Combining anchoring with financial incentives to increase physical activity: a randomized controlled trial among college students.

The purpose of this study was to: (1) compare the relative efficacy of different combinations of three behavioral intervention strategies (i.e., personalized reminders, financial incentives, and anchoring) for establishing physical activity habits using an mHealth app and (2) to examine the effects of these different combined interventions on intrinsic motivation for physical activity and daily walking habit strength. A four-arm randomized controlled trial was conducted in a sample of college students (N = 161) who had a self-reported personal wellness goal of increasing their physical activity. Receiving cue-contingent financial incentives (i.e., incentives conditional on performing physical activity within ± one hour of a prespecified physical activity cue) combined with anchoring resulted in the highest daily step counts and greatest odds of temporally consistent walking during both the four-week intervention and the full eight-week study period. Cue-contingent financial incentives were also more successful at increasing physical activity and maintaining these effects post-intervention than traditional non-cue-contingent incentives. There were no differences in intrinsic motivation or habit strength between study groups at any time point. Financial incentives, particularly cue-contingent incentives, can be effectively used to support the anchoring intervention strategy for establishing physical activity habits. Moreover, mHealth apps are a feasible method for delivering the combined intervention technique of financial incentives with anchoring.

Entity linking for biomedical literature.

BACKGROUND: The Entity Linking (EL) task links entity mentions from an unstructured document to entities in a knowledge base. Although this problem is well-studied in news and social media, this problem has not received much attention in the life science domain. One outcome of tackling the EL problem in the life sciences domain is to enable scientists to build computational models of biological processes with more efficiency. However, simply applying a news-trained entity linker produces inadequate results. METHODS: Since existing supervised approaches require a large amount of manually-labeled training data, which is currently unavailable for the life science domain, we propose a novel unsupervised collective inference approach to link entities from unstructured full texts of biomedical literature to 300 ontologies. The approach leverages the rich semantic information and structures in ontologies for similarity computation and entity ranking. RESULTS: Without using any manual annotation, our approach significantly outperforms state-of-the-art supervised EL method (9% absolute gain in linking accuracy). Furthermore, the state-of-the-art supervised EL method requires 15,000 manually annotated entity mentions for training. These promising results establish a benchmark for the EL task in the life science domain. We also provide in depth analysis and discussion on both challenges and opportunities on automatic knowledge enrichment for scientific literature. CONCLUSIONS: In this paper, we propose a novel unsupervised collective inference approach to address the EL problem in a new domain. We show that our unsupervised approach is able to outperform a current state-of-the-art supervised approach that has been trained with a large amount of manually labeled data. Life science presents an underrepresented domain for applying EL techniques. By providing a small benchmark data set and identifying opportunities, we hope to stimulate discussions across natural language processing and bioinformatics and motivate others to develop techniques for this largely untapped domain.

Accurate clinical toxicity prediction using multi-task deep neural nets and contrastive molecular explanations.

Explainable machine learning for molecular toxicity prediction is a promising approach for efficient drug development and chemical safety. A predictive ML model of toxicity can reduce experimental cost and time while mitigating ethical concerns by significantly reducing animal and clinical testing. Herein, we use a deep learning framework for simultaneously modeling in vitro, in vivo, and clinical toxicity data. Two different molecular input representations are used; Morgan fingerprints and pre-trained SMILES embeddings. A multi-task deep learning model accurately predicts toxicity for all endpoints, including clinical, as indicated by the area under the Receiver Operator Characteristic curve and balanced accuracy. In particular, pre-trained molecular SMILES embeddings as input to the multi-task model improved clinical toxicity predictions compared to existing models in MoleculeNet benchmark. Additionally, our multitask approach is comprehensive in the sense that it is comparable to state-of-the-art approaches for specific endpoints in in vitro, in vivo and clinical platforms. Through both the multi-task model and transfer learning, we were able to indicate the minimal need of in vivo data for clinical toxicity predictions. To provide confidence and explain the model's predictions, we adapt a post-hoc contrastive explanation method that returns pertinent positive and negative features, which correspond well to known mutagenic and reactive toxicophores, such as unsubstituted bonded heteroatoms, aromatic amines, and Michael receptors. Furthermore, toxicophore recovery by pertinent feature analysis captures more of the in vitro (53%) and in vivo (56%), rather than of the clinical (8%), endpoints, and indeed uncovers a preference in known toxicophore data towards in vitro and in vivo experimental data. To our knowledge, this is the first contrastive explanation, using both present and absent substructures, for predictions of clinical and in vivo molecular toxicity.

Semantically enabling clinical decision support recommendations.

