arXiv subjects

Allan Hanbury

Publications and source records attributed to Allan Hanbury.

49 records · Page 3Linked to original sources

arXiv2020

Interpretable & Time-Budget-Constrained Contextualization for Re-Ranking

Search engines operate under a strict time constraint as a fast response is paramount to user satisfaction. Thus, neural re-ranking models have a limited time-budget to re-rank documents. Given the same amount of time, a faster re-ranking model can incorporate more documents than a less efficient one, leading to a higher effectiveness. To utilize this property, we propose TK (Transformer-Kernel): a neural re-ranking model for ad-hoc search using an efficient contextualization mechanism. TK employs a very small number of Transformer layers (up to three) to contextualize query and document word embeddings. To score individual term interactions, we use a document-length enhanced kernel-pooling, which enables users to gain insight into the model. TK offers an optimal ratio between effectiveness and efficiency: under realistic time constraints (max. 200 ms per query) TK achieves the highest effectiveness in comparison to BERT and other re-ranking models. We demonstrate this on three large-scale ranking collections: MSMARCO-Passage, MSMARCO-Document, and TREC CAR. In addition, to gain insight into TK, we perform a clustered query analysis of TK's results, highlighting its strengths and weaknesses on queries with different types of information need and we show how to interpret the cause of ranking differences of two documents by comparing their internal scores.

cs.IR↗

arXiv2020

DSR: A Collection for the Evaluation of Graded Disease-Symptom Relations

The effective extraction of ranked disease-symptom relationships is a critical component in various medical tasks, including computer-assisted medical diagnosis or the discovery of unexpected associations between diseases. While existing disease-symptom relationship extraction methods are used as the foundation in the various medical tasks, no collection is available to systematically evaluate the performance of such methods. In this paper, we introduce the Disease-Symptom Relation collection (DSR-collection), created by five fully trained physicians as expert annotators. We provide graded symptom judgments for diseases by differentiating between "symptoms" and "primary symptoms". Further, we provide several strong baselines, based on the methods used in previous studies. The first method is based on word embeddings, and the second on co-occurrences of keywords in medical articles. For the co-occurrence method, we propose an adaption in which not only keywords are considered, but also the full text of medical articles. The evaluation on the DSR-collection shows the effectiveness of the proposed adaption in terms of nDCG, precision, and recall.

cs.IR↗

arXiv2019

Neural-IR-Explorer: A Content-Focused Tool to Explore Neural Re-Ranking Results

In this paper we look beyond metrics-based evaluation of Information Retrieval systems, to explore the reasons behind ranking results. We present the content-focused Neural-IR-Explorer, which empowers users to browse through retrieval results and inspect the inner workings and fine-grained results of neural re-ranking models. The explorer includes a categorized overview of the available queries, as well as an individual query result view with various options to highlight semantic connections between query-document pairs. The Neural-IR-Explorer is available at: https://neural-ir-explorer.ec.tuwien.ac.at/

cs.IR↗

arXiv2019

TU Wien @ TREC Deep Learning '19 -- Simple Contextualization for Re-ranking

The usage of neural network models puts multiple objectives in conflict with each other: Ideally we would like to create a neural model that is effective, efficient, and interpretable at the same time. However, in most instances we have to choose which property is most important to us. We used the opportunity of the TREC 2019 Deep Learning track to evaluate the effectiveness of a balanced neural re-ranking approach. We submitted results of the TK (Transformer-Kernel) model: a neural re-ranking model for ad-hoc search using an efficient contextualization mechanism. TK employs a very small number of lightweight Transformer layers to contextualize query and document word embeddings. To score individual term interactions, we use a document-length enhanced kernel-pooling, which enables users to gain insight into the model. Our best result for the passage ranking task is: 0.420 MAP, 0.671 nDCG, 0.598 P@10 (TUW19-p3 full). Our best result for the document ranking task is: 0.271 MAP, 0.465 nDCG, 0.730 P@10 (TUW19-d3 re-ranking).

