Large Language Model Pipelines

Argument Mining (AM) transforms natural language into its underlying argument structures. This transformation is typically realized through a sequence of AM tasks that form an end-to-end AM pipeline. However, AM approaches often differ in how they conceptualize these tasks, making direct comparisons between them difficult and opaque. This calls for a more nuanced, task-level analysis of AM approaches to enable clearer comparison and assessment. This work presents a preliminary meta-study that systematically reviews several state-of-the-art end-to-end AM works and analyzes their pipelines through a triple-perspective framework---a linguistic, computational and domain perspective---to understand how the pipelines model arguments as structures, computes them, and integrates domain knowledge. We further propose a general design to the linguistic and computational perspectives, illustrating how key AM tasks are designed for modeling and computation of argument structures. Our proposed framework lays the groundwork for methodology-centered descriptions across AM approaches, facilitating deeper understanding and more systematic comparisons in future research.

Know Your Client (KYC) onboarding in capital markets requires analysts to manually classify documents, extract structured data from heterogeneous sources, and validate compliance against complex regulatory policies. This process requires significant analyst time per client, with end-to-end onboarding often stretching to multiple weeks due to sequential handoffs. In this work, we analyze an on-boarding process and find that it comprises repeatable components well-suited to AI automation. We therefore propose a restructured workflow to be amenable to automation: we consolidate the traditional four-party process into two parties that share most of the work and can be automated together, eliminating intermediate handoffs that compound delays. To automate the remaining steps, we introduce Spectra, an AI-assisted document processing platform that combines a structured rules engine with LLM-based classification, extraction, and validation agents. The rules engine encodes compliance policy as a queryable database, enabling focused context injection that reduces token usage while improving extraction precision. Rather than a single monolithic prompt, the system decomposes document processing into isolated, auditable stages, each optimized independently and traceable to specific policy clauses. In evaluation on real KYC documents, Spectra achieves 100% classification accuracy and 89.4% extraction accuracy. Human review burden dropped by 96%.

Enterprise guideline documents mix narrative text, complex tables, and embedded images, and converting them into structured work artifacts still takes two to three days of manual effort each. Current language and vision-language models extract from such documents but offer no governed workflow beyond extraction: no validation, no consistency checking, no traceable artifact generation. We introduce SAGE, a governed multi-stage LLM pipeline organized around a shared versioned rule store with stable identifiers, schema-validated inter-stage contracts, and end-to-end provenance tracking. Extracted rules undergo deterministic structural validation and LLM-based semantic scoring, then a consistency module that removes duplicates, flags contradictions, and surfaces specification gaps; only uncertain or flagged items reach reviewers, while high-confidence outputs are auto-approved. On 120 documents, SAGE cuts turnaround from days to 20-100 minutes, achieving a 96% document-level success rate with 3.2% hallucination, extracting 3,896 rules and producing 812 artifacts ready for human review; without governance, hallucination rises to 15.7%.

Customers rely on specific product attributes to compare products and make purchasing decisions, but e-commerce catalogs are messy and unstructured, making it difficult to identify which attributes matter most and extract them at scale. Standard Attribute Value Extraction (AVE) systems treat all attributes equally, producing large, inconsistent attribute sets that do not reflect the factors consumers use to differentiate products. We introduce a two-stage LLM pipeline that first discovers a compact, ranked schema of purchase-discriminative attributes for each product category, then extracts their values from catalog text using a fine-tuned compact LLM (Qwen3-4B) with Hyper-Parallel Decoding (HPD). This pipeline achieves 85% extraction accuracy, on par with the foundational LLM it was distilled from, while reducing inference costs by 92% over foundational LLMs, enabling production-scale use for product discovery and catalog enrichment. The resulting category-level structured representations effectively constitute automatically constructed product knowledge bases, providing consistent, comparable attributes across varied product categories that can ground downstream knowledge-intensive applications.

