Results from the centers for disease control and prevention's predict the 2013-2014 Influenza Season Challenge.

BACKGROUND: Early insights into the timing of the start, peak, and intensity of the influenza season could be useful in planning influenza prevention and control activities. To encourage development and innovation in influenza forecasting, the Centers for Disease Control and Prevention (CDC) organized a challenge to predict the 2013-14 Unites States influenza season. METHODS: Challenge contestants were asked to forecast the start, peak, and intensity of the 2013-2014 influenza season at the national level and at any or all Health and Human Services (HHS) region level(s). The challenge ran from December 1, 2013-March 27, 2014; contestants were required to submit 9 biweekly forecasts at the national level to be eligible. The selection of the winner was based on expert evaluation of the methodology used to make the prediction and the accuracy of the prediction as judged against the U.S. Outpatient Influenza-like Illness Surveillance Network (ILINet). RESULTS: Nine teams submitted 13 forecasts for all required milestones. The first forecast was due on December 2, 2013; 3/13 forecasts received correctly predicted the start of the influenza season within one week, 1/13 predicted the peak within 1 week, 3/13 predicted the peak ILINet percentage within 1 %, and 4/13 predicted the season duration within 1 week. For the prediction due on December 19, 2013, the number of forecasts that correctly forecasted the peak week increased to 2/13, the peak percentage to 6/13, and the duration of the season to 6/13. As the season progressed, the forecasts became more stable and were closer to the season milestones. CONCLUSION: Forecasting has become technically feasible, but further efforts are needed to improve forecast accuracy so that policy makers can reliably use these predictions. CDC and challenge contestants plan to build upon the methods developed during this contest to improve the accuracy of influenza forecasts.

Agnostic Visual Recommendation Systems: Open Challenges and Future Directions.

Visualization Recommendation Systems (VRSs) are a novel and challenging field of study aiming to help generate insightful visualizations from data and support non-expert users in information discovery. Among the many contributions proposed in this area, some systems embrace the ambitious objective of imitating human analysts to identify relevant relationships in data and make appropriate design choices to represent these relationships with insightful charts. We denote these systems as "agnostic" VRSs since they do not rely on human-provided constraints and rules but try to learn the task autonomously. Despite the high application potential of agnostic VRSs, their progress is hindered by several obstacles, including the absence of standardized datasets to train recommendation algorithms, the difficulty of learning design rules, and defining quantitative criteria for evaluating the perceptual effectiveness of generated plots. This paper summarizes the literature on agnostic VRSs and outlines promising future research directions.

A self-supervised algorithm to detect signs of social isolation in the elderly from daily activity sequences.

Considering the increasing aging of the population, multi-device monitoring of the activities of daily living (ADL) of older people becomes crucial to support independent living and early detection of symptoms of mental illnesses, such as depression and Alzheimer's disease. Anomalies can anticipate the diagnosis of these pathologies in the patient's normal behavior, such as reduced hygiene, changes in sleep habits, and fewer social interactions. These abnormalities are often subtle and hard to detect. Especially using non-intrusive monitoring devices might cause anomaly detectors to generate false alarms or ignore relevant clues. This limitation may hinder their usage by caregivers. Furthermore, the notion of abnormality here is context and patient-dependent, thus requiring untrained approaches. To reduce these problems, we propose a self-supervised model for multi-sensor time series signals based on Hyperbolic uncertainty for Anomaly Detection, which we dub HypAD. HypAD estimates uncertainty end-to-end, thanks to hyperbolic neural networks, and integrates it into the "classic" notion of reconstruction loss in anomaly detection. Based on hyperbolic uncertainty, HypAD introduces the principle of a detectable anomaly. HypAD assesses whether it is sure about the input signal and fails to reconstruct it because it is anomalous or whether the high reconstruction loss is due to the model uncertainty, e.g., a complex but regular signal (cf. this parallels the residual model error upon training). The proposed solution has been incorporated into an end-to-end ADL monitoring system for elderly patients in retirement homes, developed within a funded project leveraging an interdisciplinary consortium of computer scientists, engineers, and geriatricians. Healthcare professionals were involved in the design and verification process to foster trust in the system. In addition, the system has been equipped with explainability features.

Assessment of community efforts to advance network-based prediction of protein-protein interactions.

Comprehensive understanding of the human protein-protein interaction (PPI) network, aka the human interactome, can provide important insights into the molecular mechanisms of complex biological processes and diseases. Despite the remarkable experimental efforts undertaken to date to determine the structure of the human interactome, many PPIs remain unmapped. Computational approaches, especially network-based methods, can facilitate the identification of previously uncharacterized PPIs. Many such methods have been proposed. Yet, a systematic evaluation of existing network-based methods in predicting PPIs is still lacking. Here, we report community efforts initiated by the International Network Medicine Consortium to benchmark the ability of 26 representative network-based methods to predict PPIs across six different interactomes of four different organisms: A. thaliana, C. elegans, S. cerevisiae, and H. sapiens. Through extensive computational and experimental validations, we found that advanced similarity-based methods, which leverage the underlying network characteristics of PPIs, show superior performance over other general link prediction methods in the interactomes we considered.

