arXiv subjects

Angelos Angelopoulos

Publications and source records attributed to Angelos Angelopoulos.

8 recordsLinked to original sources

arXiv2026

A Modular Agentic Framework for Synthetically Constrained Multi-Objective Hit-to-Lead Optimization

Hit-to-lead optimization requires iterative design of hit analogs across competing potency, selectivity, physicochemical, pharmacokinetic, safety, and synthetic constraints. We present SABLE (Synthetically-accessible Agentic Bayesian Ligand Exploration), an open-source framework that employs natural-language orchestration to guide chemical structure optimization. SABLE uses an LLM to interpret user-defined goals and route tasks, while specialized tools perform reaction-templated analog enumeration, physicochemical and ADMET property prediction, structure-based affinity scoring, and Bayesian optimization. The resulting workflow is a computational twin of the analytical and prioritization stages of the design-make-test-analyze cycle, providing provenance of each numerical output. Across single, and multi-objective optimization studies, SABLE enriches candidate sets for user-defined computational objectives while evaluating only a subset of the enumerated search space. Its modular architecture allows tools and characterization backends to be replaced by editing a simple config file, without modifying operational logic. SABLE provides an extensible decision-support framework for prioritizing synthetically constrained analogs in early-stage drug discovery.

cs.AI↗

arXiv2026

From Prompts to Protocols: An AI Agent for Laboratory Automation

Automating science laboratories enables faster, safer, more accurate, and more reproducible execution of protocols, accelerating the discovery and testing of new materials, drugs, and more. However, setting up and running autonomous labs requires coordinating numerous instruments and robots, forcing scientists to write code, manage configuration files, and navigate complex software infrastructure. We present an AI agent architecture that integrates large language models with laboratory orchestration, enabling scientists to interactively create and monitor automated lab protocols using natural language. Integrated into the Experiment Orchestration System (EOS), the AI agent operates under an agentic loop with automated validation and error correction, and supports the complete experimental lifecycle: creating protocols, running and monitoring both protocols and closed-loop optimization campaigns, and analyzing results. A visual graph editor renders protocols as interactive node-based diagrams synchronized with the AI agent's protocol representation, enabling seamless alternation between AI-assisted and manual protocol construction. Evaluated on three simulated automated labs spanning chemistry, biology, and materials science, the AI agent achieves a 97% first-attempt protocol generation success rate and an order of magnitude reduction in required interface actions.

cs.AI↗

arXiv2025

3-Dimensional Adaptive Unstructured Tessellated Look-up Tables for the Approximation of Compton Form Factors

We describe an iterative algorithm to construct an unstructured tessellation of simplices (irregular tetrahedra in 3-dimensions) to approximate an arbitrary function to a desired precision by interpolation. The method is applied to the generation of Compton Form Factors for simulation and analysis of nuclear femtography, as enabled by high energy exclusive processes such as electron-proton scattering producing just an electron, proton, and gamma-ray in the final state. While producing tessellations with only a 1% mean interpolation error, our results show that the use of such tessellations can significantly decrease the computation time for Monte Carlo event generation by $\sim23$ times for $10^{7}$ events (and using extrapolation, by $\sim955$ times for $10^{10}$ events).

math.NA↗

arXiv2024

PD-Insighter: A Visual Analytics System to Monitor Daily Actions for Parkinson's Disease Treatment

People with Parkinson's Disease (PD) can slow the progression of their symptoms with physical therapy. However, clinicians lack insight into patients' motor function during daily life, preventing them from tailoring treatment protocols to patient needs. This paper introduces PD-Insighter, a system for comprehensive analysis of a person's daily movements for clinical review and decision-making. PD-Insighter provides an overview dashboard for discovering motor patterns and identifying critical deficits during activities of daily living and an immersive replay for closely studying the patient's body movements with environmental context. Developed using an iterative design study methodology in consultation with clinicians, we found that PD-Insighter's ability to aggregate and display data with respect to time, actions, and local environment enabled clinicians to assess a person's overall functioning during daily life outside the clinic. PD-Insighter's design offers future guidance for generalized multiperspective body motion analytics, which may significantly improve clinical decision-making and slow the functional decline of PD and other medical conditions.

cs.HC↗

arXiv2023

Advancing Intra-operative Precision: Dynamic Data-Driven Non-Rigid Registration for Enhanced Brain Tumor Resection in Image-Guided Neurosurgery

During neurosurgery, medical images of the brain are used to locate tumors and critical structures, but brain tissue shifts make pre-operative images unreliable for accurate removal of tumors. Intra-operative imaging can track these deformations but is not a substitute for pre-operative data. To address this, we use Dynamic Data-Driven Non-Rigid Registration (NRR), a complex and time-consuming image processing operation that adjusts the pre-operative image data to account for intra-operative brain shift. Our review explores a specific NRR method for registering brain MRI during image-guided neurosurgery and examines various strategies for improving the accuracy and speed of the NRR method. We demonstrate that our implementation enables NRR results to be delivered within clinical time constraints while leveraging Distributed Computing and Machine Learning to enhance registration accuracy by identifying optimal parameters for the NRR method. Additionally, we highlight challenges associated with its use in the operating room.

eess.IV↗

arXiv2022

CLAS12 Track Reconstruction with Artificial Intelligence

In this article we describe the implementation of Artificial Intelligence models in track reconstruction software for the CLAS12 detector at Jefferson Lab. The Artificial Intelligence based approach resulted in improved track reconstruction efficiency in high luminosity experimental conditions. The track reconstruction efficiency increased by $10-12\%$ for single particle, and statistics in multi-particle physics reactions increased by $15\%-35\%$ depending on the number of particles in the reaction. The implementation of artificial intelligence in the workflow also resulted in a speedup of the tracking by $35\%$.

physics.data-an↗

arXiv2022

Convolutional Auto-Encoders for Drift Chamber data de-noising for CLAS12

In this article, we present the results of using Convolutional Auto-Encoders for de-noising raw data for CLAS12 drift chambers. The de-noising neural network provides increased efficiency in track reconstruction and also improved performance for high luminosity experimental data collection. The de-noising neural network used in conjunction with the previously developed track classifier neural network \cite{Gavalian:2022hfa} lead to a significant track reconstruction efficiency increase for current luminosity ($0.6\times10^{35}~cm^{-2}~sec^{-1}$ ). The increase in experimentally measured quantities will allow running experiments at twice the luminosity with the same track reconstruction efficiency. This will lead to huge savings in accelerator operational costs, and large savings for Jefferson Lab and collaborating institutions.

physics.ins-det↗

arXiv2022

Using Machine Learning for Particle Track Identification in the CLAS12 Detector

Particle track reconstruction is the most computationally intensive process in nuclear physics experiments. Traditional algorithms use a combinatorial approach that exhaustively tests track measurements ("hits") to identify those that form an actual particle trajectory. In this article, we describe the development of four machine learning (ML) models that assist the tracking algorithm by identifying valid track candidates from the measurements in drift chambers. Several types of machine learning models were tested, including: Convolutional Neural Networks (CNN), Multi-Layer Perceptrons (MLP), Extremely Randomized Trees (ERT) and Recurrent Neural Networks (RNN). As a result of this work, an MLP network classifier was implemented as part of the CLAS12 reconstruction software to provide the tracking code with recommended track candidates. The resulting software achieved accuracy of greater than 99\% and resulted in an end-to-end speedup of 35\% compared to existing algorithms.

cs.CV↗