Objective: Identifying study-eligible patients within clinical databases is a critical step in clinical research. However, accurate query design typically requires extensive technical and biomedical expertise. We sought to create a system capable of generating data model-agnostic queries while also providing novel logical reasoning capabilities for complex clinical trial eligibility criteria. Materials and Methods: The task of query creation from eligibility criteria requires solving several text-processing problems, including named entity recognition and relation extraction, sequence-to-sequence transformation, normalization, and reasoning. We incorporated hybrid deep learning and rule-based modules for these, as well as a knowledge base of the Unified Medical Language System (UMLS) and linked ontologies. To enable data-model agnostic query creation, we introduce a novel method for tagging database schema elements using UMLS concepts. To evaluate our system, called LeafAI, we compared the capability of LeafAI to a human database programmer to identify patients who had been enrolled in 8 clinical trials conducted at our institution. We measured performance by the number of actual enrolled patients matched by generated queries. Results: LeafAI matched a mean 43% of enrolled patients with 27,225 eligible across 8 clinical trials, compared to 27% matched and 14,587 eligible in queries by a human database programmer. The human programmer spent 26 total hours crafting queries compared to several minutes by LeafAI. Conclusions: Our work contributes a state-of-the-art data model-agnostic query generation system capable of conditional reasoning using a knowledge base. We demonstrate that LeafAI can rival an experienced human programmer in finding patients eligible for clinical trials.

As models are trained and deployed, developers need to be able to systematically debug errors that emerge in the machine learning pipeline. We present MDB, a debugging framework for interactively querying datasets and models. MDB integrates functional programming with relational algebra to build expressive queries over a database of datasets and model predictions. Queries are reusable and easily modified, enabling debuggers to rapidly iterate and refine queries to discover and characterize errors and model behaviors. We evaluate MDB on object detection, bias discovery, image classification, and data imputation tasks across self-driving videos, large language models, and medical records. Our experiments show that MDB enables up to 10x faster and 40\% shorter queries than other baselines. In a user study, we find developers can successfully construct complex queries that describe errors of machine learning models.

To address the issue of rising software maintenance cost due to program comprehension challenges, we propose SMARTKT (Smart Knowledge Transfer), a search framework, which extracts and integrates knowledge related to various aspects of an application in form of a semantic graph. This graph supports syntax and semantic queries and converts the process of program comprehension into a {\em google-like} search problem.

Knowledge graphs (KGs) are inherently incomplete because of incomplete world knowledge and bias in what is the input to the KG. Additionally, world knowledge constantly expands and evolves, making existing facts deprecated or introducing new ones. However, we would still want to be able to answer queries as if the graph were complete. In this chapter, we will give an overview of several methods which have been proposed to answer queries in such a setting. We will first provide an overview of the different query types which can be supported by these methods and datasets typically used for evaluation, as well as an insight into their limitations. Then, we give an overview of the different approaches and describe them in terms of expressiveness, supported graph types, and inference capabilities.

Although deep learning techniques have shown significant achievements, they frequently depend on extensive amounts of hand-labeled data and tend to perform inadequately in few-shot scenarios. The objective of this study is to devise a strategy that can improve the model's capability to recognize biomedical entities in scenarios of few-shot learning. By redefining biomedical named entity recognition (BioNER) as a machine reading comprehension (MRC) problem, we propose a demonstration-based learning method to address few-shot BioNER, which involves constructing appropriate task demonstrations. In assessing our proposed method, we compared the proposed method with existing advanced methods using six benchmark datasets, including BC4CHEMD, BC5CDR-Chemical, BC5CDR-Disease, NCBI-Disease, BC2GM, and JNLPBA. We examined the models' efficacy by reporting F1 scores from both the 25-shot and 50-shot learning experiments. In 25-shot learning, we observed 1.1% improvements in the average F1 scores compared to the baseline method, reaching 61.7%, 84.1%, 69.1%, 70.1%, 50.6%, and 59.9% on six datasets, respectively. In 50-shot learning, we further improved the average F1 scores by 1.0% compared to the baseline method, reaching 73.1%, 86.8%, 76.1%, 75.6%, 61.7%, and 65.4%, respectively. We reported that in the realm of few-shot learning BioNER, MRC-based language models are much more proficient in recognizing biomedical entities compared to the sequence labeling approach. Furthermore, our MRC-language models can compete successfully with fully-supervised learning methodologies that rely heavily on the availability of abundant annotated data. These results highlight possible pathways for future advancements in few-shot BioNER methodologies.

