Nirajan Acharya

Sagar Bhetwal, Rajan Bastakoti, Nirajan Acharya et al.

Biopharmaceutical manufacturing organizations operate under regulatory frameworks such as FDA guidance, EU Good Manufacturing Practice (GMP), and the EU AI Act, which can restrict the use of cloud-based artificial intelligence systems. Locally deployed large language models (LLMs) offer a privacy-preserving alternative, but their suitability for pharmaceutical manufacturing tasks remains underexplored. This study evaluates four open-source LLMs (Qwen 2.5 Coder 7B, Llama 3.1 8B, Mistral 7B, and Meditron 7B) deployed locally via Ollama for natural-language-to-SQL generation over a pharmaceutical manufacturing database. A FastAPI-based evaluation platform, PharmaBatchDB AI, was developed using a synthetic Microsoft SQL Server database containing approximately 63,000 records across Batch, Manufacturing Execution System (MES), and Clean-In-Place (CIP) modules. Models were benchmarked on 60 domain-specific natural-language questions using metrics including SQL extraction rate, SQL compliance, factual consistency, ROUGE-L, hallucination rate, throughput, and latency. Qwen 2.5 Coder 7B, Llama 3.1 8B, and Mistral 7B generated SQL for all evaluation tasks, while Meditron 7B failed on nearly all tasks due to context-window limitations and poor SQL generation capability. Llama 3.1 8B achieved the highest SQL compliance, whereas Qwen 2.5 Coder 7B achieved the strongest overall text similarity and factual consistency. Performance differences between the two leading models were not statistically significant. The results show that code-tuned general-purpose LLMs outperform a domain-specific biomedical model on structured query generation for pharmaceutical manufacturing data. Although fully local, GxP-aligned NLQ systems are feasible on consumer hardware, current performance levels still require human oversight and downstream validation for regulated use.

Rajan Bastakoti, Sagar Bhetwal, Nirajan Acharya et al.

Retrieval-Augmented Generation (RAG) has become foundational for grounding large language models in domain-specific corpora, yet conventional vector-based RAG systems are fundamentally limited in their ability to capture the structured, multi-entity relationships that underpin financial market analysis. This paper presents a comprehensive comparative study of a novel two-hop Graph-RAG architecture versus a standard vector-only baseline for cross-entity financial sentiment analysis. Our system constructs a sentiment-weighted knowledge graph of 59 equity entities from 255 news articles covering 10 major technology stocks, then augments dense retrieval with intensity-filtered graph traversal over INFLUENCES edges to surface relational evidence inaccessible to vector search alone. We evaluate both architectures on 100 grounded queries (30 Direct, 70 Relational) using semantic similarity, entity recall, RAGAS metrics, latency benchmarks, and ablation studies. Graph-RAG achieves a statistically significant improvement in entity recall (+6.4%, p < 0.001, Wilcoxon signed-rank) and delivers substantially more relevant answers for complex multi-entity queries (+11.7% Answer Relevancy), with gains concentrating in relational question types (+16.1%). Critically, these improvements come at no measurable cost to answer quality (delta = +0.001 semantic similarity, Cohen's d = 0.078), with a modest 22.6% increase in mean latency offset by an 80% reduction in latency variance. An ablation study on the graph traversal intensity threshold reveals an inverted-U relationship with answer quality, identifying tau = 0.5 as optimal over the production default of tau = 0.7. These findings characterize a precision-for-coverage trade-off inherent to graph-augmented retrieval and provide actionable architectural guidance for practitioners building RAG systems for multi-entity financial analysis.

