Fine-Grained Relevance Annotations for Multi-Task Document Ranking and Question Answering

There are many existing retrieval and question answering datasets. However, most of them either focus on ranked list evaluation or single-candidate question answering. This divide makes it challenging to properly evaluate approaches concerned with ranking documents and providing snippets or answers for a given query. In this work, we present FiRA: a novel dataset of Fine-Grained Relevance Annotations. We extend the ranked retrieval annotations of the Deep Learning track of TREC 2019 with passage and word level graded relevance annotations for all relevant documents. We use our newly created data to study the distribution of relevance in long documents, as well as the attention of annotators to specific positions of the text. As an example, we evaluate the recently introduced TKL document ranking model. We find that although TKL exhibits state-of-the-art retrieval results for long documents, it misses many relevant passages.

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).

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.

An Unbiased Approach to Quantification of Gender Inclination using Interpretable Word Representations

Recent advances in word embedding provide significant benefit to various information processing tasks. Yet these dense representations and their estimation of word-to-word relatedness remain difficult to interpret and hard to analyze. As an alternative, explicit word representations i.e. vectors with clearly-defined dimensions, which can be words, windows of words, or documents are easily interpretable, and recent methods show competitive performance to the dense vectors. In this work, we propose a method to transfer word2vec SkipGram embedding model to its explicit representation model. The method provides interpretable explicit vectors while keeping the effectiveness of the original model, tested by evaluating the model on several word association collections. Based on the proposed explicit representation, we propose a novel method to quantify the degree of the existence of gender bias in the English language (used in Wikipedia) with regard to a set of occupations. By measuring the bias towards explicit Female and Male factors, the work demonstrates a general tendency of the majority of the occupations to male and a strong bias in a few specific occupations (e.g. nurse) to female.

Is the winner really the best? A critical analysis of common research practice in biomedical image analysis competitions

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.

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.

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.

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).