Information retrieval (IR) or knowledge retrieval, is a critical component for many down-stream tasks such as open-domain question answering (QA). It is also very challenging, as it requires succinctness, completeness, and correctness. In recent works, dense retrieval models have achieved state-of-the-art (SOTA) performance on in-domain IR and QA benchmarks by representing queries and knowledge passages with dense vectors and learning the lexical and semantic similarity. However, using single dense vectors and end-to-end supervision are not always optimal because queries may require attention to multiple aspects and event implicit knowledge. In this work, we propose an information retrieval pipeline that uses entity/event linking model and query decomposition model to focus more accurately on different information units of the query. We show that, while being more interpretable and reliable, our proposed pipeline significantly improves passage coverages and denotation accuracies across five IR and QA benchmarks. It will be the go-to system to use for applications that need to perform IR on a new domain without much dedicated effort, because of its superior interpretability and cross-domain performance.

The large amount of time clinicians spend sifting through patient notes and documenting in electronic health records (EHRs) is a leading cause of clinician burnout. By proactively and dynamically retrieving relevant notes during the documentation process, we can reduce the effort required to find relevant patient history. In this work, we conceptualize the use of EHR audit logs for machine learning as a source of supervision of note relevance in a specific clinical context, at a particular point in time. Our evaluation focuses on the dynamic retrieval in the emergency department, a high acuity setting with unique patterns of information retrieval and note writing. We show that our methods can achieve an AUC of 0.963 for predicting which notes will be read in an individual note writing session. We additionally conduct a user study with several clinicians and find that our framework can help clinicians retrieve relevant information more efficiently. Demonstrating that our framework and methods can perform well in this demanding setting is a promising proof of concept that they will translate to other clinical settings and data modalities (e.g., labs, medications, imaging).

Knowledge from diverse application domains is organized as knowledge graphs (KGs) that are stored in RDF engines accessible in the web via SPARQL endpoints. Expressing a well-formed SPARQL query requires information about the graph structure and the exact URIs of its components, which is impractical for the average user. Question answering (QA) systems assist by translating natural language questions to SPARQL. Existing QA systems are typically based on application-specific human-curated rules, or require prior information, expensive pre-processing and model adaptation for each targeted KG. Therefore, they are hard to generalize to a broad set of applications and KGs. In this paper, we propose KGQAn, a universal QA system that does not need to be tailored to each target KG. Instead of curated rules, KGQAn introduces a novel formalization of question understanding as a text generation problem to convert a question into an intermediate abstract representation via a neural sequence-to-sequence model. We also develop a just-in-time linker that maps at query time the abstract representation to a SPARQL query for a specific KG, using only the publicly accessible APIs and the existing indices of the RDF store, without requiring any pre-processing. Our experiments with several real KGs demonstrate that KGQAn is easily deployed and outperforms by a large margin the state-of-the-art in terms of quality of answers and processing time, especially for arbitrary KGs, unseen during the training.

Search query variation poses a challenge in e-commerce search, as equivalent search intents can be expressed through different queries with surface-level differences. This paper introduces a framework to recognize and leverage query equivalence to enhance searcher and business outcomes. The proposed approach addresses three key problems: mapping queries to vector representations of search intent, identifying nearest neighbor queries expressing equivalent or similar intent, and optimizing for user or business objectives. The framework utilizes both surface similarity and behavioral similarity to determine query equivalence. Surface similarity involves canonicalizing queries based on word inflection, word order, compounding, and noise words. Behavioral similarity leverages historical search behavior to generate vector representations of query intent. An offline process is used to train a sentence similarity model, while an online nearest neighbor approach supports processing of unseen queries. Experimental evaluations demonstrate the effectiveness of the proposed approach, outperforming popular sentence transformer models and achieving a Pearson correlation of 0.85 for query similarity. The results highlight the potential of leveraging historical behavior data and training models to recognize and utilize query equivalence in e-commerce search, leading to improved user experiences and business outcomes. Further advancements and benchmark datasets are encouraged to facilitate the development of solutions for this critical problem in the e-commerce domain.

One of the most intriguing debates regarding a novel task is the development of search engines and recommendation-based systems in the music industry. Studies have shown a drastic depression in the search engine fields, due to concerning factors such as speed, accuracy and the format of data given for querying. Often people face difficulty in searching for a song solely based on the title, hence a solution is proposed to complete a search analysis through a single query input and is matched with the lyrics of the songs present in the database. Hence it is essential to incorporate cutting-edge technology tools for developing a user-friendly search engine. Jina AI is an MLOps framework for building neural search engines that are utilized, in order for the user to obtain accurate results. Jina AI effectively helps to maintain and enhance the quality of performance for the search engine for the query given. An effective search engine and a recommendation system for the music industry, built with JinaAI.