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Tumor documentation in Germany is largely done manually, requiring reading patient records and entering data into structured databases. Large language models (LLMs) could potentially enhance this process by improving efficiency and…
Motivation: Modeling biological signaling networks using ordinary differential equations (ODEs) has proven to be a powerful technique for generating insight into cellular dynamics, but it typically requires estimating rate parameters based…
The Statistical Toolkit is an open source system specialized in the statistical comparison of distributions. It addresses requirements common to different experimental domains, such as simulation validation (e.g. comparison of experimental…
The American Statistical Association Biopharmaceutical Section (ASA BIOP) scientific working group on real-world evidence (RWE) has been making continuous, extended efforts towards a goal of supporting and advancing regulatory science with…
For agentic systems to use external tools to solve complex, long-horizon tasks, we need a large set of diverse and controllable tool-use environments. We introduce SynthTools, a fully LLM-based pipeline spanning the entire lifecycle:…
As machine learning has become increasingly popular over the last few decades, so too has the number of machine learning interfaces for implementing these models. Whilst many R libraries exist for machine learning, very few offer extended…
Today, tool-calling agents are commonly evaluated or tested on static datasets of execution traces, including input commands, agent responses, and associated tool calls. However, internal production datasets are often insufficient or…
Many scientific-software projects test their codes inadequately, or not at all. Despite its well-known benefits, adopting routine testing is often not easy. Development teams may have doubts about establishing effective test procedures,…
Successful biomedical relation extraction can provide evidence to researchers and clinicians about possible unknown associations between biomedical entities, advancing the current knowledge we have about those entities and their inherent…
Machine learning (ML) applications become increasingly common in many domains. ML systems to execute these workloads include numerical computing frameworks and libraries, ML algorithm libraries, and specialized systems for deep neural…
Bulk_extractor is a high-performance digital forensics tool written in C++. Between 2018 and 2022 we updated the program from C++98 to C++17, performed a complete code refactoring, and adopted a unit test framework. The new version…
The process of identifying and characterizing B-cell epitopes, which are the portions of antigens recognized by antibodies, is important for our understanding of the immune system, and for many applications including vaccine development,…
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
In recent years, researchers have explored component-based synthesis, which aims to automatically construct programs that operate by composing calls to existing APIs. However, prior work has not considered efficient synthesis of methods…
AI systems, in particular with deep learning techniques, have demonstrated superior performance for various real-world applications. Given the need for tailored optimization in specific scenarios, as well as the concerns related to the…
The initiation of dose optimization has driven a paradigm shift in oncology clinical trials to determine the optimal biological dose (OBD). Early-phase trials with randomized doses can facilitate additional investigation of the identified…
In this work, we propose a new computing process, named DeepBEVdose, which is essentially distinct to the previous deep learning-based dose calculation methods.We present a novel image-domain dose calculation algorithm to automatically…
RecBole has recently attracted increasing attention from the research community. As the increase of the number of users, we have received a number of suggestions and update requests. This motivates us to make some significant improvements…
Estimating the effect of treatments from natural experiments, where treatments are pre-assigned, is an important and well-studied problem. We introduce a novel natural experiment dataset obtained from an early childhood literacy nonprofit.…
First released in 2010, the Rivet library forms an important repository for analysis code, facilitating comparisons between measurements of the final state in particle collisions and theoretical calculations of those final states. We give…