Automatic text filtering using limited supervision learning for epidemic intelligence

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Smartphone picture organization: a hierarchical approach

We live in a society where the large majority of the population has a camera-equipped smartphone. In addition, hard drives and cloud storage are getting cheaper and cheaper, leading to a tremendous growth in stored personal photos. Unlike photo collections captured by a digital camera, which typically are pre-processed by the user who organizes them into event-related folders, smartphone pictures are automatically stored in the cloud. As a consequence, photo collections captured by a smartphone are highly unstructured and because smartphones are ubiquitous, they present a larger variability compared to pictures captured by a digital camera. To solve the need of organizing large smartphone photo collections automatically, we propose here a new methodology for hierarchical photo organization into topics and topic-related categories. Our approach successfully estimates latent topics in the pictures by applying probabilistic Latent Semantic Analysis, and automatically assigns a name to each topic by relying on a lexical database. Topic-related categories are then estimated by using a set of topic-specific Convolutional Neuronal Networks. To validate our approach, we ensemble and make public a large dataset of more than 8,000 smartphone pictures from 40 persons. Experimental results demonstrate major user satisfaction with respect to state of the art solutions in terms of organization.Peer ReviewedPreprin

Beyond Frontal Faces: Improving Person Recognition Using Multiple Cues

We explore the task of recognizing peoples' identities in photo albums in an unconstrained setting. To facilitate this, we introduce the new People In Photo Albums (PIPA) dataset, consisting of over 60000 instances of 2000 individuals collected from public Flickr photo albums. With only about half of the person images containing a frontal face, the recognition task is very challenging due to the large variations in pose, clothing, camera viewpoint, image resolution and illumination. We propose the Pose Invariant PErson Recognition (PIPER) method, which accumulates the cues of poselet-level person recognizers trained by deep convolutional networks to discount for the pose variations, combined with a face recognizer and a global recognizer. Experiments on three different settings confirm that in our unconstrained setup PIPER significantly improves on the performance of DeepFace, which is one of the best face recognizers as measured on the LFW dataset

Optimizing text mining methods for improving biomedical natural language processing

The overwhelming amount and the increasing rate of publication in the biomedical domain make it difficult for life sciences researchers to acquire and maintain all information that is necessary for their research. Pubmed (the primary citation database for the biomedical literature) currently contains over 21 million article abstracts and more than one million of them were published in 2020 alone. Even though existing article databases provide capable keyword search services, typical everyday-life queries usually return thousands of relevant articles. For instance, a cancer research scientist may need to acquire a complete list of genes that interact with BRCA1 (breast cancer 1) gene. The PubMed keyword search for BRCA1 returns over 16,500 article abstracts, making manual inspection of the retrieved documents impractical. Missing even one of the interacting gene partners in this scenario may jeopardize successful development of a potential new drug or vaccine. Although manually curated databases of biomolecular interactions exist, they are usually not up-to-date and they require notable human effort to maintain. To summarize, new discoveries are constantly being shared within the community via scientific publishing, but unfortunately the probability of missing vital information for research in life sciences is increasing. In response to this problem, the biomedical natural language processing (BioNLP) community of researchers has emerged and strives to assist life sciences researchers by building modern language processing and text mining tools that can be applied at large-scale and scan the whole publicly available literature and extract, classify, and aggregate the information found within, thus keeping life sciences researchers always up-to-date with the recent relevant discoveries and facilitating their research in numerous fields such as molecular biology, biomedical engineering, bioinformatics, genetics engineering and biochemistry. My research has almost exclusively focused on biomedical relation and event extraction tasks. These foundational information extraction tasks deal with automatic detection of biological processes, interactions and relations described in the biomedical literature. Precisely speaking, biomedical relation and event extraction systems can scan through a vast amount of biomedical texts and automatically detect and extract the semantic relations of biomedical named entities (e.g. genes, proteins, chemical compounds, and diseases). The structured outputs of such systems (i.e., the extracted relations or events) can be stored as relational databases or molecular interaction networks which can easily be queried, filtered, analyzed, visualized and integrated with other structured data sources. Extracting biomolecular interactions has always been the primary interest of BioNLP researcher because having knowledge about such interactions is crucially important in various research areas including precision medicine, drug discovery, drug repurposing, hypothesis generation, construction and curation of signaling pathways, and protein function and structure prediction. State-of-the-art relation and event extraction methods are based on supervised machine learning, requiring manually annotated data for training. Manual annotation for the biomedical domain requires domain expertise and it is time-consuming. Hence, having minimal training data for building information extraction systems is a common case in the biomedical domain. This demands development of methods that can make the most out of available training data and this thesis gathers all my research efforts and contributions in that direction. It is worth mentioning that biomedical natural language processing has undergone a revolution since I started my research in this field almost ten years ago. As a member of the BioNLP community, I have witnessed the emergence, improvement– and in some cases, the disappearance–of many methods, each pushing the performance of the best previous method one step further. I can broadly divide the last ten years into three periods. Once I started my research, feature-based methods that relied on heavy feature engineering were dominant and popular. Then, significant advancements in the hardware technology, as well as several breakthroughs in the algorithms and methods enabled machine learning practitioners to seriously utilize artificial neural networks for real-world applications. In this period, convolutional, recurrent, and attention-based neural network models became dominant and superior. Finally, the introduction of transformer-based language representation models such as BERT and GPT impacted the field and resulted in unprecedented performance improvements on many data sets. When reading this thesis, I demand the reader to take into account the course of history and judge the methods and results based on what could have been done in that particular period of the history

