arXiv subjects

Carsten Eickhoff

Publications and source records attributed to Carsten Eickhoff.

At least 91 records · Page 5Linked to original sources

arXiv2020

Are "Undocumented Workers" the Same as "Illegal Aliens"? Disentangling Denotation and Connotation in Vector Spaces

In politics, neologisms are frequently invented for partisan objectives. For example, "undocumented workers" and "illegal aliens" refer to the same group of people (i.e., they have the same denotation), but they carry clearly different connotations. Examples like these have traditionally posed a challenge to reference-based semantic theories and led to increasing acceptance of alternative theories (e.g., Two-Factor Semantics) among philosophers and cognitive scientists. In NLP, however, popular pretrained models encode both denotation and connotation as one entangled representation. In this study, we propose an adversarial neural network that decomposes a pretrained representation as independent denotation and connotation representations. For intrinsic interpretability, we show that words with the same denotation but different connotations (e.g., "immigrants" vs. "aliens", "estate tax" vs. "death tax") move closer to each other in denotation space while moving further apart in connotation space. For extrinsic application, we train an information retrieval system with our disentangled representations and show that the denotation vectors improve the viewpoint diversity of document rankings.

cs.CL↗

arXiv2020

Drug-Drug Interaction Prediction with Wasserstein Adversarial Autoencoder-based Knowledge Graph Embeddings

Interaction between pharmacological agents can trigger unexpected adverse events. Capturing richer and more comprehensive information about drug-drug interactions (DDI) is one of the key tasks in public health and drug development. Recently, several knowledge graph embedding approaches have received increasing attention in the DDI domain due to their capability of projecting drugs and interactions into a low-dimensional feature space for predicting links and classifying triplets. However, existing methods only apply a uniformly random mode to construct negative samples. As a consequence, these samples are often too simplistic to train an effective model. In this paper, we propose a new knowledge graph embedding framework by introducing adversarial autoencoders (AAE) based on Wasserstein distances and Gumbel-Softmax relaxation for drug-drug interactions tasks. In our framework, the autoencoder is employed to generate high-quality negative samples and the hidden vector of the autoencoder is regarded as a plausible drug candidate. Afterwards, the discriminator learns the embeddings of drugs and interactions based on both positive and negative triplets. Meanwhile, in order to solve vanishing gradient problems on the discrete representation--an inherent flaw in traditional generative models--we utilize the Gumbel-Softmax relaxation and the Wasserstein distance to train the embedding model steadily. We empirically evaluate our method on two tasks, link prediction and DDI classification. The experimental results show that our framework can attain significant improvements and noticeably outperform competitive baselines.

cs.LG↗

arXiv2020

Extracting Angina Symptoms from Clinical Notes Using Pre-Trained Transformer Architectures

Anginal symptoms can connote increased cardiac risk and a need for change in cardiovascular management. This study evaluated the potential to extract these symptoms from physician notes using the Bidirectional Encoder from Transformers language model fine-tuned on a domain-specific corpus. The history of present illness section of 459 expert annotated primary care physician notes from consecutive patients referred for cardiac testing without known atherosclerotic cardiovascular disease were included. Notes were annotated for positive and negative mentions of chest pain and shortness of breath characterization. The results demonstrate high sensitivity and specificity for the detection of chest pain or discomfort, substernal chest pain, shortness of breath, and dyspnea on exertion. Small sample size limited extracting factors related to provocation and palliation of chest pain. This study provides a promising starting point for the natural language processing of physician notes to characterize clinically actionable anginal symptoms.

cs.AI↗

arXiv2020

Brown University at TREC Deep Learning 2019

This paper describes Brown University's submission to the TREC 2019 Deep Learning track. We followed a 2-phase method for producing a ranking of passages for a given input query: In the the first phase, the user's query is expanded by appending 3 queries generated by a transformer model which was trained to rephrase an input query into semantically similar queries. The expanded query can exhibit greater similarity in surface form and vocabulary overlap with the passages of interest and can therefore serve as enriched input to any downstream information retrieval method. In the second phase, we use a BERT-based model pre-trained for language modeling but fine-tuned for query - document relevance prediction to compute relevance scores for a set of 1000 candidate passages per query and subsequently obtain a ranking of passages by sorting them based on the predicted relevance scores. According to the results published in the official Overview of the TREC Deep Learning Track 2019, our team ranked 3rd in the passage retrieval task (including full ranking and re-ranking), and 2nd when considering only re-ranking submissions.

cs.IR↗

arXiv2020

Mining Misdiagnosis Patterns from Biomedical Literature

Diagnostic errors can pose a serious threat to patient safety, leading to serious harm and even death. Efforts are being made to develop interventions that allow physicians to reassess for errors and improve diagnostic accuracy. Our study presents an exploration of misdiagnosis patterns mined from PubMed abstracts. Article titles containing certain phrases indicating misdiagnosis were selected and frequencies of these misdiagnoses calculated. We present the resulting patterns in the form of a directed graph with frequency-weighted misdiagnosis edges connecting diagnosis vertices. We find that the most commonly misdiagnosed diseases were often misdiagnosed as many different diseases, with each misdiagnosis having a relatively low frequency, rather than as a single disease with greater probability. Additionally, while a misdiagnosis relationship may generally exist, the relationship was often found to be one-sided.

