Generative AI & LLM Systems for
Enterprise Pharmaceutical Workflows
An executive, operational, and technical seminar syllabus tailored for corporate pharmaceutical teams. Master Microsoft 365 Copilot Enterprise, local ETL augmentation, RAG architectures, medical speech-to-text, and secure on-premise AI while safeguarding sensitive clinical trials, drug formulas, and regulatory compliance.
Important: This curriculum is educational. Each organization remains responsible for validating intended uses, access controls, records, and approvals under its own quality system.
5-Step Delivery: Lecture → Hands-On → Q&A → Assignment → Reviews
Engineered specifically for regulated pharmaceutical environments. We bridge high-level conceptual understanding with immediate software application, real-world team challenges, and strict regulatory audit verification.
Conceptual Lecture & Grounding
Demystifying transformer mechanics, token economics, context limits, and data security boundaries with clear life-science analogies.
- Eliminate public model hype
- Contrast ML vs. Generative AI
- Explain next-token prediction
Hands-On Live Software Labs
Instructor demonstrates live on screen, followed by attendees executing step-by-step in M365 Copilot, Python, and local tools.
- Word SOP generation
- Excel clinical batch formulas
- PPT board briefing outlines
Socratic Q&A & Enterprise Checkpoints
Dedicated checkpoints to address team skepticism, proprietary data boundary questions, and edge cases in clinical workflows.
- Address corporate IT fears
- Test hallucination awareness
- Real-time prompt debugging
Applied Assignments & Challenges
Small breakout groups solve realistic synthetic pharma scenarios to prove autonomous problem-solving capabilities.
- Plain-language CSR summaries
- MedDRA symptom categorization
- Competitor FDA deck creation
Peer Reviews & GxP Audit Verification
Enforcing rigorous quality control with 21 CFR Part 11 validation checklists, prompt version logging, and qualified sign-offs.
- Hallucination audit score
- Data classification adherence
- Qualified human verification
Core Terminology & Foundations
Clear, precise definitions bridging consumer hype to enterprise pharmaceutical reality.
Computational systems capable of performing tasks typically requiring human intelligence, including pattern recognition, reasoning, document synthesis, and statistical inference.
Deep transformer models trained on massive corpora to predict subsequent tokens. They possess broad language understanding, world knowledge, and translation/synthesis abilities.
A framework that retrieves proprietary private documents from an indexed knowledge base before prompting an LLM to generate answers grounded strictly in retrieved context.
Chatbots converse. Assistants summarize & suggest. Agents take multi-step tool actions. Workflows follow deterministic orchestration with AI nodes.
Prompt Engineering: Crafting phrasing, roles, and instructions. Context Engineering: Dynamically assembling relevant document chunks, system constraints, metadata, and schemas into the limited context window.
Tokens: Sub-word chunks (~0.75 words). Embeddings: High-dimensional numerical arrays capturing semantic meaning so similar medical terms sit close together in geometric space.
Controls the randomness of next-token selection. Low temperature (0.0 - 0.2) enforces deterministic, analytical adherence. Higher temperature (0.7 - 1.0) introduces creative variability.
An open protocol allowing LLMs and AI assistants to securely connect to external data sources, local databases, and enterprise file servers through standardized, permissioned interfaces.
Fine-Tuning: Updates internal weights to learn specific syntax/tone (costly, stale). RAG: Grounds base model with live external facts without updating weights (fast, source-traceable).
Running open-weights models (Llama-3, Mistral, BioMistral) directly on local GPU servers (Ollama, vLLM) entirely inside the corporate intranet without outbound internet traffic.
The operational discipline of evaluating, deploying, monitoring, and tracing LLM pipelines for latency, token costs, hallucination rates, and drift over time.
Models processing and cross-correlating text, image, tabular, and audio data simultaneously (e.g. OCR on scanned batch records, Whisper audio transcription of doctor interviews).
The gold-standard Computerized System Validation (CSV) framework categorizing software into risk tiers (Category 4 Configured vs Category 5 Custom), paired with ALCOA+ data integrity criteria.
