Engineering Notes

Engineering Notes

Thoughts and Ideas on AI by Muthukrishnan

Deep Research Applications of Modern LLMs Generated through Deep Research

22 Mar 2025

Artificial Intelligence is moving beyond conversational chatbots to become autonomous research agents. Unlike conventional LLM assistants that answer questions based on pre-trained knowledge, these new systems—collectively called Deep Research AI—can:

This process, while slower, achieves comprehensive, verifiable insights comparable to a PhD-level literature review.

How Deep Research Works

Core Stages:

  1. Planning: Breaks the main query into a structured research plan.
  2. Agentic Search: Iteratively refines queries and gathers data across sources.
  3. Analysis and Synthesis: Compares, contextualizes, and integrates information.
  4. Reporting: Produces structured documents with citations.

Comparative Overview of Leading Platforms

FeatureGoogle GeminiOpenAI ChatGPTAnthropic ClaudeManus
ArchitectureAgentic, multi-step planningAdvanced reasoning models (o1-Pro, o3)Multi-agent orchestrationMulti-agent with Claude 3.5 Sonnet & 29 tools
StrengthsTransparent sourcing, Google integrationProactive prompt refinement, advanced data analysisEnterprise integrations, breadth-first queriesFull autonomy across workflows
Data IntegrationWeb, file uploads, Google WorkspaceWeb, extensive file uploadsWeb, Gmail, Calendar, DocsWeb, full file system, APIs, terminal access
Ideal Use CasesMarket research, literature reviewsData analysis, investigative researchSales prep, knowledge managementSoftware prototyping, workflow automation

Few Key ways people are using Deep Research across industries

  1. Market Intelligence Reports

    • Automates comprehensive market analysis.
    • Gemini excels in structured reporting and transparency.
    • ChatGPT assists with prompt refinement and digestible summaries.

    Sample Prompt:

    Conduct a comprehensive market analysis for [INDUSTRY/PRODUCT]. Include:
    - Market size, growth rate, and key trends
    - Competitive landscape with top 5 players
    - Customer segments and pain points
    - Regulatory environment and challenges
    - Future opportunities and threats
    Provide sources for all data points and create executive summary.
    
  2. Competitive Intelligence

    • Compares competitor strategies, pricing, and sentiment.
    • Gemini offers structured comparison tables and critical evaluation.

    Sample Prompt:

    Analyze competitors [COMPANY A, B, C] in [INDUSTRY]:
    - Product offerings and pricing strategies
    - Marketing approaches and brand positioning
    - Customer sentiment from reviews and social media
    - Recent news, partnerships, and strategic moves
    - SWOT analysis for each competitor
    Create comparison table with strengths/weaknesses assessment.
    
  3. Product Development Research

    • Processes user feedback and creates product requirement documents.
    • ChatGPT’s advanced reasoning supports deep technical analysis.
  4. Strategic Briefings

    • Fuses private internal data with public context.
    • Claude integrates Gmail, Docs, and the web for holistic overviews.
  5. Financial Forecasting and M&A

    • Transforms unstructured commentary into quantifiable signals.
    • FinLLMs (BloombergGPT, FinGPT) are tailored for finance.
  6. Legal E-Discovery

    • Moves beyond keyword search to reconstruct event narratives.
    • LLMs embedded in platforms like Relativity aiR enhance transparency.
  7. Contract Review & Due Diligence

    • Automates first-pass legal review.
    • Studies show LLMs match junior lawyers in accuracy and reduce costs by over 99%.

II. Scientific and Technical Research

  1. Systematic Literature Reviews

    • Automates evidence synthesis from sources like PubMed.
    • Gemini integrates with NotebookLM for deeper analysis.
  2. Quantitative Data Analysis

    • ChatGPT ADA supports data cleaning, regression, and visualization.
  3. Pharmaceutical Discovery

    • Llamole (MIT-IBM) generates molecules and synthesis plans.
    • Achieves higher chemical synthesis success rates.
  4. Bioinformatics

    • Assists in data preparation and code development across languages.
  5. Autonomous Software Development

    • Manus agents plan, code, debug, and deploy applications end-to-end.
  6. Game Development

    • Generates fully functional video game prototypes rapidly.