Data Scarcity in Event Analysis and Abusive Language Detection

Lack of data is almost always the cause of the suboptimal performance of neural networks. Even though data scarce scenarios can be simulated for any task by assuming limited access to training data, we study two problem areas where data scarcity is a practical challenge: event analysis and abusive content detection} Journalists, social scientists and political scientists need to retrieve and analyze event mentions in unstructured text to compute useful statistical information to understand society. We claim that it is hard to specify information need about events using keyword-based representation and propose a Query by Example (QBE) setting for event retrieval. In the QBE setting, we assume that there are a few example sentences mentioning the event class a user is interested in and we aim to retrieve relevant events using only the examples as a query. Traditional event detection approaches are not applicable in this setting as event detection datasets are constructed based on pre-defined schemas which limits them to a small set of event and event-argument types. Moreover, the amount of annotated data in event detection datasets is limited that only allows us to build a retrieval corpus for evaluation. Thus we assume that there are no relevance judgments to train an event retrieval model -- except for the few examples of a specific event type. We create three QBE evaluation settings from three event detection datasets: PoliceKilling, ACE, and IndiaPoliceEvents. For the PoliceKilling dataset, where a relevant sentence describes a police killing event, we show that a query model constructed from the NLP features extracted from the few given examples is effective compared to event detection baselines. For the ACE dataset, where there are thirty-three types of events, we construct a QBE setting for each type and show that a sentence embedding approach effectively transfers for event matching. Finally, we conducted a unified evaluation of all three datasets using the sentence-embedding-based model and showed that it outperforms strong baselines. We further examine the effect of data scarcity in abusive language detection. We first study a specific type of abusive language -- hate speech. Neural hate speech detection models trained from one dataset poorly generalize to another dataset from a different domain. This is because characteristics of hate speech vary based on racial and cultural aspects. Our data scarcity scenario assumes that we have a hate speech dataset from a domain and it needs to generalize to a test set from another domain using the unlabeled data from the test domain only. Thus we assume zero target domain data in this scenario. To tackle the data scarcity, we propose an unsupervised domain adaptation approach to augment labeled data for hate speech detection. We evaluate the approach with three different models (character CNNs, BiLSTMs, and BERT) on three different collections. We show our approach improves Area under the Precision/Recall curve by as much as 42% and recall by as much as 278%, with no loss (and in some cases a significant gain) in precision. Finally, we examine the cross-lingual abusive language detection problem. Abusive language is a superclass of hate speech that includes profanity, aggression, offensiveness, cyberbullying, toxicity, and hate speech itself. There is a large collection of abusive language detection datasets in English such as Jigsaw. For other languages there exist datasets for abusive language detection but with very limited data. We propose a cross-lingual transfer learning approach to learn an effective neural abusive language classifier for such low-resource languages with help from a dataset from a resource-rich language. The framework is based on a nearest-neighbor architecture and is thus interpretable by design. It is a modern instantiation of the classic k-nearest neighbor model, as we use transformer representations in all its components. Unlike prior work on neighborhood-based approaches, we encode the neighborhood information based on query-neighbor interactions. We propose two encoding schemes and show their effectiveness using both qualitative and quantitative analyses. Our evaluation results on eight languages from two different datasets for abusive language detection show sizable improvements in F1 over strong baselines