A formal triad metric measuring: Context Relevance (did retrieval pull the right SOP?), Groundedness / Faithfulness (is the answer backed 100% by context?), and Answer Relevance (does it satisfy the prompt?).
The 6 Core Curriculum Modules
A comprehensive, modular roadmap designed for business leaders, laboratory scientists, data engineers, and regulatory analysts. Click any module to explore granular lecture topics, hands-on labs, and pharma use cases.
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Embeddings & High-Dimensional Semantic Search
How mathematical text vectors capture bio-medical semantic relationships. Cosine similarity, Euclidean distance, and hybrid search combining BM25 keyword matching with dense vectors.
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Vector Databases: Architecture & Indexing
How enterprise vector stores (Azure AI Search, Qdrant, Chroma, PGVector) index millions of scientific publications, clinical trial records, and patent filings using HNSW algorithms.
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Hyperparameter Tuning: Temperature, Top_P, Frequency Penalties
Setting temperature to 0.0 for auditing, regulatory tables, and data extraction vs. 0.6 for brainstorming slide titles. Deep dive into repetition penalties and system prompt grounding.
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MCP (Model Context Protocol) & Secure Tool Calling
Anthropic's open standard for connecting AI clients to local files, databases, and enterprise APIs. Building safe read-only MCP bridges into laboratory information systems (LIMS).
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Local AI Deployment (Ollama, vLLM, GGUF/AWQ Quantization)
Setting up local, air-gapped inference servers inside the pharma corporate firewall. Memory sizing (VRAM requirements, 4-bit/8-bit quantization) for open weights models like Llama 3 and Mistral.
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Fine-Tuning Architectures (LoRA, QLoRA, PEFT) vs In-Context Grounding
When parameter-efficient fine-tuning is justified (specialized chemical nomenclature, proprietary SMILES tokens, structured JSON dialects) vs. when fine-tuning creates regulatory liability (catastrophic forgetting, stale knowledge cutoff, high Computerized System Validation re-audit costs).
- Ability to architect scalable vector retrieval pipelines without vendor lock-in.
- Mastery of local offline model execution for confidential chemical IPs.
- Understanding the MCP specification to replace custom fragile API wrappers.
Interactive Lab
Spinning up a local Ollama instance on an enterprise workstation and running vector queries on a confidential research paper.
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RAG Lifecycle for Life Sciences
Document ingestion (parsing complex clinical trial PDFs, tables, and headers), intelligent chunking (parent-child, markdown-aware, recursive), embedding generation, and metadata tagging (drug name, phase, date).
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Advanced Retrieval: Re-Ranking, Hybrid Search & Citation Grounding
Why basic vector search fails on pharma acronyms. Deploying Cross-Encoder re-rankers (Cohere, BGE) and enforcing mandatory source citation page numbers for 100% auditability.
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RAG Evaluation Triad & Quality Benchmarking (RAGAS / TruLens)
Quantitatively auditing retrieval before production deployment. Evaluating the RAG Triad: Context Relevance (precision of retrieved SOP chunks), Faithfulness (100% adherence without hallucination), and Answer Relevance against golden validation datasets.
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Audio Intelligence & Medical Speech-to-Text (Whisper)
OpenAI Whisper architectures (Tiny, Base, Large-v3) deployed locally. Handling clinical terminology, drug brand names, speaker diarization (identifying speaker 1 vs speaker 2), and background lab noise.
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End-to-End Audio Ingestion Pipeline
Audio file -> Local Whisper transcription -> PII de-identification -> LLM clinical meeting summary -> Action item extraction into Microsoft Planner / Jira.
- End-to-end blueprint for building an internal "Chat with SOPs" system.
- Automated transcription pipeline saving 5+ hours weekly per clinical team.
- Mitigation strategies for medical acronym hallucinations in audio models.
Interactive Lab
Live audio transcription of a simulated clinical trial investigator meeting, extracting Adverse Drug Reaction (ADR) bullet points into a structured memo.