A Network-Based Analysis of Disease Modules From a Taxonomic Perspective.

OBJECTIVE: Human-curated diseaseontologies are widely used for diagnostic evaluation, treatment and data comparisons over time, and clinical decision support. The classification principles underlying these ontologies are guided by the analysis of observable pathological similarities between disorders, often based on anatomical or histological principles. Although, thanks to recent advances in molecular biology, disease ontologies are slowly changing to integrate the etiological and genetic origins of diseases, nosology still reflects this "reductionist" perspective. Proximity relationships of disease modules (hereafter DMs) in the human interactome network are now increasingly used in diagnostics, to identify pathobiologically similar diseases and to support drug repurposing and discovery. On the other hand, similarity relations induced from structural proximity of DMs also have several limitations, such as incomplete knowledge of disease-gene relationships and reliability of clinical trials to assess their validity. The purpose of the study described in this paper is to shed more light on disease similarities by analyzing the relationship between categorical proximity of diseases in human-curated ontologies and structural proximity of the related DMs in the interactome. METHOD: We propose a method (and related algorithms) to automatically induce a hierarchical structure from proximity relations between DMs, and to compare this structure with a human-curated disease taxonomy. RESULTS: We demonstrate that the proposed method allows to systematically analyze commonalities and differences among structural and categorical similarity of human diseases, help refine and extend human disease classification systems, and identify promising network areas where new disease-gene interactions can be discovered.

Integrating categorical and structural proximity in Disease Ontologies.

The purpose of the study described in this paper is to shed more light on disease similarities by analyzing the relationship between categorical proximity of diseases in human-curated ontologies and structural proximity of the related disease module (DM) in the interactome. We propose a methodology (and related algorithms) to automatically induce a hierarchical structure from proximity relations between DMs, and to compare this structure with a human-curated disease taxonomy.Clinical relevance- Disease ontologies are extensively used for diagnostic evaluation and clinical decision support but still reflect the clinical reductionist perspective. We demonstrate that the proposed network-based methodology allows us to analyze commonalities and differences among structural and categorical similarity of human diseases, help refine human disease classification systems, and identify promising network areas where new disease-gene interactions can be discovered.

The social phenotype: Extracting a patient-centered perspective of diabetes from health-related blogs.

MOTIVATIONS: It has recently been argued [1] that the effectiveness of a cure depends on the doctor-patient shared understanding of an illness and its treatment. Although a better communication between doctor and patient can be pursued through dedicated training programs, or by collecting patients' experiences and symptoms by means of questionnaires, the impact of these actions is limited by time and resources. In this paper we suggest that a patient-centered view of a disease - as well as potential misalignment between patient and doctor focuses - can be inferred at a larger scale through automated textual analysis of health-related forums. People are generating an enormous amount of social data to describe their health care experiences, and continuously search information about diseases, symptoms, diagnoses, doctors, treatment options and medicines. By automatically collecting, analyzing and exploiting this information, it is possible to obtain a more detailed and nuanced vision of patients' experience, that we call the "social phenotype" of diseases. MATERIALS AND METHODS: As a use-case for our analysis, we consider diabetes, a widespread disease in most industrialized countries. We create a high quality data sample of diabetic patients' messages in Italy, extracted from popular medical forums during more than 10 years. Next, we use a state-of-the-art topic extraction technique based on generative statistical models improved with word embeddings, to identify the main complications, the frequently reported symptoms and the common concerns of these patients. Finally, in order to detect differences in focus, we compare the results of our analysis with available quality of life (QoL) assessments obtained with standard methodologies, such as questionnaires and survey studies. RESULTS: We show that patients with diabetes, when accessing on-line forums, express a perception of their disease in a way that might be noticeably different from what is inferred from published QoL assessments on diabetes. In our study, we found that issues reported to have a daily impact on these patients are diet, glycemic control, drugs and clinical tests. These problems are not commonly considered in QoL assessments, since they are not perceived by doctors as representing severe limitations. Although limited to the case of Italian diabetic patients, we suggest that the methodology described in this paper, which is language and disease agnostic, could be applied to other diseases and countries, since misalignment between doctor and patients, and the importance of collecting unbiased patient perceptions, has been emphasized in many studies ([2,3]inter alia). Extracting the social phenotype of a disease might help acquiring patient-centered information on health care experiences on a much wider scale.

Structural semantic interconnections: a knowledge-based approach to word sense disambiguation.

