A Search Engine for Discovery of Scientific Challenges and Directions

Keeping track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine. In experiments with 19 researchers and clinicians using our system, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain and to AI papers, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org/

A Search Engine for Discovery of Biomedical Challenges and Directions

The ability to keep track of scientific challenges, advances and emerging directions is a fundamental part of research. However, researchers face a flood of papers that hinders discovery of important knowledge. In biomedicine, this directly impacts human lives. To address this problem, we present a novel task of extraction and search of scientific challenges and directions, to facilitate rapid knowledge discovery. We construct and release an expert-annotated corpus of texts sampled from full-length papers, labeled with novel semantic categories that generalize across many types of challenges and directions. We focus on a large corpus of interdisciplinary work relating to the COVID-19 pandemic, ranging from biomedicine to areas such as AI and economics. We apply a model trained on our data to identify challenges and directions across the corpus and build a dedicated search engine for this information. In studies with researchers, including those working directly on COVID-19, we outperform a popular scientific search engine in assisting knowledge discovery. Finally, we show that models trained on our resource generalize to the wider biomedical domain, highlighting its broad utility. We make our data, model and search engine publicly available. https://challenges.apps.allenai.org

Bridger: Toward Bursting Scientific Filter Bubbles and Boosting Innovation via Novel Author Discovery

Scientific silos can hinder innovation. These information "filter bubbles" and the growing challenge of information overload limit awareness across the literature, making it difficult to keep track of even narrow areas of interest, let alone discover new ones. Algorithmic curation and recommendation, which often prioritize relevance, can further reinforce these bubbles. In response, we describe Bridger, a system for facilitating discovery of scholars and their work, to explore design tradeoffs among relevant and novel recommendations. We construct a faceted representation of authors using information extracted from their papers and inferred personas. We explore approaches both for recommending new content and for displaying it in a manner that helps researchers to understand the work of authors who they are unfamiliar with. In studies with computer science researchers, our approach substantially improves users' abilities to do so. We develop an approach that locates commonalities and contrasts between scientists---retrieving partially similar authors, rather than aiming for strict similarity. We find this approach helps users discover authors useful for generating novel research ideas of relevance to their work, at a higher rate than a state-of-art neural model. Our analysis reveals that Bridger connects authors who have different citation profiles, publish in different venues, and are more distant in social co-authorship networks, raising the prospect of bridging diverse communities and facilitating discovery.

Domain-Specific Pretraining for Vertical Search: Case Study on Biomedical Literature

Information overload is a prevalent challenge in many high-value domains. A prominent case in point is the explosion of the biomedical literature on COVID-19, which swelled to hundreds of thousands of papers in a matter of months. In general, biomedical literature expands by two papers every minute, totalling over a million new papers every year. Search in the biomedical realm, and many other vertical domains is challenging due to the scarcity of direct supervision from click logs. Self-supervised learning has emerged as a promising direction to overcome the annotation bottleneck. We propose a general approach for vertical search based on domain-specific pretraining and present a case study for the biomedical domain. Despite being substantially simpler and not using any relevance labels for training or development, our method performs comparably or better than the best systems in the official TREC-COVID evaluation, a COVID-related biomedical search competition. Using distributed computing in modern cloud infrastructure, our system can scale to tens of millions of articles on PubMed and has been deployed as Microsoft Biomedical Search, a new search experience for biomedical literature: https://aka.ms/biomedsearch.

Platform for Situated Intelligence

We introduce Platform for Situated Intelligence, an open-source framework created to support the rapid development and study of multimodal, integrative-AI systems. The framework provides infrastructure for sensing, fusing, and making inferences from temporal streams of data across different modalities, a set of tools that enable visualization and debugging, and an ecosystem of components that encapsulate a variety of perception and processing technologies. These assets jointly provide the means for rapidly constructing and refining multimodal, integrative-AI systems, while retaining the efficiency and performance characteristics required for deployment in open-world settings.

Formation of Social Ties Influences Food Choice: A Campus-Wide Longitudinal Study

Nutrition is a key determinant of long-term health, and social influence has long been theorized to be a key determinant of nutrition. It has been difficult to quantify the postulated role of social influence on nutrition using traditional methods such as surveys, due to the typically small scale and short duration of studies. To overcome these limitations, we leverage a novel source of data: logs of 38 million food purchases made over an 8-year period on the Ecole Polytechnique Federale de Lausanne (EPFL) university campus, linked to anonymized individuals via the smartcards used to make on-campus purchases. In a longitudinal observational study, we ask: How is a person's food choice affected by eating with someone else whose own food choice is healthy vs. unhealthy? To estimate causal effects from the passively observed log data, we control confounds in a matched quasi-experimental design: we identify focal users who at first do not have any regular eating partners but then start eating with a fixed partner regularly, and we match focal users into comparison pairs such that paired users are nearly identical with respect to covariates measured before acquiring the partner, where the two focal users' new eating partners diverge in the healthiness of their respective food choice. A difference-in-differences analysis of the paired data yields clear evidence of social influence: focal users acquiring a healthy-eating partner change their habits significantly more toward healthy foods than focal users acquiring an unhealthy-eating partner. We further identify foods whose purchase frequency is impacted significantly by the eating partner's healthiness of food choice. Beyond the main results, the work demonstrates the utility of passively sensed food purchase logs for deriving insights, with the potential of informing the design of public health interventions and food offerings.

