Identifying symptom etiologies using syntactic patterns and large language models.

Differential diagnosis is a crucial aspect of medical practice, as it guides clinicians to accurate diagnoses and effective treatment plans. Traditional resources, such as medical books and services like UpToDate, are constrained by manual curation, potentially missing out on novel or less common findings. This paper introduces and analyzes two novel methods to mine etiologies from scientific literature.

Extending the boundaries of cancer therapeutic complexity with literature text mining.

Drug combination therapy is a main pillar of cancer therapy. As the number of possible drug candidates for combinations grows, the development of optimal high complexity combination therapies (involving 4 or more drugs per treatment) such as RCHOP-I and FOLFIRINOX becomes increasingly challenging due to combinatorial explosion. In this paper, we propose a text mining (TM) based tool and workflow for rapid generation of high complexity combination treatments (HCCT) in order to extend the boundaries of complexity in cancer treatments.

From centralized to ad-hoc knowledge base construction for hypotheses generation.

Objective: To demonstrate and develop an approach enabling individual researchers or small teams to create their own ad-hoc, lightweight knowledge bases tailored for specialized scientific interests, using text-mining over scientific literature, and demonstrate the effectiveness of these knowledge bases in hypothesis generation and literature-based discovery (LBD).

Methods: We propose a lightweight process using an extractive search framework to create ad-hoc knowledge bases, which require minimal training and no background in bio-curation or computer science. These knowledge bases are particularly effective for LBD and hypothesis generation using Swanson's ABC method.

Using topic models to identify clients' functioning levels and alliance ruptures in psychotherapy.

Computerized natural language processing techniques can analyze psychotherapy sessions as texts, thus generating information about the therapy process and outcome and supporting the scaling-up of psychotherapy research. We used topic modeling to identify topics discussed in psychotherapy sessions and explored (a) which topics best identified clients' functioning and alliance ruptures and (b) whether changes in these topics were associated with changes in outcome. Transcripts of 873 sessions from 58 clients treated by 52 therapists were analyzed.

Using computerized text analysis to examine associations between linguistic features and clients' distress during psychotherapy.

Raw linguistic data within psychotherapy sessions may provide important information about clients' progress and well-being. In the current study, computerized text analytic techniques were applied to examine whether linguistic features were associated with clients' experiences of distress within and between clients and whether changes in linguistic features were associated with changes in treatment outcome. Transcripts of 729 psychotherapy sessions from 58 clients treated by 52 therapists were analyzed.

Mining fall-related information in clinical notes: Comparison of rule-based and novel word embedding-based machine learning approaches.

Background: Natural language processing (NLP) of health-related data is still an expertise demanding, and resource expensive process. We created a novel, open source rapid clinical text mining system called NimbleMiner. NimbleMiner combines several machine learning techniques (word embedding models and positive only labels learning) to facilitate the process in which a human rapidly performs text mining of clinical narratives, while being aided by the machine learning components.

Rich parameterization improves RNA structure prediction.

Current approaches to RNA structure prediction range from physics-based methods, which rely on thousands of experimentally measured thermodynamic parameters, to machine-learning (ML) techniques. While the methods for parameter estimation are successfully shifting toward ML-based approaches, the model parameterizations so far remained fairly constant. We study the potential contribution of increasing the amount of information utilized by RNA folding prediction models to the improvement of their prediction quality.