Pratip Rana

Protiva Das, Sovon Chakraborty, Sidhant Narula et al.

The rapid advancement of Large Language Models (LLMs) in biological research has significantly lowered the barrier to accessing complex bioinformatics knowledge, ex perimental design strategies, and analytical workflows. While these capabilities accelerate innovation, they also introduce serious dual-use risks, as Bio-LLMs can be exploited to generate harmful biological insights under the guise of legitimate research queries. Existing safeguards, such as static prompt filtering and policy-based restrictions, are insufficient when LLMs are embedded within dynamic biological workflows and application-layer systems. In this paper, we present BioShield, a context-aware application-level firewall designed to secure Bio LLMs against dual-use attacks. At the core of BioShield is a domain-specific prompt scanner that performs contextual risk analysis of incoming queries. The scanner leverages a harmful scoring mechanism tailored to biological dual-use threat cat egories to identify prompts that attempt to conceal malicious intent within seemingly benign research requests. Queries ex ceeding a predefined risk threshold are blocked before reaching the model, effectively preventing unsafe knowledge generation at the source. In addition to pre-generation protection, BioShield deploys a post-generation output verification module that inspects model responses for actionable or weaponizable biological content. If an unsafe response is detected, the system triggers controlled regeneration under strengthened safety constraints. By combining contextual prompt scanning with response-level validation, BioShield provides a layered defense framework specifically designed for bio-domain LLM deployments. Our framework advances cyberbiosecurity by formalizing dual-use threat detection in Bio-LLMs and proposing a structured mitigation strategy for secure, responsible AI driven biological research.

Ross Gore, Eranga Bandara, Sachin Shetty et al.

Mild Traumatic Brain Injury (TBI) detection presents significant challenges due to the subtle and often ambiguous presentation of symptoms in medical imaging, making accurate diagnosis a complex task. To address these challenges, we propose Proof-of-TBI, a medical diagnosis support system that integrates multiple fine-tuned vision-language models with the OpenAI-o3 reasoning large language model (LLM). Our approach fine-tunes multiple vision-language models using a labeled dataset of TBI MRI scans, training them to diagnose TBI symptoms effectively. The predictions from these models are aggregated through a consensus-based decision-making process. The system evaluates the predictions from all fine-tuned vision language models using the OpenAI-o3 reasoning LLM, a model that has demonstrated remarkable reasoning performance, to produce the most accurate final diagnosis. The LLM Agents orchestrates interactions between the vision-language models and the reasoning LLM, managing the final decision-making process with transparency, reliability, and automation. This end-to-end decision-making workflow combines the vision-language model consortium with the OpenAI-o3 reasoning LLM, enabled by custom prompt engineering by the LLM agents. The prototype for the proposed platform was developed in collaboration with the U.S. Army Medical Research team in Newport News, Virginia, incorporating five fine-tuned vision-language models. The results demonstrate the transformative potential of combining fine-tuned vision-language model inputs with the OpenAI-o3 reasoning LLM to create a robust, secure, and highly accurate diagnostic system for mild TBI prediction. To the best of our knowledge, this research represents the first application of fine-tuned vision-language models integrated with a reasoning LLM for TBI prediction tasks.

Kusal Debnath, Pratip Rana, Preetam Ghosh

Drug-target affinity (DTA) prediction is a critical aspect of drug discovery. The meaningful representation of drugs and targets is crucial for accurate prediction. Using 1D string-based representations for drugs and targets is a common approach that has demonstrated good results in drug-target affinity prediction. However, these approach lacks information on the relative position of the atoms and bonds. To address this limitation, graph-based representations have been used to some extent. However, solely considering the structural aspect of drugs and targets may be insufficient for accurate DTA prediction. Integrating the functional aspect of these drugs at the genetic level can enhance the prediction capability of the models. To fill this gap, we propose GramSeq-DTA, which integrates chemical perturbation information with the structural information of drugs and targets. We applied a Grammar Variational Autoencoder (GVAE) for drug feature extraction and utilized two different approaches for protein feature extraction: Convolutional Neural Network (CNN) and Recurrent Neural Network (RNN). The chemical perturbation data is obtained from the L1000 project, which provides information on the upregulation and downregulation of genes caused by selected drugs. This chemical perturbation information is processed, and a compact dataset is prepared, serving as the functional feature set of the drugs. By integrating the drug, gene, and target features in the model, our approach outperforms the current state-of-the-art DTA prediction models when validated on widely used DTA datasets (BindingDB, Davis, and KIBA). This work provides a novel and practical approach to DTA prediction by merging the structural and functional aspects of biological entities, and it encourages further research in multi-modal DTA prediction.

Abhishek Phadke, Shakib Mahmud Dipto, Pratip Rana

This paper presents a simulation workflow for generating synthetic LiDAR datasets to support autonomous vehicle perception, robotics research, and sensor security analysis. Leveraging the CoppeliaSim simulation environment and its Python API, we integrate time-of-flight LiDAR, image sensors, and two dimensional scanners onto a simulated vehicle platform operating within an urban scenario. The workflow automates data capture, storage, and annotation across multiple formats (PCD, PLY, CSV), producing synchronized multimodal datasets with ground truth pose information. We validate the pipeline by generating large-scale point clouds and corresponding RGB and depth imagery. The study examines potential security vulnerabilities in LiDAR data, such as adversarial point injection and spoofing attacks, and demonstrates how synthetic datasets can facilitate the evaluation of defense strategies. Finally, limitations related to environmental realism, sensor noise modeling, and computational scalability are discussed, and future research directions, such as incorporating weather effects, real-world terrain models, and advanced scanner configurations, are proposed. The workflow provides a versatile, reproducible framework for generating high-fidelity synthetic LiDAR datasets to advance perception research and strengthen sensor security in autonomous systems. Documentation and examples accompany this framework; samples of animated cloud returns and image sensor data can be found at this Link.