BACKGROUND: Clinical decision support systems have been widely deployed to guide healthcare decisions on patient diagnosis, treatment choices, and patient management through evidence-based recommendations. These recommendations are typically derived from clinical practice guidelines created by clinical specialties or healthcare organizations. Although there have been many different technical approaches to encoding guideline recommendations into decision support systems, much of the previous work has not focused on enabling system generated recommendations through the formalization of changes in a guideline, the provenance of a recommendation, and applicability of the evidence. Prior work indicates that healthcare providers may not find that guideline-derived recommendations always meet their needs for reasons such as lack of relevance, transparency, time pressure, and applicability to their clinical practice. RESULTS: We introduce several semantic techniques that model diseases based on clinical practice guidelines, provenance of the guidelines, and the study cohorts they are based on to enhance the capabilities of clinical decision support systems. We have explored ways to enable clinical decision support systems with semantic technologies that can represent and link to details in related items from the scientific literature and quickly adapt to changing information from the guidelines, identifying gaps, and supporting personalized explanations. Previous semantics-driven clinical decision systems have limited support in all these aspects, and we present the ontologies and semantic web based software tools in three distinct areas that are unified using a standard set of ontologies and a custom-built knowledge graph framework: (i) guideline modeling to characterize diseases, (ii) guideline provenance to attach evidence to treatment decisions from authoritative sources, and (iii) study cohort modeling to identify relevant research publications for complicated patients. CONCLUSIONS: We have enhanced existing, evidence-based knowledge by developing ontologies and software that enables clinicians to conveniently access updates to and provenance of guidelines, as well as gather additional information from research studies applicable to their patients' unique circumstances. Our software solutions leverage many well-used existing biomedical ontologies and build upon decades of knowledge representation and reasoning work, leading to explainable results.

A Response to Núñez et al.'s (2019) "What Happened to Cognitive Science?"

Núñez et al.'s (2019) negative assessment of the field of cognitive science derives from evaluation criteria that fail to reflect the true nature of the field. In reality, the field is thriving on both the research and educational fronts, and it shows great promise for the future.

Liberal Entity Extraction: Rapid Construction of Fine-Grained Entity Typing Systems.

The ability of automatically recognizing and typing entities in natural language without prior knowledge (e.g., predefined entity types) is a major challenge in processing such data. Most existing entity typing systems are limited to certain domains, genres, and languages. In this article, we propose a novel unsupervised entity-typing framework by combining symbolic and distributional semantics. We start from learning three types of representations for each entity mention: general semantic representation, specific context representation, and knowledge representation based on knowledge bases. Then we develop a novel joint hierarchical clustering and linking algorithm to type all mentions using these representations. This framework does not rely on any annotated data, predefined typing schema, or handcrafted features; therefore, it can be quickly adapted to a new domain, genre, and/or language. Experiments on genres (news and discussion forum) show comparable performance with state-of-the-art supervised typing systems trained from a large amount of labeled data. Results on various languages (English, Chinese, Japanese, Hausa, and Yoruba) and domains (general and biomedical) demonstrate the portability of our framework.

Understanding Emergency Department 72-Hour Revisits Among Medicaid Patients Using Electronic Healthcare Records.

Electronic Healthcare Records (EHRs) have the potential to improve healthcare quality and to decrease costs by providing quality metrics, discovering actionable insights, and supporting decision-making to improve future outcomes. Within the United States Medicaid Program, rates of recidivism among emergency department (ED) patients serve as metrics of hospital performance that help ensure efficient and effective treatment within the ED. We analyze ED Medicaid patient data from 1,149,738 EHRs provided by a hospital over a 2-year period to understand the characteristics of the ED return visits within a 72-hour time frame. Frequent flyer patients with multiple revisits account for 47% of Medicaid patient revisits over this period. ED encounters by frequent flyer patients with prior 72-hour revisits in the last 6 months are thrice more likely to result in a readmit than those of infrequent patients. Statistical L1-logistic regression and random forest analyses reveal distinct patterns of ED usage and patient diagnoses between frequent and infrequent patient encounters, suggesting distinct opportunities for interventions to improve efficacy of care and streamline ED workflow. This work forms a foundation for future development of predictive models, which could flag patients at high risk of revisiting.

Data Integration for Heterogenous Datasets.

More and more, the needs of data analysts are requiring the use of data outside the control of their own organizations. The increasing amount of data available on the Web, the new technologies for linking data across datasets, and the increasing need to integrate structured and unstructured data are all driving this trend. In this article, we provide a technical overview of the emerging "broad data" area, in which the variety of heterogeneous data being used, rather than the scale of the data being analyzed, is the limiting factor in data analysis efforts. The article explores some of the emerging themes in data discovery, data integration, linked data, and the combination of structured and unstructured data.

Changing the equation on scientific data visualization.

An essential facet of the data deluge is the need for different types of users to apply visualizations to understand how data analyses and queries relate to each other. Unfortunately, visualization too often becomes an end product of scientific analysis, rather than an exploration tool that scientists can use throughout the research life cycle. However, new database technologies, coupled with emerging Web-based technologies, may hold the key to lowering the cost of visualization generation and allow it to become a more integral part of the scientific process.