Towards the extraction of cross-sentence relations through event extraction and entity coreference

Cross-sentence relation extraction deals with the extraction of relations beyond the sentence boundary. This thesis focuses on two of the NLP tasks which are of importance to the successful extraction of cross-sentence relation mentions: event extraction and coreference resolution. The first part of the thesis focuses on addressing data sparsity issues in event extraction. We propose a self-training approach for obtaining additional labeled examples for the task. The process starts off with a Bi-LSTM event tagger trained on a small labeled data set which is used to discover new event instances in a large collection of unstructured text. The high confidence model predictions are selected to construct a data set of automatically-labeled training examples. We present several ways in which the resulting data set can be used for re-training the event tagger in conjunction with the initial labeled data. The best configuration achieves statistically significant improvement over the baseline on the ACE 2005 test set (macro-F1), as well as in a 10-fold cross validation (micro- and macro-F1) evaluation. Our error analysis reveals that the augmentation approach is especially beneficial for the classification of the most under-represented event types in the original data set. The second part of the thesis focuses on the problem of coreference resolution. While a certain level of precision can be reached by modeling surface information about entity mentions, their successful resolution often depends on semantic or world knowledge. This thesis investigates an unsupervised source of such knowledge, namely distributed word representations. We present several ways in which word embeddings can be utilized to extract features for a supervised coreference resolver. Our evaluation results and error analysis show that each of these features helps improve over the baseline coreference system’s performance, with a statistically significant improvement (CoNLL F1) achieved when the proposed features are used jointly. Moreover, all features lead to a reduction in the amount of precision errors in resolving references between common nouns, demonstrating that they successfully incorporate semantic information into the process

Combining brain-computer interfaces and assistive technologies: state-of-the-art and challenges

In recent years, new research has brought the field of EEG-based Brain-Computer Interfacing (BCI) out of its infancy and into a phase of relative maturity through many demonstrated prototypes such as brain-controlled wheelchairs, keyboards, and computer games. With this proof-of-concept phase in the past, the time is now ripe to focus on the development of practical BCI technologies that can be brought out of the lab and into real-world applications. In particular, we focus on the prospect of improving the lives of countless disabled individuals through a combination of BCI technology with existing assistive technologies (AT). In pursuit of more practical BCIs for use outside of the lab, in this paper, we identify four application areas where disabled individuals could greatly benefit from advancements in BCI technology, namely,“Communication and Control”, “Motor Substitution”, “Entertainment”, and “Motor Recovery”. We review the current state of the art and possible future developments, while discussing the main research issues in these four areas. In particular, we expect the most progress in the development of technologies such as hybrid BCI architectures, user-machine adaptation algorithms, the exploitation of users’ mental states for BCI reliability and confidence measures, the incorporation of principles in human-computer interaction (HCI) to improve BCI usability, and the development of novel BCI technology including better EEG devices

Large-Scale Pattern-Based Information Extraction from the World Wide Web

Extracting information from text is the task of obtaining structured, machine-processable facts from information that is mentioned in an unstructured manner. It thus allows systems to automatically aggregate information for further analysis, efficient retrieval, automatic validation, or appropriate visualization. This work explores the potential of using textual patterns for Information Extraction from the World Wide Web