25 April 2025 in Journal of Radiological Protection
Colossus is designed to meet a growing need for survival analysis software capable of analyzing tens of millions of rows of radiation epidemiological data. Colossus is an R package devised to offer scalable survival analysis for the Million Person Study. The total and relative rate equations available in Colossus are outlined in this article, which are used in conjunction with Cox proportional hazards, Poisson, and Fine-Grey regression models. Following a comparison with existing software, validation with epidemiological cohort data is described. Exposure data and specific causes of death among workers at Los Alamos National Laboratory and U.S. nuclear power plants were analyzed by Colossus and 32-bit Epicure and compared with published results. Colossus results agreed with the results of existing software and previous publications.
1 July 2014 in Environmental Modelling & Software
As the volume of collected data continues to increase in the environmental sciences, so too does the need for effective means for accessing those data. We have developed an Open Modeling Interface (OpenMI) data component that retrieves input data for model components from environmental information systems and delivers output data to those systems. The adoption of standards for both model component input–output interfaces and web services make it possible for the component to be reconfigured for use with different linked models and various online systems. The data component employs three techniques tailored to the unique design of the OpenMI that enable efficient operation: caching, prefetching, and buffering, making it capable of scaling to large numbers of simultaneous simulations executing on a computational grid. We present the design of the component, an evaluation of its performance, and a case study demonstrating how it can be incorporated into modeling studies
1 June 2026 in Neurocomputing
Accurate identification of animal behaviors is fundamental to behavioral neuroscience, yet manual annotation remains a major bottleneck due to its subjectivity, limited scalability, and high labor cost. This work presents a unified deep learning and heuristic-based framework for automated behavior classification in the Novel Object Recognition Test (NORT), a widely used paradigm for assessing memory and cognitive function in rodents. We fine-tuned a YOLOv11 Pose model to detect nose and tail-base keypoints specific to Long-Evans rats, and used these keypoints to derive spatial heuristics for identifying NORT behaviors. In parallel, we trained YOLOv11 classification models to predict Standing, Object Interaction, and Other behaviors from individual frames, using datasets containing either 2-object or 5-object videos, as well as a combined dataset containing both 2-object and 5-object videos. Our model trained on the combined dataset, enhanced with heuristic-based post-processing to identify the specific objects that the rat is interacting with, achieved the best overall accuracy and generalization across arenas, outperforming heuristic-only and subset-specific 2-object or 5-object models. Detailed confusion matrices and error analyses reveal that most errors occur near behavioral transitions, reflecting the inherent ambiguity of manual labels at frame-level. The proposed framework enables scalable, reproducible, and objective annotation of NORT videos and provides a foundation for future extensions toward temporally-aware behavioral analysis. All the code and model weights, together with sample NORT videos, will be made publicly available to support future rodent behavior recognition research.