The Asset Administration Shell (AAS) is a cornerstone of Industry 4.0 and the Digital Product Passport, providing standardized digital representations of industrial assets. While manufacturers already maintain extensive technical product documentation, generating AAS instances from existing product datasheets remains a labor-intensive task because technical information is extracted from heterogeneous document structures and often involves company-specific terminology and conventions. In this work, we present AAS-RAIL, a retrieval-augmented information extraction (IE) approach that automatically generates Asset Administration Shells from PDF product datasheets using large language models (LLMs). Instead of relying on a fixed set of few-shot examples, the proposed retrieval-augmented in-context learning (RAIL) approach retrieves LLM-generated extraction helpers from similar Asset Administration Shells to provide instance-specific in-context learning (ICL). This enables the model to adapt its extraction behavior to company-specific naming conventions and formatting styles without fine-tuning. Our core contribution is the dynamic selection of company-specific AAS examples for each datasheet, replacing static prompting with an extraction pipeline that adapts to instances and combines semantic retrieval and structured information extraction. The proposed approach is evaluated on a collection of industrial product datasheets using a selection of open- and closed-weight LLMs. Experimental results show that RAIL consistently improves extraction quality over conventional few-shot prompting, yielding relative improvements of 30.4-52.4%. These results demonstrate that our approach provides an effective improvement for company-specific AAS generation.

Process mining (PM) provides a powerful framework for discovering and optimizing operational processes from event data. However, the efficacy of PM techniques is strictly predicated on the availability of structured event logs. Thus far, event logs have often been laboriously created by domain and process mining experts. This costly effort causes large portions of organizational knowledge, including incident tickets, manuals, and textual reports, to remain underutilized. We address this bottleneck by investigating the efficacy of Large Language Models (LLMs) as automated data translators. We propose a scalable framework that leverages LLMs as data translators to bridge the gap between unstructured textual resources and structured event data. We finetune LLMs on a newly created text-to-log dataset, demonstrating that the resulting models can extract high-fidelity event logs from unstructured resources. Our results show that this finetuning approach outperforms few-shot or zero-shot prompting by a large amount, highlighting finetuning as a necessary pre-condition for generating reliable event data. We conclude that our method provides a promising pipeline for making previously unused data available to process mining ecosystems, effectively expanding the possibilities of using PM to further investigate organizational workflows.

This paper presents Murano, an open source framework for designing, running, and reproducing mechanistic interpretability studies of large language models, intended for researchers across disciplines. These studies often combine loading, recording, attribution, intervention, and evaluation, while existing libraries tend to focus on different parts of this workflow. As a result, researchers using several libraries may need to adapt outputs from one for use by another. To bridge this gap, Murano represents operations from these five areas as composable steps. Steps exchange named result artifacts and declare the inputs they require and the outputs they produce. A pipeline executes its steps in the order supplied, and Murano uses canonical addresses when component identities pass between operations. Murano builds on existing interpretability and machine learning libraries. We demonstrate Murano through two reproductions of established interpretability studies and one illustrative sparse autoencoder case study.

IT service management (ITSM) systems accumulate large volumes of heterogeneous ticket data that are difficult for sales and executive stakeholders to convert into actionable intelligence. This paper presents a sociotechnical AI pipeline, designed and evaluated following design science research principles, that transforms raw ITSM exports into a multilevel decision-support artifact. The pipeline combines LLM-based schema normalization, HDBSCAN sub-topic clustering, and hierarchical agglomerative clustering to generate executive-facing Main-topics and granular Sub-topics. A stakeholder evaluation across six artifacts and five raters from Sales Engineering and customer success roles shows that all four decision-support metrics, interpretability, actionability, trust, and likelihood of use, on average exceed 4.0 out of 5.0, with trust as the most consistent signal. The findings position ITSM analytics as an Information Systems (IS) problem of transformation, abstraction, and human-centered design.

