K-Dense-AI

GPU-accelerate Python code using CuPy, Numba CUDA, Warp, cuDF, cuML, cuGraph, KvikIO, cuCIM, cuxfilter, cuVS, cuSpatial, and RAFT. Use whenever the user mentions GPU/CUDA/NVIDIA acceleration, or wants to speed up NumPy, pandas, scikit-learn, scikit-image, NetworkX, GeoPandas, or Faiss workloads. Covers physics simulation, differentiable rendering, mesh ray casting, particle systems (DEM/SPH/fluids), vector/similarity search, GPUDirect Storage file IO, interactive dashboards, geospatial analysis, medical imaging, and sparse eigensolvers. Also use when you see CPU-bound Python code (loops, large arrays, ML pipelines, graph analytics, image processing) that would benefit from GPU acceleration, even if not explicitly requested.

Search 10 academic literature APIs for papers, preprints, citations, and open-access full text, and return results with reproducible provenance. Covers PubMed, PMC (full text), bioRxiv, medRxiv, arXiv, OpenAlex, Crossref, Semantic Scholar, CORE, Unpaywall. Use when searching for papers, citations, DOI/PMID/arXiv lookups, abstracts, full text, open-access PDFs, preprints, citation graphs, author publications, or any scholarly literature query. Triggers on mentions of any supported database or requests like "find papers on X", "look up this DOI", "who cites this paper", or "get me the PDF".

Look up current research and scientific information across three backends: fast web search via parallel-cli (default), the Parallel Chat API for deep multi-source synthesis, and Perplexity sonar-pro-search for scholarly paper searches. Automatically routes each query to the best backend and saves every result to sources/ for reproducible citation. Use this whenever you need to find papers, gather statistics or market data, verify a scientific claim, collect citations, or research any topic for scientific/technical writing — even if the user does not say "research" explicitly. Note: query text is sent to api.parallel.ai (PARALLEL_API_KEY) and, for academic searches, to openrouter.ai (OPENROUTER_API_KEY).

Guided statistical analysis for research data - test selection, assumption checking, effect sizes, power analysis, Bayesian alternatives, and APA-formatted reporting. Use whenever a user wants to compare groups, test a hypothesis, analyze experimental or survey data, check statistical assumptions, compute required sample sizes, or write up results - even if they never name a specific test. Covers t-tests, ANOVA, chi-square, correlation, regression, non-parametric and Bayesian methods. For low-level model APIs, see the statsmodels and pymc skills.

Query documented public database APIs with explicit endpoints, filters, pagination, and provenance. Use when a scientific, regulatory, financial, or other database-backed fact must be retrieved reproducibly from a named source rather than inferred from general knowledge.

Query the 1000 Genomes Project dataset (3,202 whole-genome-sequenced individuals, GRCh38) at the level of individual participants. Use when a question is about individuals or variants in the 1000 Genomes Project cohort: which individuals carry variants matching specific criteria in a gene or region, which individuals are homozygous-reference at a position, which variants exist in the dataset or carried by specified individuals in a gene or region, the relatedness between two specified individuals. Variants are returned with 1000 Genomes allele frequencies (AF), gnomAD v4.1 exome and genome AF, AlphaMissense score, and HGVSp annotations.

Access a collection of open-source molecular design and structural biology tools on the Tamarind Bio platform, via its REST API or MCP server — no local GPUs required. Tamarind bundles popular open-source models for structure prediction (AlphaFold, Boltz, Chai, ESMFold), protein, binder, and de novo design (RFdiffusion, ProteinMPNN, BoltzGen), antibody and nanobody design and developability, protein-ligand docking (DiffDock, Autodock Vina), binding-affinity prediction, MSA generation, and molecular dynamics. Use when the user mentions Tamarind or tamarind.bio, wants to run any of these open-source tools in the cloud, references app.tamarind.bio/api or the x-api-key header, or needs to submit batches of sequences for structural or biophysical characterization.

Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run protein expression and purification (cell-free, E. coli, or Pichia), HiBiT or A280 or LabChip quantification, IVT mRNA/circRNA synthesis, thermal shift / developability assays, Echo-MS enzyme or analyte methods, SPR target onboarding, fluorescent pixel art, or otherwise interact with Ginkgo Cloud Lab services. Covers protocol selection, input preparation, pricing, and ordering workflows.