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Microsoft Copilot Enterprise Architecture
How Microsoft Graph grounding works. Understanding Commercial Data Protection: why prompts stay within the enterprise tenant, never leak into public models, and are isolated across user access permissions.
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Word Mastery: Regulatory & Scientific Writing
Drafting Clinical Study Report (CSR) sections, translating technical jargon into plain-language summaries (PLS) for patient leaflets, reformatting text into strict ICH-GCP templates, and comparing revisions.
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Excel Mastery: Clinical Data Prep & Formulas
Prompting Copilot in Excel to generate nested XLOOKUP/INDEX-MATCH formulas, parse dirty patient demographic strings, detect batch number anomalies, and summarize clinical trial adverse event rates.
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PowerPoint Mastery: Executive & Scientific Decks
Converting 40-page regulatory review PDFs into crisp 8-slide executive decks. Structuring trial efficacy visualizations, generating speaker notes, and ensuring on-brand pharma styling.
- 50%+ reduction in initial draft time for SOPs and regulatory summary memos.
- Instant formula debugging and exploratory data analysis in Excel.
- Rapid executive deck generation with accurate scientific talking points.
Interactive Lab
Live session transforming raw clinical trial Excel rows into a clean summary table, drafting a Word regulatory memo, and generating a 4-slide executive briefing.
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Modernizing Traditional ETL with LLM Nodes
Where regex and rule engines fail: using LLMs inside ETL pipelines for fuzzy entity resolution, physician handwritten note normalization, and messy lab unit conversions.
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Structured Outputs with Python & Pydantic
Guaranteeing 100% parseable JSON schema compliance using instructor and OpenAI/Azure structured output mode. Ensuring downstream SQL pipelines never crash from malformed responses.
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Adverse Event & MedDRA Classification Automation
Automating mapping of patient unstructured adverse incident logs to standardized Medical Dictionary for Regulatory Activities (MedDRA) SOC/PT codes with confidence scoring.
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JavaScript / Office Scripts & Webhook Automation
Writing TypeScript/JavaScript Office Scripts in Excel to trigger automated REST calls to Azure OpenAI or internal microservices, enabling one-click data enrichment.
- High-throughput asynchronous batch processing scripts in Python.
- Zero schema breakdown in ETL pipelines via Pydantic validators.
- Automated rate limiting, exponential backoff, and fallback models.
Interactive Lab
Writing a Python script that ingests a CSV of 100 unstructured patient doctor notes, maps them to standard MedDRA categories, and outputs validated JSON for SQL insertion.
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The "Is My Data Used for Training?" Reality
The critical difference between consumer ChatGPT and Microsoft Copilot Enterprise / Azure OpenAI. Explaining Zero Data Retention (ZDR), customer tenant isolation, and legal guarantees that proprietary data is never used to train base models.
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Data Classification Matrix: What Can & Cannot Be Shared
Clear guidelines for staff: Tier 1 (Public Literature & Generic Text) vs. Tier 2 (Internal SOPs in Copilot Enterprise) vs. Tier 3 (Proprietary Molecular SMILES & Patient PHI - Air-Gapped Local Only).
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GAMP 5 System Classification & ALCOA+ Data Integrity
Auditing AI tools under GAMP 5 Category 4 (Configured Commercial Software like M365 Copilot) vs Category 5 (Custom Python/ETL/RAG code). Enforcing ALCOA+ data integrity (Attributable, Legible, Contemporaneous, Original, Accurate) across system prompt logs, temperature seeds, and qualified reviewer electronic records.
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GxP & 21 CFR Part 11 Validation for AI Systems
Computerized System Validation (CSV) requirements. Managing probabilistic outputs in deterministic validation frameworks: Human-in-the-Loop (HITL) mandatory sign-offs, seed logging, and versioned audit logs.
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Hallucination Mitigation & Citation Verification
Implementing the "Trust but Verify" workflow. Prompt constraints forbidding external knowledge assumptions, strict page/paragraph citation enforcement, and automated fact-checking checks.
- Complete peace of mind on intellectual property protection and IP leakage.
- A defensible AI governance policy aligned with FDA/EMA digital health guidance.