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arXiv2019

Why rankings of biomedical image analysis competitions should be interpreted with care

International challenges have become the standard for validation of biomedical image analysis methods. Given their scientific impact, it is surprising that a critical analysis of common practices related to the organization of challenges has not yet been performed. In this paper, we present a comprehensive analysis of biomedical image analysis challenges conducted up to now. We demonstrate the importance of challenges and show that the lack of quality control has critical consequences. First, reproducibility and interpretation of the results is often hampered as only a fraction of relevant information is typically provided. Second, the rank of an algorithm is generally not robust to a number of variables such as the test data used for validation, the ranking scheme applied and the observers that make the reference annotations. To overcome these problems, we recommend best practice guidelines and define open research questions to be addressed in the future.

cs.CV↗

arXiv2019

Deep Learning architectures for generalized immunofluorescence based nuclear image segmentation

Separating and labeling each instance of a nucleus (instance-aware segmentation) is the key challenge in segmenting single cell nuclei on fluorescence microscopy images. Deep Neural Networks can learn the implicit transformation of a nuclear image into a probability map indicating the class membership of each pixel (nucleus or background), but the use of post-processing steps to turn the probability map into a labeled object mask is error-prone. This especially accounts for nuclear images of tissue sections and nuclear images across varying tissue preparations. In this work, we aim to evaluate the performance of state-of-the-art deep learning architectures to segment nuclei in fluorescence images of various tissue origins and sample preparation types without post-processing. We compare architectures that operate on pixel to pixel translation and an architecture that operates on object detection and subsequent locally applied segmentation. In addition, we propose a novel strategy to create artificial images to extend the training set. We evaluate the influence of ground truth annotation quality, image scale and segmentation complexity on segmentation performance. Results show that three out of four deep learning architectures (U-Net, U-Net with ResNet34 backbone, Mask R-CNN) can segment fluorescent nuclear images on most of the sample preparation types and tissue origins with satisfactory segmentation performance. Mask R-CNN, an architecture designed to address instance aware segmentation tasks, outperforms other architectures. Equal nuclear mean size, consistent nuclear annotations and the use of artificially generated images result in overall acceptable precision and recall across different tissues and sample preparation types.

cs.CV↗

arXiv2019

Let's measure run time! Extending the IR replicability infrastructure to include performance aspects

Establishing a docker-based replicability infrastructure offers the community a great opportunity: measuring the run time of information retrieval systems. The time required to present query results to a user is paramount to the users satisfaction. Recent advances in neural IR re-ranking models put the issue of query latency at the forefront. They bring a complex trade-off between performance and effectiveness based on a myriad of factors: the choice of encoding model, network architecture, hardware acceleration and many others. The best performing models (currently using the BERT transformer model) run orders of magnitude more slowly than simpler architectures. We aim to broaden the focus of the neural IR community to include performance considerations -- to sustain the practical applicability of our innovations. In this position paper we supply our argument with a case study exploring the performance of different neural re-ranking models. Finally, we propose to extend the OSIRRC docker-based replicability infrastructure with two performance focused benchmark scenarios.

cs.IR↗

arXiv2019

On the Effect of Low-Frequency Terms on Neural-IR Models

Low-frequency terms are a recurring challenge for information retrieval models, especially neural IR frameworks struggle with adequately capturing infrequently observed words. While these terms are often removed from neural models - mainly as a concession to efficiency demands - they traditionally play an important role in the performance of IR models. In this paper, we analyze the effects of low-frequency terms on the performance and robustness of neural IR models. We conduct controlled experiments on three recent neural IR models, trained on a large-scale passage retrieval collection. We evaluate the neural IR models with various vocabulary sizes for their respective word embeddings, considering different levels of constraints on the available GPU memory. We observe that despite the significant benefits of using larger vocabularies, the performance gap between the vocabularies can be, to a great extent, mitigated by extensive tuning of a related parameter: the number of documents to re-rank. We further investigate the use of subword-token embedding models, and in particular FastText, for neural IR models. Our experiments show that using FastText brings slight improvements to the overall performance of the neural IR models in comparison to models trained on the full vocabulary, while the improvement becomes much more pronounced for queries containing low-frequency terms.

cs.IR↗

arXiv2018

Uncertainty in Neural Network Word Embedding: Exploration of Threshold for Similarity

Word embedding, specially with its recent developments, promises a quantification of the similarity between terms. However, it is not clear to which extent this similarity value can be genuinely meaningful and useful for subsequent tasks. We explore how the similarity score obtained from the models is really indicative of term relatedness. We first observe and quantify the uncertainty factor of the word embedding models regarding to the similarity value. Based on this factor, we introduce a general threshold on various dimensions which effectively filters the highly related terms. Our evaluation on four information retrieval collections supports the effectiveness of our approach as the results of the introduced threshold are significantly better than the baseline while being equal to or statistically indistinguishable from the optimal results.