Understanding Failures of Deep Networks via Robust Feature Extraction

Traditional evaluation metrics for learned models that report aggregate scores over a test set are insufficient for surfacing important and informative patterns of failure over features and instances. We introduce and study a method aimed at characterizing and explaining failures by identifying visual attributes whose presence or absence results in poor performance. In distinction to previous work that relies upon crowdsourced labels for visual attributes, we leverage the representation of a separate robust model to extract interpretable features and then harness these features to identify failure modes. We further propose a visualization method to enable humans to understand the semantic meaning encoded in such features and test the comprehensibility of the features. An evaluation of the methods on the ImageNet dataset demonstrates that: (i) the proposed workflow is effective for discovering important failure modes, (ii) the visualization techniques help humans to understand the extracted features, and (iii) the extracted insights can assist engineers with error analysis and debugging.

Extracting a Knowledge Base of Mechanisms from COVID-19 Papers

The urgency of mitigating COVID-19 has spawned a large and diverse body of scientific literature that is challenging for researchers to navigate. This explosion of information has stimulated interest in automated tools to help identify useful knowledge. We have pursued the use of methods for extracting diverse forms of mechanism relations from the natural language of scientific papers. We seek to identify concepts in COVID-19 and related literature which represent activities, functions, associations and causal relations, ranging from cellular processes to economic impacts. We formulate a broad, coarse-grained schema targeting mechanism relations between open, free-form entities. Our approach strikes a balance between expressivity and breadth that supports generalization across diverse concepts. We curate a dataset of scientific papers annotated according to our novel schema. Using an information extraction model trained on this new corpus, we construct a knowledge base (KB) of 2M mechanism relations, which we make publicly available. Our model is able to extract relations at an F1 at least twice that of baselines such as open IE or related scientific IE systems. We conduct experiments examining the ability of our system to retrieve relevant information on viral mechanisms of action, and on applications of AI to COVID-19 research. In both cases, our system identifies relevant information from our automatically-constructed knowledge base with high precision.

An Empirical Analysis of Backward Compatibility in Machine Learning Systems

In many applications of machine learning (ML), updates are performed with the goal of enhancing model performance. However, current practices for updating models rely solely on isolated, aggregate performance analyses, overlooking important dependencies, expectations, and needs in real-world deployments. We consider how updates, intended to improve ML models, can introduce new errors that can significantly affect downstream systems and users. For example, updates in models used in cloud-based classification services, such as image recognition, can cause unexpected erroneous behavior in systems that make calls to the services. Prior work has shown the importance of "backward compatibility" for maintaining human trust. We study challenges with backward compatibility across different ML architectures and datasets, focusing on common settings including data shifts with structured noise and ML employed in inferential pipelines. Our results show that (i) compatibility issues arise even without data shift due to optimization stochasticity, (ii) training on large-scale noisy datasets often results in significant decreases in backward compatibility even when model accuracy increases, and (iii) distributions of incompatible points align with noise bias, motivating the need for compatibility aware de-noising and robustness methods.

SciSight: Combining faceted navigation and research group detection for COVID-19 exploratory scientific search

The COVID-19 pandemic has sparked unprecedented mobilization of scientists, already generating thousands of new papers that join a litany of previous biomedical work in related areas. This deluge of information makes it hard for researchers to keep track of their own research area, let alone explore new directions. Standard search engines are designed primarily for targeted search and are not geared for discovery or making connections that are not obvious from reading individual papers. In this paper, we present our ongoing work on SciSight, a novel framework for exploratory search of COVID-19 research. Based on formative interviews with scientists and a review of existing tools, we build and integrate two key capabilities: first, exploring interactions between biomedical facets (e.g., proteins, genes, drugs, diseases, patient characteristics); and second, discovering groups of researchers and how they are connected. We extract entities using a language model pre-trained on several biomedical information extraction tasks, and enrich them with data from the Microsoft Academic Graph (MAG). To find research groups automatically, we use hierarchical clustering with overlap to allow authors, as they do, to belong to multiple groups. Finally, we introduce a novel presentation of these groups based on both topical and social affinities, allowing users to drill down from groups to papers to associations between entities, and update query suggestions on the fly with the goal of facilitating exploratory navigation. SciSight has thus far served over 10K users with over 30K page views and 13% returning users. Preliminary user interviews with biomedical researchers suggest that SciSight complements current approaches and helps find new and relevant knowledge.