- Clear employee SOP on acceptable AI usage and data classifications.
Interactive Lab
Auditing a simulated AI output against 21 CFR Part 11 requirements: documenting prompt version, model version, temperature, and qualified human reviewer electronic sign-off.
Pharma Copilot & Automation Prompt Bank
Ready-to-use, enterprise-grade prompts engineered specifically for pharmaceutical workflows in Word, Excel, PowerPoint, and Python ETL pipelines. Click copy to test in your workflow.
You are an expert pharmaceutical quality assurance and regulatory affairs specialist. Based strictly on the attached laboratory test protocol [insert document], draft a Standard Operating Procedure (SOP) following GxP standards. Include the following standardized sections: 1. PURPOSE & SCOPE 2. REGULATORY REFERENCES (ICH Q2(R1), 21 CFR Part 211) 3. RESPONSIBILITIES & ROLES 4. REAGENTS, STANDARDS & EQUIPMENT SPECIFICATIONS 5. STEP-BY-STEP PROCEDURE (imperative voice, sequential numbering) 6. QUALITY CONTROL CRITERIA & ACCEPTANCE LIMITS 7. DEVIATION & OUT-OF-SPECIFICATION (OOS) REPORTING PROTOCOL 8. REVISION HISTORY TABLE Constraints: - Maintain an unambiguous, authoritative tone. - Do not assume missing numerical thresholds; if a parameter is not in the source, insert [PARAMETER TO BE SPECIFIED BY QA]. - Do not add information from outside the provided protocol.
Act as a medical communicator specializing in health literacy. Read the attached Clinical Study Report (CSR) summary section for Phase III Trial [Trial_ID]. Translate this scientific text into a Plain Language Summary (PLS) intended for trial participants and the general public. Guidelines: - Target a 6th to 8th grade reading level (Flesch-Kincaid grade level ≤ 8). - Replace medical terminology with clear everyday equivalents (e.g., replace 'hypertension' with 'high blood pressure', 'adverse event' with 'side effect', 'myocardial infarction' with 'heart attack'). - Organize with clear subheadings: * Why was this study done? * What treatments were compared? * What were the main findings? * What side effects did patients experience? - Clearly state that patients should consult their physician before changing any medication.
Analyze the stability testing data in Columns A through H: - Column A: Batch Number - Column B: Storage Condition (e.g., 25°C/60% RH, 40°C/75% RH) - Column C: Time Point (Months: 0, 3, 6, 9, 12) - Column D: Active Pharmaceutical Ingredient (API) Assay % (Specification: 95.0% - 105.0%) - Column E: Total Degradation Impurities % (Specification: NMT 1.5%) Tasks: 1. Provide an Excel formula for Column F that flags "OUT OF SPEC (OOS)" if Assay < 95.0% or > 105.0%, or if Impurities > 1.5%. Otherwise output "PASS". 2. Write a formula to calculate the degradation rate (slope of impurities vs time) for each batch. 3. Suggest conditional formatting rules to highlight accelerating degradation before it breaches OOS limits.
In Column C, I have messy clinical site demographic entries that mix age and gender (e.g., "54 yr M", "Female, 62", "M - 41 years old", "Age: 29 / F"). Provide formulas or Power Query steps to: 1. Extract numerical AGE into Column D as an integer. 2. Standardize GENDER into Column E strictly as either "M", "F", or "UNKNOWN". 3. Provide a data validation formula for Column F that flags rows where Age is outside the protocol inclusion criteria (18 to 75 years inclusive).