Model Cards and Data Cards have demonstrated the value of structured, human-readable documentation for machine learning artifacts, capturing their context, parameters, limitations, and intended use. However, these practices remain focused on static artifacts (the datasets and trained models themselves) while overlooking the workflow executions that produce, transform, and evaluate them. Such executions hold critical details about data preparation, parameter choice, runtime behavior, resource use, and intermediate transformations, precisely where bias, performance variation, and reproducibility gaps tend to originate. To close this gap, we introduce Workflow Cards: structured summaries that condense the machine-readable provenance data of a workflow execution into a form both humans and large language models (LLMs) can read and analyze. This paper has two main parts. First, it defines a Workflow Card template informed by a representative set of provenance questions that surface from the execution-level data missing from Model and Data Cards. Second, it evaluates how effectively LLMs use Workflow Cards to understand workflow executions compared with querying provenance databases through a schema-based interface. Results show that Workflow Cards provide execution-level information absent from existing card types, such as Model Cards and Data Cards, thereby filling an important documentation gap; and that Workflow Cards nearly double answer quality compared with schema-based querying, consistently across LLM-as-a-Judge and human assessments.

Reranking medical procedures against patient queries is a critical component of health insurance information retrieval, complicated by a substantial lexical gap between patient language and clinical nomenclature. We present a systematic comparison of two reranking paradigms for this production task: (1) small cross-encoders (MedCPT, MiniLM-L12) fine-tuned with listwise learning-to-rank objectives across layer freezing configurations, and (2) Qwen3-Reranker-4B, a 4B-parameter instruction reranker whose prompt is iteratively refined via an agentic optimization loop driven by GPT-4.1. On a purpose-built dataset of 2,647 queries across 708 insurance services, we find that a 109M-parameter cross-encoder fine-tuned with ListNet outperforms the 4B-parameter model by 2.6 percentage points on NDCG@3 and 13.3 points on Spearman correlation - at 37x fewer parameters. We report practical findings, a scalable LLM based dataset construction pipeline, and deployment trade-offs relevant to production reranking systems. We release our code and a sample dataset to support reproducibility and adaptation to other domains.

Depression is a major mental disorder for which diagnosis relies primarily on clinical assessments. Automated methods to support its detection via the psychiatric MADRS scale are getting more and more attention. While existing solutions primarily focus on detecting the disorder from different text sources (e.g., online text, social media), there is still limited support for clinical trials, where clinical assessments are conducted through structured interviews based on standard guidelines such as SIGMA. In this work, we develop a LLM pipeline specifically designed to support clinicians in supporting the assessment of depression in patients enrolled in clinical trials. Our pipeline converts audio interviews into transcripts, maps them into the ten MADRS symptom items, estimates their severity, and identify problematic clinical ratings associated with them. Evaluation on real clinical interviews shows a strong overall correlation of 0.867 with expert ratings, providing interpretable support for future assessments in clinical trials.

Pretraining data processing is critical to the downstream performance of Large Language Models (LLMs). However, many existing approaches define a fixed processing strategy at the corpus or domain level and apply it uniformly to many examples, without adapting to the needs of each example. We propose DataOrchestra, a framework that unifies different processing operations and orchestrates an example-specific pipeline for each example. Given a chunk of pretraining data, an orchestrator decides whether to drop, untouch, or clean it. For a chunk to be cleaned, it selects one or more downstream operations, ranging from programmatic editing to different forms of LLM-based rewriting. For each rewriting step, it further generates a concrete instruction, which is executed by the corresponding downstream tool model. We pretrain models from 0.5B to 7B from scratch on web data processed by DataOrchestra and observe stable average gains over individual data-processing methods across 11 benchmarks. DataOrchestra is also effective for math continued pretraining and outperforms stronger processing baselines, while reducing processing compute by skipping unnecessary downstream operations.

