MOTIVATION: Integrating Large Language Models (LLMs) with research tools presents technical and reproducibility challenges for biomedical research. While commercial artificial intelligence (AI) systems are easy to adopt, they obscure data provenance, lack transparency, and can generates false information, making them unfit for many research problems. To address these challenges, we developed the Bioinformatics Retrieval Augmented Digital (BRAD) agent software system. RESULTS: Here, we introduce BRAD, an agentic system that integrates LLMs with external tools and data to streamline research workflows. BRAD's modular agents retrieve information from literature, custom software, and online databases while maintaining transparent protocols to increase the reliability of AI generated results. We apply BRAD to a biomarker discovery pipeline, automating both execution and the generation of enrichment reports. This workflow contextualizes user data within the literature, enabling a level of interpretation and automation that surpasses conventional research tools. Beyond the workflow we highlight here, BRAD is a flexible system that has been deployed in other applications including a chatbot, video RAG, and analysis of single cell data. AVAILABILITY AND IMPLEMENTATION: The source code for BRAD is available at https://github.com/Jpickard1/BRAD; Information for pip installation, tutorials, documentation, and further information can be found at: ReadTheDocs.

This paper describes an efficient reverse-mode differentiation algorithm for contraction operations for arbitrary and unconventional tensor network topologies. The approach leverages the tensor contraction tree of Evenbly and Pfeifer (2014), which provides an instruction set for the contraction sequence of a network. We show that this tree can be efficiently leveraged for differentiation of a full tensor network contraction using a recursive scheme that exploits (1) the bilinear property of contraction and (2) the property that trees have a single path from root to leaves. While differentiation of tensor-tensor contraction is already possible in most automatic differentiation packages, we show that exploiting these two additional properties in the specific context of contraction sequences can improve efficiency. Following a description of the algorithm and computational complexity analysis, we investigate its utility for gradient-based supervised learning for low-rank function recovery and for fitting real-world unstructured datasets. We demonstrate improved performance over alternating least-squares optimization approaches and the capability to handle heterogeneous and arbitrary tensor network formats. When compared to alternating minimization algorithms, we find that the gradient-based approach requires a smaller oversampling ratio (number of samples compared to number model parameters) for recovery. This increased efficiency extends to fitting unstructured data of varying dimensionality and when employing a variety of tensor network formats. Here, we show improved learning using the hierarchical Tucker method over the tensor-train in high-dimensional settings on a number of benchmark problems.

We explore an approach to behavioral cloning in video games. We are motivated to pursue a learning architecture that is data efficient and provides opportunity for interpreting player strategies and replicating player actions in unseen situations. To this end, we have developed a generative model that learns latent features of a game that can be used for training an action predictor. Specifically, our architecture combines a Variational Autoencoder with a discriminator mapping the latent space to action predictions (predictor). We compare our model performance to two different behavior cloning architectures: a discriminative model (a Convolutional Neural Network) mapping game states directly to actions, and a Variational Autoencoder with a predictor trained separately. Finally, we demonstrate how we can use the advantage of generative modeling to sample new states from the latent space of the Variational Autoencoder to analyze player actions and provide meaning to certain latent features.

The development of fast, agile micro Unmanned Aerial Vehicles (UAVs) has been limited by (i) on-board computing hardware restrictions, (ii) the lack of sophisticated vision-based perception and vision-in-the-loop control algorithms, and (iii) the absence of development environments where such systems and algorithms can be rapidly and easily designed, implemented, and validated. Here, we first present a new micro UAV platform that integrates high-rate cameras, inertial sensors, and an NVIDIA Jetson Tegra X1 system-on-chip compute module that boasts 256 GPU cores. The UAV mechanics and electronics were designed and built in house, and are described in detail. Second, we present a novel “virtual reality” development environment, in which photorealistically-rendered synthetic on-board camera images are generated in real time while the UAV is in flight. This development environment allows us to rapidly prototype computing and sensing hardware as well as perception and control algorithms, using real physics, real interoceptive sensor data (e.g., from the on-board inertial measurement unit), and synthetic exteroceptive sensor data (e.g., from synthetic cameras). Third, we demonstrate repeated agile maneuvering with closed-loop vision-based perception and control algorithms, which we have developed using this environment.