Using the attached Phase IIb Efficacy Summary for Compound [XYZ-101], generate an outline for a high-impact 6-slide executive presentation for the Senior Scientific Advisory Board. Structure each slide with: - Slide Title (action-oriented, e.g. "Primary Endpoint Met with Statistically Significant Efficacy") - Visual Concept (describe recommended chart: Kaplan-Meier curve, waterfall plot, or 3-column metric cards) - 3 Bullet Points (succinct, bold key metric first, max 15 words per bullet) - Speaker Talking Points (2-3 sentences providing regulatory and clinical context) Slides required: Slide 1: Study Design & Patient Demographics (n=450) Slide 2: Primary Efficacy Endpoint (p-value, hazard ratio, 95% CI) Slide 3: Secondary Biomarker Outcomes Slide 4: Safety & Tolerability Profile (treatment-emergent adverse events) Slide 5: Competitive Landscape & Differentiation Slide 6: Phase III Recommendation & Regulatory Timeline
Create a 4-slide competitive intelligence briefing based on the newly published FDA approval package for [Competitor Drug Name]. Focus on: 1. Mechanism of Action (MoA) Comparison vs our in-house molecule. 2. Dosing Convenience & Administration Routes (Oral QD vs SC Bi-weekly). 3. Boxed Warnings or Special Monitoring Requirements. 4. Opportunities for our medical affairs positioning. Make each slide clean, professional, and suitable for commercial sales and medical science liaisons (MSLs).
You are an automated Pharmacovigilance (PV) data extraction node in a high-throughput GxP ETL pipeline. Your task is to ingest unstructured patient incident reports or physician notes and output strictly validated, parseable JSON conforming to ICH E2A safety guidelines. INPUT TEXT: """ [Insert raw clinician note / EHR excerpt] """ EXTRACTION RULES: 1. Extract every reported adverse event into an array under the key "adverse_events". 2. For each event, include: - "verbatim_term": Exact symptom phrase quoted directly from the input text. - "suspect_drug": Trade name or active ingredient mentioned, or "NOT_SPECIFIED". - "severity": Must be strictly one of ["MILD", "MODERATE", "SEVERE", "LIFE_THREATENING"]. - "causality_assessment": Strictly one of ["UNRELATED", "POSSIBLE", "PROBABLE", "DEFINITE"]. - "action_taken_with_drug": Strictly one of ["DOSE_NOT_CHANGED", "DOSE_REDUCED", "DRUG_INTERRUPTED", "DRUG_WITHDRAWN", "UNKNOWN"]. - "regulatory_seriousness": Boolean (true if hospitalization, disability, life-threatening, or death occurred; false otherwise). - "confidence_score": Decimal between 0.0 and 1.0 indicating extraction certainty. 3. If no adverse events are detected, return an empty array for "adverse_events". 4. Set "requires_expedited_15_day_review": true if any event meets regulatory expedited criteria. OUTPUT CONSTRAINT: Output ONLY raw, valid JSON with zero conversational filler, zero markdown backticks, and zero preamble.
You are an audio intelligence and clinical documentation node in an automated medical speech-to-text pipeline. You will ingest raw, noisy speech-to-text transcripts generated from investigator meetings, advisory boards, or patient monitoring calls. RAW TRANSCRIPT: """ [Insert raw Whisper audio transcript here] """ TRANSFORMATION DIRECTIVES: 1. Medical Vocabulary Normalization: - Detect phonetically misheard pharmaceutical terms and correct them to standard INN (International Nonproprietary Names) or trade names (e.g., correct "pembro" or "keytruder" to "Keytruda / pembrolizumab", "humira" to "adalimumab", "ozempick" to "Ozempic / semaglutide"). - Standardize clinical trial abbreviations (AUC, Cmax, OOS, SAE, MedDRA, eCRF). 2. Automated PHI / PII Redaction (HIPAA Safe Harbor): - Replace any identifiable patient names, hospital room numbers, physician phone numbers, dates of birth, or Medical Record Numbers (MRNs) with standard redaction tokens like [PATIENT_NAME_REDACTED], [MRN_REDACTED], [PHONE_REDACTED]. 3. Structured Clinical Synthesis: - Provide an Executive Scientific Summary (bulleted trial efficacy, pharmacokinetics, and safety observations). - Document any Unresolved Protocol Questions or Investigator Concerns. - Output an Action Item Table with columns: [Action Item, Responsible Function (QA / Clinical Ops / Data Mgmt), Target Milestone]. OUTPUT FORMAT: Return clean, audit-ready Markdown with strict separation between clinical facts and operational deliverables.