Computational nutrition needs precise ingredient data, but current databases are incomplete, inconsistent, and built for human reference rather than automated reasoning. LLMs could help fill these gaps, but single-pass outputs are unreliable and can introduce silent errors into downstream computation. We present a quality-controlled LLM pipeline for ingredient data acquisition that combines robust statistical estimation, domain-specific invariant checks, and a web-fetch fallback. An illustrative Heap's Law fit to 233 recipes suggests that unique-ingredient growth is sub-linear and front-loaded: the projected ratio of unique ingredients to recipes falls from 1.74 at 100 recipes to 0.19 at 5,000. For each ingredient attribute, repeated LLM queries are treated as samples from a model-induced answer distribution, and we apply robust point estimators and normalised confidence scores across numerical, Boolean, multiple-choice, open categorical, and optional integer types. An invariant guard layer enforces nutritional and logical self-consistency within each ingredient record. Minor numeric inconsistencies are reconciled via a linear program that minimises worst-case percentage deviation while preserving semantic zeros, and major violations are escalated to web-evidence-grounded repair, then human review only if that fails. On a curated 30-ingredient reference set, the pipeline achieves 98.4% exact match on nutrient flags and cuts median absolute percentage error on nutrient ratios from 31.9% for the median-aggregated baseline to 10.1%, a reduction of 21.8 percentage points, at an API cost of about $1 per ingredient. This frames LLM-assisted database construction as a controlled data-engineering workflow that makes uncertainty operational rather than discarding it.

Multi-stage LLM hiring pipelines (resume improvement, interview question generation, answer feedback) can fabricate credentials, inflate qualifiers, and invent experience. We evaluate two mitigations, prompt guardrails and human-in-the-loop (HITL) checkpoints, against a fully automated baseline. In a controlled experiment (10 synthetic resumes x 2 job descriptions x 3 repetitions x 3 conditions; 180 runs), the baseline (C1) produced at least one unsupported claim in 96.7% of outputs (mean 6.80 findings/output). Prompt guardrails (C2) reduced finding density by 86% (6.80 to 0.92/output), but 50.0% of outputs still contained a fabrication, showing prompt-level mitigation alone is insufficient. A human checkpoint after resume improvement (C3) eliminated all identity fabrications, reduced finding density by 59% (6.88 to 2.82/output), reduced item-level fabrication from 96.7% to 75.0% (p=.022), and cut capture of JD-embedded trap requirements from 47% to 2% (vs. 5% under the guardrail). An exploratory analysis of multi-specialty resumes shows contamination rising monotonically with domain distance between specialties, suggesting career changers are especially exposed. The reviewer in this study caught all flagrant fabrications, but subtle qualifier drops and plausible new claims survived review roughly half the time (54.5% removal). Neither mitigation degraded the deliverable: claim retention exceeded 99% under both. The interventions are complementary: the guardrail eliminates unprompted additions and qualifier inflation cheaply, while the checkpoint gives near-categorical guarantees against the most severe failures, invented identities and JD-baited claims. These results support a layered architecture combining guardrails with a human checkpoint. A supplementary run with a newer-generation model (90.0% baseline fabrication rate) suggests the problem is not resolved by model progress alone.

Large language models (LLMs) are increasingly used to automate data-processing workflows, yet coding agents typically produce scripts that are not automatically materialized as persistent, editable platform artifacts. We call this disconnect the \textit{NL2Pipeline gap}. To bridge it, we introduce \textsc{DataFlow-Harness}, a platform that guides an LLM agent to construct platform-native directed acyclic graphs (DAGs) through typed, incremental mutations rather than free-form scripts. The platform combines \textsc{DataFlow-Skills} for procedural guidance, a Model Context Protocol (MCP) layer that exposes the live operator registry and current pipeline state, and \textsc{DataFlow-WebUI}, which synchronizes conversational authoring with a visual DAG editor. On a 12-task data-engineering benchmark, \textsc{DataFlow-Harness} achieves a 93.3% observed end-to-end pass rate. Relative to Vanilla Claude Code, it reduces measured monetary cost by 72.5% and generation latency by 49.9%; its observed pass rate is within 0.9 percentage points of the Context-Aware Claude Code baseline while its cost is 42.8% lower. Per-task analysis indicates that Skills are most useful when construction depends on implicit procedural knowledge. These results show that live platform grounding can produce persistent, editable workflow artifacts with an observed reliability close to script-generation baselines and with lower measured construction cost and latency.