III. Media, Creative Work, and Personal Productivity

  1. Investigative Journalism

    • Custom GPTs (e.g., COA Beat Assistant) analyze public reports to uncover stories.
  2. Novel Writing and Plot Development

    • Tools like Sudowrite and Novelcrafter assist with outlining and character creation.
  3. Worldbuilding

    • Deep Realms generates coherent lore, cultures, and visuals.
  4. Administrative Automation

    • Manus automates multi-step workflows such as résumé screening.
  5. Personal Information Management

    • Claude synthesizes schedules, emails, and public data into actionable plans.
  6. Personalized Learning Plans

    • Combines student materials with online resources for tailored study paths.
  7. Fact-Checking and Source Verification

    • Gemini transparently displays sourcing and conflicting information resolution.

Practical Prompts for Key Applications

Business Applications

Product Development Research:

Analyze user feedback for [PRODUCT] and create product requirements:
- Categorize feedback into themes (bugs, features, usability)
- Identify top 10 most requested features
- Prioritize based on impact and feasibility
- Create user stories and acceptance criteria
- Suggest technical implementation approaches
Include market research on similar features in competing products.

Strategic Briefings:

Create strategic briefing for [COMPANY] board meeting:
- Synthesize recent email communications about [PROJECT]
- Integrate with public market data and industry trends
- Identify key risks and opportunities
- Provide recommendations with supporting evidence
- Create timeline for next quarter initiatives
Format as executive presentation with key takeaways.

Financial Forecasting:

Analyze M&A opportunity for [TARGET COMPANY]:
- Extract financial metrics from earnings calls and reports
- Identify synergies and integration risks
- Calculate valuation using DCF and comparable analysis
- Assess market reaction and analyst sentiment
- Create deal structure recommendations
Provide quantitative model with sensitivity analysis.

Legal E-Discovery:

Analyze legal documents for [CASE] discovery:
- Identify key events and timeline reconstruction
- Extract relevant communications between parties
- Highlight potential privileged information
- Categorize documents by relevance and responsiveness
- Create narrative summary of key findings
Maintain chain of custody and provide source citations.

Scientific Research Applications

Literature Review:

Conduct systematic literature review on [RESEARCH TOPIC]:
- Search PubMed, arXiv, and Google Scholar
- Identify key papers and citation patterns
- Synthesize findings across studies
- Identify research gaps and contradictions
- Create evidence hierarchy and quality assessment
Generate comprehensive review with methodology section.

Data Analysis:

Analyze dataset [DATASET] for [RESEARCH QUESTION]:
- Perform exploratory data analysis
- Identify patterns and correlations
- Apply appropriate statistical tests
- Create visualizations and interpretations
- Validate findings with cross-validation
Generate complete analysis report with code.

Pharmaceutical Research:

Research drug discovery for [CONDITION]:
- Identify potential molecular targets
- Analyze existing compounds and mechanisms
- Assess safety and efficacy data
- Review clinical trial outcomes
- Suggest optimization strategies
Create comprehensive research summary with references.

Creative and Media Applications

Investigative Journalism:

Investigate [TOPIC] for news story:
- Gather public records and documents
- Identify key stakeholders and sources
- Analyze financial and legal connections
- Verify claims and cross-reference sources
- Create timeline of events
Produce fact-checked article with source attribution.

Content Creation:

Develop [CONTENT TYPE] about [TOPIC]:
- Research audience preferences and trends
- Analyze competitor content performance
- Create outline with key messages
- Develop engaging narrative structure
- Optimize for SEO and platform algorithms
Generate complete content calendar with metrics.

Educational Planning:

Create personalized learning plan for [SUBJECT]:
- Assess current knowledge level
- Identify learning objectives and gaps
- Curate resources from multiple sources
- Design progressive skill-building sequence
- Include assessment and feedback mechanisms
Provide adaptive learning pathway with milestones.

Deep Research AI systems mark a shift from AI as a tool to AI as an autonomous collaborator. As these agents evolve, human involvement is becoming more strategic, focusing on:

The future will likely involve ecosystems of specialized agents collaborating seamlessly, supported by open standards for interoperability.