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Aaron Karlsberg

Publications and source records attributed to Aaron Karlsberg.

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Compiled AI: Deterministic Code Generation for LLM-Based Workflow Automation

We study compiled AI, a paradigm in which large language models generate executable code artifacts during a compilation phase, after which workflows execute deterministically without further model invocation. This paradigm has antecedents in prior work on declarative pipeline optimization (DSPy) and hybrid neural-symbolic planning (LLM+P); our contribution is a systems-oriented study of its application to high-stakes enterprise workflows, with particular emphasis on healthcare settings where reliability and auditability are critical. By constraining generation to narrow business-logic functions embedded in validated templates, compiled AI trades runtime flexibility for predictability, auditability, cost efficiency, and reduced security exposure. We introduce (i) a system architecture for constrained LLM-based code generation, (ii) a four-stage generation-and-validation pipeline that converts probabilistic model output into production-ready code artifacts, and (iii) an evaluation framework measuring operational metrics including token amortization, determinism, reliability, security, and cost. We evaluate on two task types: function-calling (BFCL, n=400) and document intelligence (DocILE, n=5,680 invoices). On function-calling, compiled AI achieves 96% task completion with zero execution tokens, breaking even with runtime inference at approximately 17 transactions and reducing token consumption by 57x at 1,000 transactions. On document intelligence, our Code Factory variant matches Direct LLM on key field extraction (KILE: 80.0%) while achieving the highest line item recognition accuracy (LIR: 80.4%). Security evaluation across 135 test cases demonstrates 96.7% accuracy on prompt injection detection and 87.5% on static code safety analysis with zero false positives.

cs.SE

RNA-seq data science: From raw data to effective interpretation

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community to develop accurate and scalable computational tools. RNA-seq is a method of analyzing the RNA content of a sample using the modern sequencing platforms. It generates enormous amounts of transcriptomic data in the form of nucleotide sequences, known as reads. RNA-seq analysis enables the probing of genes and corresponding transcripts which is essential for answering important biological questions, such as detecting novel exons, transcripts, gene expressions, and studying alternative splicing structure. However, obtaining meaningful biological signals from raw data using computational methods is challenging due to the limitations of modern sequencing technologies. The need to leverage these technological challenges have pushed the rapid development of many novel computational tools which have evolved and diversified in accordance with technological advancements, leading to the current myriad population of RNA-seq tools. Our review provides a systemic overview of RNA-seq technology and 235 available RNA-seq tools across various domains published from 2008 to 2020, discussing the interdisciplinary nature of bioinformatics involved in RNA sequencing, analysis, and software development.

q-bio.GN