Applies the epidemiological reasoning and population-health frameworks of Albert Hofman (Harvard epidemiologist, Rotterdam Study). Trigger this skill whenever you are analyzing public health strategies, preventive medicine, cohort study design, cardiovascular or neurodegenerative disease risks, or healthy aging. Use it when evaluating whether to use population-wide interventions versus individual screening, assessing risk factors in elderly populations, or tracing adult chronic diseases back to early-life or fetal origins.

Applies the mental models and frameworks of Andrej Karpathy (deep learning, former Director of AI at Tesla, founding member of OpenAI, Eureka Labs). Use this skill whenever you are helping the user build neural networks from scratch, debug deep learning pipelines, evaluate AI agent workflows, design LLM apps, or navigate the transition to Software 3.0 (vibe coding). It is highly relevant for pedagogy (untangling complex knowledge), assessing AI capabilities vs. limitations (jagged intelligence, tokenization limits), and architectural decisions (end-to-end optimization vs. complex pipelines). Reach for this whenever discussing LLM training, autonomous systems, or AI-assisted coding.

Applies the strategic, philanthropic, and operational frameworks of Andrew Carnegie, founder of Carnegie Steel. Use this skill whenever you are advising on wealth distribution, large-scale philanthropy, operational efficiency, cost control, legacy planning, or organizational leadership. Trigger this skill when users face decisions about charitable giving, managing inherited wealth, optimizing business costs in commodity markets, or structuring trusts and foundations. Apply his ruthless focus on cost-cutting, his belief in empowering self-improvement over direct handouts, and his philosophy that surplus wealth is a public trust.

Applies the reasoning, principles, and frameworks of Andrew Ng (machine learning pioneer, co-founder of Coursera and DeepLearning.AI, Stanford University, and former Google Brain lead). Use this skill whenever the user is navigating AI application development, agentic workflows, automation strategy, AI-native software engineering, or rapid prototyping. Trigger this skill when discussing career advice in the AI era, evaluating AI regulations, structuring machine learning projects, or deciding how to integrate AI into a business. It emphasizes task-based automation, data-centric ML, and driving the cost of proof-of-concepts to zero.

Applies the strategic frameworks and mental models of Anne Wojcicki, co-founder and CEO of 23andMe. Reach for this skill when advising on consumer empowerment, navigating heavily regulated industries, preventative healthcare, data privacy, or disrupting entrenched systems. Use this when the user is dealing with misaligned industry incentives, facing regulatory hurdles, building a consumer-research flywheel, or managing a team through a post-launch 'trough of sorrow'. Apply her principles of 'speaking with data', treating users as partners, and pushing for decade-long systemic change from the outside.

Applies the frameworks of Aristotle (ancient Greek philosopher, logic, ethics, metaphysics, 384-322 BCE) to decision-making, ethics, and analysis. Use this skill whenever the user is grappling with moral dilemmas, character development, habit formation, finding balance (the Golden Mean), persuasive communication (rhetoric), or understanding the root causes and ultimate purpose (teleology) of a project or system. Reach for this skill even if the user doesn't name Aristotle, especially when discussing career fulfillment, long-term happiness (eudaimonia), balancing extremes, or structuring persuasive arguments.

Applies the computational biology and AI-driven reasoning of Aviv Regev (computational biologist, Genentech, single-cell genomics). Use this skill whenever the user is dealing with experimental design, high-dimensional data analysis, integrating AI into scientific workflows, scaling biological research, or navigating noisy, complex systems. Trigger this for topics like single-cell genomics, drug discovery, biological atlases, interdisciplinary research strategy, or when deciding between depth vs. breadth in data collection.

Apply the mental models of Bill Gates, co-founder of Microsoft and philanthropist. Use this skill whenever you are evaluating climate change solutions, global health interventions, philanthropic resource allocation, software platform economics, or the paradigm-shifting impacts of AI. Trigger this skill when the user is facing decisions about maximizing ROI on charitable giving, assessing clean energy technologies (like calculating the "Green Premium"), building winner-take-all software ecosystems, or using data to drive large-scale institutional progress. Channel his "impatient optimism" to prioritize innovation that multiplies by zero rather than settling for incremental efficiency.