cs.IR↗

arXiv2020

Diagnosis Prevalence vs. Efficacy in Machine-learning Based Diagnostic Decision Support

Many recent studies use machine learning to predict a small number of ICD-9-CM codes. In practice, on the other hand, physicians have to consider a broader range of diagnoses. This study aims to put these previously incongruent evaluation settings on a more equal footing by predicting ICD-9-CM codes based on electronic health record properties and demonstrating the relationship between diagnosis prevalence and system performance. We extracted patient features from the MIMIC-III dataset for each admission. We trained and evaluated 43 different machine learning classifiers. Among this pool, the most successful classifier was a Multi-Layer Perceptron. In accordance with general machine learning expectation, we observed all classifiers' F1 scores to drop as disease prevalence decreased. Scores fell from 0.28 for the 50 most prevalent ICD-9-CM codes to 0.03 for the 1000 most prevalent ICD-9-CM codes. Statistical analyses showed a moderate positive correlation between disease prevalence and efficacy (0.5866).

stat.AP↗

arXiv2019

DC3 -- A Diagnostic Case Challenge Collection for Clinical Decision Support

In clinical care, obtaining a correct diagnosis is the first step towards successful treatment and, ultimately, recovery. Depending on the complexity of the case, the diagnostic phase can be lengthy and ridden with errors and delays. Such errors have a high likelihood to cause patients severe harm or even lead to their death and are estimated to cost the U.S. healthcare system several hundred billion dollars each year. To avoid diagnostic errors, physicians increasingly rely on diagnostic decision support systems drawing from heuristics, historic cases, textbooks, clinical guidelines and scholarly biomedical literature. The evaluation of such systems, however, is often conducted in an ad-hoc fashion, using non-transparent methodology, and proprietary data. This paper presents DC3, a collection of 31 extremely difficult diagnostic case challenges, manually compiled and solved by clinical experts. For each case, we present a number of temporally ordered physician-generated observations alongside the eventually confirmed true diagnosis. We additionally provide inferred dense relevance judgments for these cases among the PubMed collection of 27 million scholarly biomedical articles.

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

Embedding Electronic Health Records for Clinical Information Retrieval

Neural network representation learning frameworks have recently shown to be highly effective at a wide range of tasks ranging from radiography interpretation via data-driven diagnostics to clinical decision support. This often superior performance comes at the price of dramatically increased training data requirements that cannot be satisfied in every given institution or scenario. As a means of countering such data sparsity effects, distant supervision alleviates the need for scarce in-domain data by relying on a related, resource-rich, task for training. This study presents an end-to-end neural clinical decision support system that recommends relevant literature for individual patients (few available resources) via distant supervision on the well-known MIMIC-III collection (abundant resource). Our experiments show significant improvements in retrieval effectiveness over traditional statistical as well as purely locally supervised retrieval models.

cs.IR↗

arXiv2018

Web2Text: Deep Structured Boilerplate Removal

Web pages are a valuable source of information for many natural language processing and information retrieval tasks. Extracting the main content from those documents is essential for the performance of derived applications. To address this issue, we introduce a novel model that performs sequence labeling to collectively classify all text blocks in an HTML page as either boilerplate or main content. Our method uses a hidden Markov model on top of potentials derived from DOM tree features using convolutional neural networks. The proposed method sets a new state-of-the-art performance for boilerplate removal on the CleanEval benchmark. As a component of information retrieval pipelines, it improves retrieval performance on the ClueWeb12 collection.

cs.IR↗

arXiv2018

Unsupervised Learning of Parsimonious General-Purpose Embeddings for User and Location Modelling

Many social network applications depend on robust representations of spatio-temporal data. In this work, we present an embedding model based on feed-forward neural networks which transforms social media check-ins into dense feature vectors encoding geographic, temporal, and functional aspects for modelling places, neighborhoods, and users. We employ the embedding model in a variety of applications including location recommendation, urban functional zone study, and crime prediction. For location recommendation, we propose a Spatio-Temporal Embedding Similarity algorithm (STES) based on the embedding model. In a range of experiments on real life data collected from Foursquare, we demonstrate our model's effectiveness at characterizing places and people and its applicability in aforementioned problem domains. Finally, we select eight major cities around the globe and verify the robustness and generality of our model by porting pre-trained models from one city to another, thereby alleviating the need for costly local training.

cs.IR↗

arXiv2018

Biomedical Question Answering via Weighted Neural Network Passage Retrieval

The amount of publicly available biomedical literature has been growing rapidly in recent years, yet question answering systems still struggle to exploit the full potential of this source of data. In a preliminary processing step, many question answering systems rely on retrieval models for identifying relevant documents and passages. This paper proposes a weighted cosine distance retrieval scheme based on neural network word embeddings. Our experiments are based on publicly available data and tasks from the BioASQ biomedical question answering challenge and demonstrate significant performance gains over a wide range of state-of-the-art models.

