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Open-weight bio-foundation models present a dual-use dilemma. While holding great promise for accelerating scientific research and drug development, they could also enable bad actors to develop more deadly bioweapons. To mitigate the risk…
This work introduces the Burdened Bayesian Logistic Regression Model (BBLRM), an enhancement of the Bayesian Logistic Regression Model (BLRM) for dose-finding in phase I oncology trials. The BLRM determines the maximum tolerated dose (MTD)…
Biometrics and biometric-enabled decision support systems (DSS) have become a mandatory part of complex dynamic systems such as security checkpoints, personal health monitoring systems, autonomous robots, and epidemiological surveillance.…
The US Food and Drug Administration launched Project Optimus with the aim of shifting the paradigm of dose-finding and selection towards identifying the optimal biological dose that offers the best balance between benefit and risk, rather…
Software defect detection is a critical task in software engineering. However, no prior studies have specifically addressed defect detection in bioinformatics software. Given that the performance of defect detection tasks is primarily…
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics…
Health policy decisions are often informed by estimates of long-term survival based primarily on short-term data. A range of methods are available to include longer-term information, but there has previously been no comprehensive and…
The main objective of dose finding trials is to find an optimal dose amongst a candidate set for further research. The trial design in oncology proceeds in stages with a decision as to how to treat the next group of patients made at every…
We consider a formal statistical design that allows simultaneous enrollment of a main cohort and a backfill cohort of patients in a dose-finding trial. The goal is to accumulate more information at various doses to facilitate dose…
Deep Learning (DL) components are routinely integrated into software systems that need to perform complex tasks such as image or natural language processing. The adequacy of the test data used to test such systems can be assessed by their…
Context: Mining software repositories is a popular means to gain insights into a software project's evolution, monitor project health, support decisions and derive best practices. Tools supporting the mining process are commonly applied by…
Tools constitute an essential contribution to natural language processing for requirements engineering (NLP4RE) research. They are executable instruments that make research usable and applicable in practice. In this chapter, we first…
Simflowny is an open platform which automatically generates efficient parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support simultaneously a quite…
In this work, we investigate the concept of biometric backdoors: a template poisoning attack on biometric systems that allows adversaries to stealthily and effortlessly impersonate users in the long-term by exploiting the template update…
Clinical trials often seek to determine the superiority, equivalence, or non-inferiority of an experimental condition (e.g., a new drug) compared to a control condition (e.g., a placebo or an already existing drug). The use of frequentist…
BioSimplify is an open source tool written in Java that introduces and facilitates the use of a novel model for sentence simplification tuned for automatic discourse analysis and information extraction (as opposed to sentence simplification…
This work provides documentation for a suite of R functions contained in gonogo.R. The functions provide sensitivity testing practitioners and researchers with an ability to conduct, analyze and simulate various sensitivity experiments…
Intentional threats are a major risk factor related to vulnerabilities in critical infrastructure assets, and an accurate risk assessment is necessary to analyze threats, assess vulnerabilities, and evaluate potential impacts on assets and…
Background: Mathematical models based on ordinary differential equations (ODEs) are essential tools across various scientific disciplines, including biology, ecology, and healthcare informatics. They are used to simulate complex dynamic…
The rising rate of drug-related deaths in the United States, largely driven by fentanyl, requires timely and accurate surveillance. However, critical overdose data are often buried in free-text coroner reports, leading to delays and…