Comprehensive citation management for academic research. Search Google Scholar and PubMed for papers, extract accurate metadata, validate citations, and generate properly formatted BibTeX entries. This skill should be used when you need to find papers, verify citation information, convert DOIs to BibTeX, or ensure reference accuracy in scientific writing.

Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommendation reports (evidence-based guidelines with decision algorithms). Supports GRADE evidence grading, statistical analysis (hazard ratios, survival curves, waterfall plots), biomarker integration, and regulatory compliance. Outputs publication-ready LaTeX/PDF format optimized for drug development, clinical research, and evidence synthesis.

Write comprehensive clinical reports including case reports (CARE guidelines), diagnostic reports (radiology/pathology/lab), clinical trial reports (ICH-E3, SAE, CSR), and patient documentation (SOAP, H&P, discharge summaries). Full support with templates, regulatory compliance (HIPAA, FDA, ICH-GCP), and validation tools.

Generate testable hypotheses. Formulate from observations, design experiments, explore competing explanations, develop predictions, propose mechanisms, for scientific inquiry across domains.

Create professional research posters in LaTeX using beamerposter, tikzposter, or baposter. This is the default poster skill for conference presentations, academic posters, and scientific communication. Includes layout design, color schemes, multi-column formats, figure integration, and poster-specific best practices. For editable PowerPoint output, use pptx-posters (HTML/CSS-based) or poster-presentation (python-pptx-based) instead.

Conduct comprehensive, systematic literature reviews using multiple academic databases (PubMed, arXiv, bioRxiv, Semantic Scholar, etc.). This skill should be used when conducting systematic literature reviews, meta-analyses, research synthesis, or comprehensive literature searches across biomedical, scientific, and technical domains. Creates professionally formatted markdown documents and PDFs with verified citations in multiple citation styles (APA, Nature, Vancouver, etc.).

Convert files and office documents to Markdown. Supports PDF, DOCX, PPTX, XLSX, images (with OCR), audio (with transcription), HTML, CSV, JSON, XML, ZIP, YouTube URLs, EPubs and more.

This skill should be used when converting academic papers into promotional and presentation formats including interactive websites (Paper2Web), presentation videos (Paper2Video), and conference posters (Paper2Poster). Use this skill for tasks involving paper dissemination, conference preparation, creating explorable academic homepages, generating video abstracts, or producing print-ready posters from LaTeX or PDF sources.

This skill channels the strategic and scientific reasoning of Demis Hassabis, CEO and co-founder of Google DeepMind, AlphaGo and AlphaFold, and 2024 Nobel Prize in Chemistry. Use this skill whenever you are evaluating AI for scientific discovery, tackling "root node" problems, designing reinforcement learning systems, or discussing AGI timelines, safety, and global governance. Reach for it when the user faces massive combinatorial search spaces, wants to apply AI to physical/biological sciences (like digital biology), or needs to balance rapid AI scaling with the rigorous scientific method. Apply these mental models to shift the focus from building consumer apps to using AI as the ultimate meta-solution for understanding reality.

Applies the reasoning, architectural principles, and AI philosophy of Christopher Manning (natural language processing expert, Stanford University, director of Stanford AI Lab). Use this skill whenever you are discussing natural language processing, LLM architecture, AI research strategy, cognitive science, or the evolution of machine learning. Trigger this skill for questions about AGI timelines, academic vs. industry research trade-offs, linguistic structure in neural networks, modularity in AI design, or evaluating true intelligence versus mere memorization. Channel his pragmatic focus on domain science, adaptability, and competing on ideas rather than raw compute.

Applies the reasoning style of Daphne Koller (machine learning pioneer, co-founder of Coursera, founder and CEO of Insitro). Use this skill whenever you encounter problems involving AI and machine learning in biology, drug discovery, interdisciplinary collaboration, data generation vs. data mining, or transitioning from academia to industry. Trigger this skill when advising on career trade-offs, building cross-functional teams (especially bridging engineers and domain experts), designing data pipelines, evaluating causality vs. correlation, or applying AI to physical systems ('where bits meet atoms'). Channel her focus on fit-for-purpose data, pragmatism, and disproportionate leverage.