cs.IR↗

arXiv2017

Evaluating Music Recommender Systems for Groups

Recommendation to groups of users is a challenging and currently only passingly studied task. Especially the evaluation aspect often appears ad-hoc and instead of truly evaluating on groups of users, synthesizes groups by merging individual preferences. In this paper, we present a user study, recording the individual and shared preferences of actual groups of participants, resulting in a robust, standardized evaluation benchmark. Using this benchmarking dataset, that we share with the research community, we compare the respective performance of a wide range of music group recommendation techniques proposed in the

cs.AI↗

arXiv2017

Computing Web-scale Topic Models using an Asynchronous Parameter Server

Topic models such as Latent Dirichlet Allocation (LDA) have been widely used in information retrieval for tasks ranging from smoothing and feedback methods to tools for exploratory search and discovery. However, classical methods for inferring topic models do not scale up to the massive size of today's publicly available Web-scale data sets. The state-of-the-art approaches rely on custom strategies, implementations and hardware to facilitate their asynchronous, communication-intensive workloads. We present APS-LDA, which integrates state-of-the-art topic modeling with cluster computing frameworks such as Spark using a novel asynchronous parameter server. Advantages of this integration include convenient usage of existing data processing pipelines and eliminating the need for disk writes as data can be kept in memory from start to finish. Our goal is not to outperform highly customized implementations, but to propose a general high-performance topic modeling framework that can easily be used in today's data processing pipelines. We compare APS-LDA to the existing Spark LDA implementations and show that our system can, on a 480-core cluster, process up to 135 times more data and 10 times more topics without sacrificing model quality.

cs.DC↗

arXiv2016

Neural Document Embeddings for Intensive Care Patient Mortality Prediction

We present an automatic mortality prediction scheme based on the unstructured textual content of clinical notes. Proposing a convolutional document embedding approach, our empirical investigation using the MIMIC-III intensive care database shows significant performance gains compared to previously employed methods such as latent topic distributions or generic doc2vec embeddings. These improvements are especially pronounced for the difficult problem of post-discharge mortality prediction.

cs.CL↗

arXiv2016

A Cross-Platform Collection of Social Network Profiles

The proliferation of Internet-enabled devices and services has led to a shifting balance between digital and analogue aspects of our everyday lives. In the face of this development there is a growing demand for the study of privacy hazards, the potential for unique user de-anonymization and information leakage between the various social media profiles many of us maintain. To enable the structured study of such adversarial effects, this paper presents a dedicated dataset of cross-platform social network personas (i.e., the same person has accounts on multiple platforms). The corpus comprises 850 users who generate predominantly English content. Each user object contains the online footprint of the same person in three distinct social networks: Twitter, Instagram and Foursquare. In total, it encompasses over 2.5M tweets, 340k check-ins and 42k Instagram posts. We describe the collection methodology, characteristics of the dataset, and how to obtain it. Finally, we discuss a common use case, cross-platform user identification.

cs.IR↗

arXiv2016

Implicit Negative Feedback in Clinical Information Retrieval

In this paper, we reflect on ways to improve the quality of bio-medical information retrieval by drawing implicit negative feedback from negated information in noisy natural language search queries. We begin by studying the extent to which negations occur in clinical texts and quantify their detrimental effect on retrieval performance. Subsequently, we present a number of query reformulation and ranking approaches that remedy these shortcomings by resolving natural language negations. Our experimental results are based on data collected in the course of the TREC Clinical Decision Support Track and show consistent improvements compared to state-of-the-art methods. Using our novel algorithms, we are able to reduce the negative impact of negations on early precision by up to 65%.

cs.IR↗

arXiv2016

Privacy Leakage through Innocent Content Sharing in Online Social Networks

The increased popularity and ubiquitous availability of online social networks and globalised Internet access have affected the way in which people share content. The information that users willingly disclose on these platforms can be used for various purposes, from building consumer models for advertising, to inferring personal, potentially invasive, information. In this work, we use Twitter, Instagram and Foursquare data to convey the idea that the content shared by users, especially when aggregated across platforms, can potentially disclose more information than was originally intended. We perform two case studies: First, we perform user de-anonymization by mimicking the scenario of finding the identity of a user making anonymous posts within a group of users. Empirical evaluation on a sample of real-world social network profiles suggests that cross-platform aggregation introduces significant performance gains in user identification. In the second task, we show that it is possible to infer physical location visits of a user on the basis of shared Twitter and Instagram content. We present an informativeness scoring function which estimates the relevance and novelty of a shared piece of information with respect to an inference task. This measure is validated using an active learning framework which chooses the most informative content at each given point in time. Based on a large-scale data sample, we show that by doing this, we can attain an improved inference performance. In some cases this performance exceeds even the use of the user's full timeline.

cs.SI↗