Word Sense Disambiguation (WSD) is traditionally considered an Al-hard problem. A break-through in this field would have a significant impact on many relevant Web-based applications, such as Web information retrieval, improved access to Web services, information extraction, etc. Early approaches to WSD, based on knowledge representation techniques, have been replaced in the past few years by more robust machine learning and statistical techniques. The results of recent comparative evaluations of WSD systems, however, show that these methods have inherent limitations. On the other hand, the increasing availability of large-scale, rich lexical knowledge resources seems to provide new challenges to knowledge-based approaches. In this paper, we present a method, called structural semantic interconnections (SSI), which creates structural specifications of the possible senses for each word in a context and selects the best hypothesis according to a grammar G, describing relations between sense specifications. Sense specifications are created from several available lexical resources that we integrated in part manually, in part with the help of automatic procedures. The SSI algorithm has been applied to different semantic disambiguation problems, like automatic ontology population, disambiguation of sentences in generic texts, disambiguation of words in glossary definitions. Evaluation experiments have been performed on specific knowledge domains (e.g., tourism, computer networks, enterprise interoperability), as well as on standard disambiguation test sets.

Can Twitter Be a Source of Information on Allergy? Correlation of Pollen Counts with Tweets Reporting Symptoms of Allergic Rhinoconjunctivitis and Names of Antihistamine Drugs.

Pollen forecasts are in use everywhere to inform therapeutic decisions for patients with allergic rhinoconjunctivitis (ARC). We exploited data derived from Twitter in order to identify tweets reporting a combination of symptoms consistent with a case definition of ARC and those reporting the name of an antihistamine drug. In order to increase the sensitivity of the system, we applied an algorithm aimed at automatically identifying jargon expressions related to medical terms. We compared weekly Twitter trends with National Allergy Bureau weekly pollen counts derived from US stations, and found a high correlation of the sum of the total pollen counts from each stations with tweets reporting ARC symptoms (Pearson's correlation coefficient: 0.95) and with tweets reporting antihistamine drug names (Pearson's correlation coefficient: 0.93). Longitude and latitude of the pollen stations affected the strength of the correlation. Twitter and other social networks may play a role in allergic disease surveillance and in signaling drug consumptions trends.

Twitter mining for fine-grained syndromic surveillance.

BACKGROUND: Digital traces left on the Internet by web users, if properly aggregated and analyzed, can represent a huge information dataset able to inform syndromic surveillance systems in real time with data collected directly from individuals. Since people use everyday language rather than medical jargon (e.g. runny nose vs. respiratory distress), knowledge of patients' terminology is essential for the mining of health related conversations on social networks. OBJECTIVES: In this paper we present a methodology for early detection and analysis of epidemics based on mining Twitter messages. In order to reliably trace messages of patients that actually complain of a disease, first, we learn a model of naïve medical language, second, we adopt a symptom-driven, rather than disease-driven, keyword analysis. This approach represents a major innovation compared to previous published work in the field. METHOD: We first developed an algorithm to automatically learn a variety of expressions that people use to describe their health conditions, thus improving our ability to detect health-related "concepts" expressed in non-medical terms and, in the end, producing a larger body of evidence. We then implemented a Twitter monitoring instrument to finely analyze the presence and combinations of symptoms in tweets. RESULTS: We first evaluate the algorithm's performance on an available dataset of diverse medical condition synonyms, then, we assess its utility in a case study of five common syndromes for surveillance purposes. We show that, by exploiting physicians' knowledge on symptoms positively or negatively related to a given disease, as well as the correspondence between patients' "naïve" terminology and medical jargon, not only can we analyze large volumes of Twitter messages related to that disease, but we can also mine micro-blogs with complex queries, performing fine-grained tweets classification (e.g. those reporting influenza-like illness (ILI) symptoms vs. common cold or allergy). CONCLUSIONS: Our approach yields a very high level of correlation with flu trends derived from traditional surveillance systems. Compared with Google Flu, another popular tool based on query search volumes, our method is more flexible and less sensitive to changes in web search behaviors.

Influenza-like illness surveillance on Twitter through automated learning of naïve language.

Twitter has the potential to be a timely and cost-effective source of data for syndromic surveillance. When speaking of an illness, Twitter users often report a combination of symptoms, rather than a suspected or final diagnosis, using naïve, everyday language. We developed a minimally trained algorithm that exploits the abundance of health-related web pages to identify all jargon expressions related to a specific technical term. We then translated an influenza case definition into a Boolean query, each symptom being described by a technical term and all related jargon expressions, as identified by the algorithm. Subsequently, we monitored all tweets that reported a combination of symptoms satisfying the case definition query. In order to geolocalize messages, we defined 3 localization strategies based on codes associated with each tweet. We found a high correlation coefficient between the trend of our influenza-positive tweets and ILI trends identified by US traditional surveillance systems.