Enterprise Security, Data Boundaries & GxP
Essential guidelines answering: What can be shared? Where does data go? Is data used to train public models? And how do we satisfy regulatory audits?
| Data Classification Level | Example Pharma Data Assets | Public Consumer AI (ChatGPT/Gemini Free) | Microsoft Copilot Enterprise (M365) | Private / Air-Gapped Local AI (Ollama/vLLM) |
|---|---|---|---|---|
| Tier 1: Public / Generic | Published PubMed papers, FDA guidance documents, public patents, generic meeting summaries. | Allowed (No IP) | Recommended | Supported |
| Tier 2: Confidential Corporate | Standard Operating Procedures (SOPs), internal training, non-confidential department memos, general financial reports. | STRICTLY PROHIBITED | Protected by Tenant Boundary | Fully Secured |
| Tier 3: Clinical & Patient Data (PHI/PII) | Patient medical notes, adverse event filings with identifiers, unblinded clinical trial patient logs. | STRICTLY PROHIBITED | De-identified Only (HIPAA/GDPR) | Recommended (Air-Gapped) |
| Tier 4: Core Intellectual Property | Unpublished chemical synthesis pathways, molecular SMILES, upcoming patent claims, trade secrets. | STRICTLY PROHIBITED | Executive Clearance Required | Mandatory (Zero Egress) |
Model Training & Retention Truths
In Microsoft Copilot Enterprise and Azure OpenAI with enterprise agreements, customer prompts, completions, and documents are never used to train foundation models. Zero Data Retention (ZDR) agreements ensure data is processed in memory and not logged on third-party servers.
21 CFR Part 11 & GxP Validation
Automated AI systems in GxP cannot act as final unreviewed signatories. Every AI-assisted regulatory document requires an audit trail documenting the prompt version, model version, and an explicit Human-in-the-Loop (HITL) qualified review signature.
Hallucination Defenses & RAG Triad
Implement deterministic safeguards: enforce temperature=0.0, use negative prompting ("If not found in context, state UNKNOWN"), require page-level citations for every quantitative claim, and benchmark retrieval using RAG Triad metrics (Context Relevance, Groundedness, Answer Relevance).
GAMP 5 & ALCOA+ Data Integrity
Classify AI implementations under GAMP 5 risk tiers (Category 4 Configured M365 Copilot vs Category 5 Custom ETL/RAG). Guarantee ALCOA+ principles (Attributable, Legible, Contemporaneous, Original, Accurate) with immutable prompt-response audit logging and qualified CSV sign-offs.
Seminar & Lecture Delivery Options
Choose the format that aligns with your organization's timeline, from high-level leadership overviews to multi-day technical workshops.
Executive & Leadership Primer
For Directors, VPs, Quality Heads, and Department Leads.
- High-level Generative AI & LLM landscape
- Copilot Enterprise ROI & capability limits
- Intellectual property & data privacy risks
- GxP regulatory compliance roadmap
- Executive Q&A & strategic prioritization
Comprehensive Corporate Seminar
For Cross-Functional Pharma Teams, Analysts, & Power Users.
- Everything in the Executive Primer
- Deep dive into Word, Excel, & PPT Copilot
- RAG architecture & internal SOP searching
- Speech-to-text (Whisper) for meetings
- Hands-on prompt engineering workshop
- "What Can Be Shared" governance checklist
Technical & Engineering Deep Dive
For Data Engineers, IT Architects, ETL Developers, & Bioinformaticians.
- Modules 1 through 6 complete coverage
- Python ETL pipeline augmentation with Pydantic
- Local AI setup with Ollama and vLLM
- Model Context Protocol (MCP) tool integration
- End-to-end RAG pipeline building lab
- 21 CFR Part 11 software validation artifacts
Krishna Kanth B
AI Consultant, Solutions Architect & Corporate Educator
Specializing in enterprise AI adoption, Retrieval-Augmented Generation (RAG), workflow automation, and custom LLM systems for regulated industries. Empowering corporate teams to bridge modern language models with everyday business tools safely and effectively.