cs.CL↗

arXiv2018

Toward Incorporation of Relevant Documents in word2vec

Recent advances in neural word embedding provide significant benefit to various information retrieval tasks. However as shown by recent studies, adapting the embedding models for the needs of IR tasks can bring considerable further improvements. The embedding models in general define the term relatedness by exploiting the terms' co-occurrences in short-window contexts. An alternative (and well-studied) approach in IR for related terms to a query is using local information i.e. a set of top-retrieved documents. In view of these two methods of term relatedness, in this work, we report our study on incorporating the local information of the query in the word embeddings. One main challenge in this direction is that the dense vectors of word embeddings and their estimation of term-to-term relatedness remain difficult to interpret and hard to analyze. As an alternative, explicit word representations propose vectors whose dimensions are easily interpretable, and recent methods show competitive performance to the dense vectors. We introduce a neural-based explicit representation, rooted in the conceptual ideas of the word2vec Skip-Gram model. The method provides interpretable explicit vectors while keeping the effectiveness of the Skip-Gram model. The evaluation of various explicit representations on word association collections shows that the newly proposed method out- performs the state-of-the-art explicit representations when tasked with ranking highly similar terms. Based on the introduced ex- plicit representation, we discuss our approaches on integrating local documents in globally-trained embedding models and discuss the preliminary results.

cs.IR↗

arXiv2018

Addressing Cross-Lingual Word Sense Disambiguation on Low-Density Languages: Application to Persian

We explore the use of unsupervised methods in Cross-Lingual Word Sense Disambiguation (CL-WSD) with the application of English to Persian. Our proposed approach targets the languages with scarce resources (low-density) by exploiting word embedding and semantic similarity of the words in context. We evaluate the approach on a recent evaluation benchmark and compare it with the state-of-the-art unsupervised system (CO-Graph). The results show that our approach outperforms both the standard baseline and the CO-Graph system in both of the task evaluation metrics (Out-Of-Five and Best result).

cs.CL↗

arXiv2017

Volatility Prediction using Financial Disclosures Sentiments with Word Embedding-based IR Models

Volatility prediction--an essential concept in financial markets--has recently been addressed using sentiment analysis methods. We investigate the sentiment of annual disclosures of companies in stock markets to forecast volatility. We specifically explore the use of recent Information Retrieval (IR) term weighting models that are effectively extended by related terms using word embeddings. In parallel to textual information, factual market data have been widely used as the mainstream approach to forecast market risk. We therefore study different fusion methods to combine text and market data resources. Our word embedding-based approach significantly outperforms state-of-the-art methods. In addition, we investigate the characteristics of the reports of the companies in different financial sectors.

cs.IR↗

arXiv2015

Evaluation-as-a-Service: Overview and Outlook

Evaluation in empirical computer science is essential to show progress and assess technologies developed. Several research domains such as information retrieval have long relied on systematic evaluation to measure progress: here, the Cranfield paradigm of creating shared test collections, defining search tasks, and collecting ground truth for these tasks has persisted up until now. In recent years, however, several new challenges have emerged that do not fit this paradigm very well: extremely large data sets, confidential data sets as found in the medical domain, and rapidly changing data sets as often encountered in industry. Also, crowdsourcing has changed the way that industry approaches problem-solving with companies now organizing challenges and handing out monetary awards to incentivize people to work on their challenges, particularly in the field of machine learning. This white paper is based on discussions at a workshop on Evaluation-as-a-Service (EaaS). EaaS is the paradigm of not providing data sets to participants and have them work on the data locally, but keeping the data central and allowing access via Application Programming Interfaces (API), Virtual Machines (VM) or other possibilities to ship executables. The objective of this white paper are to summarize and compare the current approaches and consolidate the experiences of these approaches to outline the next steps of EaaS, particularly towards sustainable research infrastructures. This white paper summarizes several existing approaches to EaaS and analyzes their usage scenarios and also the advantages and disadvantages. The many factors influencing EaaS are overviewed, and the environment in terms of motivations for the various stakeholders, from funding agencies to challenge organizers, researchers and participants, to industry interested in supplying real-world problems for which they require solutions.

cs.CY↗