Applies the reasoning of David Silver, lead researcher on AlphaGo and AlphaZero at DeepMind, to problems of AI design, reinforcement learning, and open-ended discovery. Use this skill whenever you are designing AI systems, evaluating learning algorithms, balancing exploration vs. exploitation, choosing research problems, or discussing how to break past human performance ceilings. Reach for this whenever the user asks about self-play, Monte-Carlo Tree Search, tabula rasa learning, AGI, or moving from human-curated data to autonomous experience. It helps shift the focus from hardcoding human knowledge to building systems that learn for themselves.

Applies the engineering and research philosophies of Jeff Dean, Chief Scientist at Google DeepMind and Google Research. Reach for this skill whenever you are designing large-scale distributed systems, optimizing latency and energy efficiency, or making architectural decisions about machine learning infrastructure. It should trigger automatically for topics involving hardware-ML co-design, model distillation, sparse activation, massively multi-task models, or scaling systems by 5x to 10x. Use this skill to evaluate system bottlenecks, transition from specialized to unified models, and optimize experimental velocity. Apply his mental models to avoid premature 100x scaling and to treat AI models as reasoning engines rather than memorization databases.

Applies the reasoning style of Kaiming He, computer vision pioneer and creator of ResNet. Use this skill whenever you are designing deep learning architectures, debugging neural network optimization, formulating generative AI problems, or bridging AI with other scientific domains. Trigger this skill for discussions on network depth, weight initialization, residual learning, flow matching, or when reframing discriminative tasks as conditional generation. It emphasizes simplicity in complex visual problems, end-to-end optimization, and viewing AI as a universal language for science.

Applies the reasoning, principles, and mental models of Sebastian Thrun (robotics and self-driving cars pioneer, founder of Google X, Waymo, Udacity, Stanford University). Reach for this skill whenever Claude is asked to advise on hardware/software systems engineering, autonomous vehicles, moonshot ideation, probabilistic robotics (SLAM), or leading high-stakes engineering teams. Trigger this skill for discussions on democratizing education, regulating AI, transitioning from academic research to product development, or managing technical teams with empathy. Use it to shift focus from incremental component debates to end-to-end execution and audacious goals.

Applies the reasoning, principles, and frameworks of Andrew Ng (machine learning pioneer, co-founder of Coursera and DeepLearning.AI, Stanford University, and former Google Brain lead). Use this skill whenever the user is navigating AI application development, agentic workflows, automation strategy, AI-native software engineering, or rapid prototyping. Trigger this skill when discussing career advice in the AI era, evaluating AI regulations, structuring machine learning projects, or deciding how to integrate AI into a business. It emphasizes task-based automation, data-centric ML, and driving the cost of proof-of-concepts to zero.

Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifying questions

You MUST use this before any data analysis or investigation - before exploring a dataset, loading or profiling data, running a model, computing a statistic, or testing an idea, and before any outcome data is touched

Use when you have an approved research question and need a concrete analysis plan, before touching outcome data or fitting any model

Use when facing 2+ independent investigations that can proceed without shared state - parallel literature survey, multi-dataset replication, or pre-specified robustness checks

Use when you have a pre-registered analysis plan to execute inline in this session with review checkpoints, on a platform without subagents

Use when a result is surprising, impossible, contradicts a sanity check, a pipeline fails, a model won't converge, or a replication fails - before adjusting anything

Use before running any confirmatory analysis or looking at outcome data, when testing a hypothesis, computing a p-value, or about to claim an effect - locks predictions and decision rules before results are seen

Use when receiving critical feedback on an analysis or manuscript, before implementing suggestions, especially if feedback seems unclear or methodologically questionable - requires verification, not performative agreement or blind changes

Rewrite dense or technical text into a clear plain-language summary with a fixed structure (TL;DR, why it matters, key points, caveats). Use when the user asks to summarize, simplify, explain, "put this in plain language", or make something readable for a general / non-expert audience.