Nirajan Acharya, Gaurav Kumar Gupta

The Model Context Protocol (MCP), introduced by Anthropic in November 2024 and now governed by the Linux Foundation's Agentic AI Foundation, has rapidly become the de facto standard for connecting large language model (LLM)-based agents to external tools and data sources, with over 97 million monthly SDK downloads and more than 177000 registered tools. However, this explosive adoption has exposed a critical gap: the absence of a unified, formal security framework capable of systematically characterizing, analyzing, and mitigating the diverse threats facing MCP-based agent ecosystems. Existing security research remains fragmented across individual attack papers, isolated benchmarks, and point defense mechanisms. This paper presents MCPSHIELD, a comprehensive formal security framework for MCP-based AI agents. We make four principal contributions: (1) a hierarchical threat taxonomy comprising 7 threat categories and 23 distinct attack vectors organized across four attack surfaces, grounded in the analysis of over 177000 MCP tools; (2) a formal verification model based on labeled transition systems with trust boundary annotations that enables static and runtime analysis of MCP tool interaction chains; (3) a systematic comparative evaluation of 12 existing defense mechanisms, identifying coverage gaps across our threat taxonomy; and (4) a defense in depth reference architecture integrating capability based access control, cryptographic tool attestation, information flow tracking, and runtime policy enforcement. Our analysis reveals that no existing single defense covers more than 34 percent of the identified threat landscape, whereas MCPSHIELD's integrated architecture achieves theoretical coverage of 91 percent. We further identify seven open research challenges that must be addressed to secure the next generation of agentic AI systems.

Gaurav Kumar Gupta, Pranal Pande, Nirajan Acharya et al.

Large Language Models (LLMs) are revolutionizing medical diagnostics by enhancing both disease classification and clinical decision-making. In this study, we evaluate the performance of two LLM- based diagnostic tools, DeepSeek R1 and O3 Mini, using a structured dataset of symptoms and diagnoses. We assessed their predictive accuracy at both the disease and category levels, as well as the reliability of their confidence scores. DeepSeek R1 achieved a disease-level accuracy of 76% and an overall accuracy of 82%, outperforming O3 Mini, which attained 72% and 75% respectively. Notably, DeepSeek R1 demonstrated exceptional performance in Mental Health, Neurological Disorders, and Oncology, where it reached 100% accuracy, while O3 Mini excelled in Autoimmune Disease classification with 100% accuracy. Both models, however, struggled with Respiratory Disease classification, recording accuracies of only 40% for DeepSeek R1 and 20% for O3 Mini. Additionally, the analysis of confidence scores revealed that DeepSeek R1 provided high-confidence predictions in 92% of cases, compared to 68% for O3 Mini. Ethical considerations regarding bias, model interpretability, and data privacy are also discussed to ensure the responsible integration of LLMs into clinical practice. Overall, our findings offer valuable insights into the strengths and limitations of LLM-based diagnostic systems and provide a roadmap for future enhancements in AI-driven healthcare.

Gaurav Kumar Gupta, Nirajan Acharya, Pranal Pande

Diabetes mellitus is a major global health challenge, affecting over half a billion adults worldwide with prevalence projected to rise. Although the American Diabetes Association (ADA) provides clear diagnostic thresholds, early recognition remains difficult due to vague symptoms, borderline laboratory values, gestational complexity, and the demands of long-term monitoring. Advances in large language models (LLMs) offer opportunities to enhance decision support through structured, interpretable, and patient-friendly outputs. This study evaluates GPT-5, the latest generative pre-trained transformer, using a simulation framework built entirely on synthetic cases aligned with ADA Standards of Care 2025 and inspired by public datasets including NHANES, Pima Indians, EyePACS, and MIMIC-IV. Five representative scenarios were tested: symptom recognition, laboratory interpretation, gestational diabetes screening, remote monitoring, and multimodal complication detection. For each, GPT-5 classified cases, generated clinical rationales, produced patient explanations, and output structured JSON summaries. Results showed strong alignment with ADA-defined criteria, suggesting GPT-5 may function as a dual-purpose tool for clinicians and patients, while underscoring the importance of reproducible evaluation frameworks for responsibly assessing LLMs in healthcare.