scheme, our approach embeds the multi-index subspace structure into the new indexes with sparse constraint, thus it has little additional memory consumption in online query stage. Experimental evaluation on three benchmark datasets reveals that the proposed approach achieves the state-of-the-art performance, i.e., N-score 3.94 on UKBench, mAP 94.1\% on Holiday and 62.39\% on Market-1501.Comment: 12 page

Webly Supervised Joint Embedding for Cross-Modal Image-Text Retrieval

Cross-modal retrieval between visual data and natural language description remains a long-standing challenge in multimedia. While recent image-text retrieval methods offer great promise by learning deep representations aligned across modalities, most of these methods are plagued by the issue of training with small-scale datasets covering a limited number of images with ground-truth sentences. Moreover, it is extremely expensive to create a larger dataset by annotating millions of images with sentences and may lead to a biased model. Inspired by the recent success of webly supervised learning in deep neural networks, we capitalize on readily-available web images with noisy annotations to learn robust image-text joint representation. Specifically, our main idea is to leverage web images and corresponding tags, along with fully annotated datasets, in training for learning the visual-semantic joint embedding. We propose a two-stage approach for the task that can augment a typical supervised pair-wise ranking loss based formulation with weakly-annotated web images to learn a more robust visual-semantic embedding. Experiments on two standard benchmark datasets demonstrate that our method achieves a significant performance gain in image-text retrieval compared to state-of-the-art approaches.Comment: ACM Multimedia 201

Beyond Precision: A Study on Recall of Initial Retrieval with Neural Representations

Vocabulary mismatch is a central problem in information retrieval (IR), i.e., the relevant documents may not contain the same (symbolic) terms of the query. Recently, neural representations have shown great success in capturing semantic relatedness, leading to new possibilities to alleviate the vocabulary mismatch problem in IR. However, most existing efforts in this direction have been devoted to the re-ranking stage. That is to leverage neural representations to help re-rank a set of candidate documents, which are typically obtained from an initial retrieval stage based on some symbolic index and search scheme (e.g., BM25 over the inverted index). This naturally raises a question: if the relevant documents have not been found in the initial retrieval stage due to vocabulary mismatch, there would be no chance to re-rank them to the top positions later. Therefore, in this paper, we study the problem how to employ neural representations to improve the recall of relevant documents in the initial retrieval stage. Specifically, to meet the efficiency requirement of the initial stage, we introduce a neural index for the neural representations of documents, and propose two hybrid search schemes based on both neural and symbolic indices, namely the parallel search scheme and the sequential search scheme. Our experiments show that both hybrid index and search schemes can improve the recall of the initial retrieval stage with small overhead

An Information Retrieval Approach to Short Text Conversation

Human computer conversation is regarded as one of the most difficult problems in artificial intelligence. In this paper, we address one of its key sub-problems, referred to as short text conversation, in which given a message from human, the computer returns a reasonable response to the message. We leverage the vast amount of short conversation data available on social media to study the issue. We propose formalizing short text conversation as a search problem at the first step, and employing state-of-the-art information retrieval (IR) techniques to carry out the task. We investigate the significance as well as the limitation of the IR approach. Our experiments demonstrate that the retrieval-based model can make the system behave rather "intelligently", when combined with a huge repository of conversation data from social media.Comment: 21 pages, 4 figure

Learning to Rank Using Localized Geometric Mean Metrics

Many learning-to-rank (LtR) algorithms focus on query-independent model, in which query and document do not lie in the same feature space, and the rankers rely on the feature ensemble about query-document pair instead of the similarity between query instance and documents. However, existing algorithms do not consider local structures in query-document feature space, and are fragile to irrelevant noise features. In this paper, we propose a novel Riemannian metric learning algorithm to capture the local structures and develop a robust LtR algorithm. First, we design a concept called \textit{ideal candidate document} to introduce metric learning algorithm to query-independent model. Previous metric learning algorithms aiming to find an optimal metric space are only suitable for query-dependent model, in which query instance and documents belong to the same feature space and the similarity is directly computed from the metric space. Then we extend the new and extremely fast global Geometric Mean Metric Learning (GMML) algorithm to develop a localized GMML, namely L-GMML. Based on the combination of local learned metrics, we employ the popular Normalized Discounted Cumulative Gain~(NDCG) scorer and Weighted Approximate Rank Pairwise (WARP) loss to optimize the \textit{ideal candidate document} for each query candidate set. Finally, we can quickly evaluate all candidates via the similarity between the \textit{ideal candidate document} and other candidates. By leveraging the ability of metric learning algorithms to describe the complex structural information, our approach gives us a principled and efficient way to perform LtR tasks. The experiments on real-world datasets demonstrate that our proposed L-GMML algorithm outperforms the state-of-the-art metric learning to rank methods and the stylish query-independent LtR algorithms regarding accuracy and computational efficiency.Comment: To appear in SIGIR'1