Large language model (LLM) trading agents show promising performance in equity markets, yet remain narrowly focused on US equities with little evidence from live deployment. We present Fin-Analyst, a hybrid agent for FinMMEval 2026 Task 3: an eight-specialist LLM pipeline over news, SEC filings, fundamentals, analyst forecasts, technical indicators, and social sentiment, aggregated by a Meta-Agent for Tesla (TSLA), and a lightweight rule based three-signal vote for Bitcoin (BTC). On the final official leaderboard (accessed 2026-07-05), Fin-Analyst ranks first of all agents on TSLA with a +13.51% return, +28.33 points over Buy-and-Hold (Sharpe 4.10, 88% win rate), while the BTC vote ends flat yet well above a sharply falling baseline. Relative to the interim performance, the asset ranking reversed, indicating that short live windows yield volatility-sensitive rankings. Ablation identifies event-driven 8-K disclosures as the most influential TSLA signal. Error analysis shows that the memoryless agents repeat wrong calls for days at a time, and that the fixed-threshold BTC rules lost money by trading on noise in a sideways market while the LLM pipeline gained under similar conditions, motivating a memory-aware, LLM-based successor for both assets.

Open physiological corpora are heterogeneous: they use different sensors, labels, sampling rates, recording settings, and clinical endpoints. They can support detector design, but they do not directly specify which detector rules should be built for a new contactless monitoring platform. We report a controlled four-analyst large-language-model (LLM) workflow for converting 68 public physiological corpora, screened for commercial-use compatibility, into an auditable library of candidate rule shapes for prospective validation. Four independent commercial LLM families read the corpus documentation under a controlled prompt and produced 695 candidate rule markers (top-markers). Deduplication retained 649 rule records; a threshold-bounds audit then flagged 51 sanity violations for clamping or curator review. Cross-corpus consolidation produced 436 unique rule shapes. Gate-tagging against two hard invariants, native target-hardware channel availability and no multi-night per-patient personalization, identified 94 build-now detector components across four detector-family buckets. The pipeline does not produce a validated clinical detector. It produces an auditable engineering cascade in which analyst disagreement, threshold checks, curator review, and automated continuous-integration (CI) checks route literature-derived rules toward prospective hardware validation.

Biomedical question answering requires not only accurate extraction of information from scientific literature but also reliable integration of evidence across multiple documents. This study presents a question-type-specific large language model (LLM) framework for BioASQ 14b Task B, designed to improve answer robustness and evidence grounding in biomedical question answering. Rather than applying a single prompting strategy to all questions, the framework selects different inference procedures for yes/no, factoid, and list questions according to their distinct reasoning and evaluation requirements. For yes/no questions, snippet shuffling and self-reflection are used to reduce sensitivity to evidence ordering and improve decision stability. For factoid questions, full-snippet input is combined with chain-of-thought-based in-context learning to support accurate biomedical entity identification. For list questions, a multi-agent architecture is employed, in which evidence extraction, candidate generation, answer verification, and final aggregation are handled collaboratively. Preliminary experiments on BioASQ 13b were used to identify effective inference strategies for each question type, and the resulting framework was subsequently evaluated in the official BioASQ 14b Task B challenge. In the official evaluation, our framework showed competitive performance across multiple batches and achieved first place in the factoid subtask of Batch 4. These results demonstrate the effectiveness of combining question-type-specific inference, ensemble prediction, and agent-based verification for reliable biomedical question answering.

Real estate property listings expose structured metadata through the API. Still, the richest property-level information (i.e., legal status, structural condition, utility supplies, heating systems) sits in attached questionnaire documents that no automated system currently processes at scale. These documents are heterogeneous. Some are digitally generated with selectable text, others are scanned physical forms. There are even more complex layouts that contain checkbox annotations that defeat conventional text extraction. In this paper, we present an end-to-end pipeline for acquiring, classifying, and extracting structured data from selectable text documents. The pipeline was applied to 3965 questionnaire documents collected from a live property platform via reverse-engineered REST APIs. First, we classified each document into one of three structural categories (text_only, scanned, and special_char), then extracted 35 predefined property attributes from eligible documents using DeepSeek R1 as the Large Language Model, prompted to return a structured JSON object. All 2781 submitted documents were processed successfully, producing a final dataset of 2766 unique property records. Downstream validation confirmed the data quality. Cosine similarity matching achieves a Jaccard consistency score of 0.82, and K-Means clustering produces interpretable market segments with a silhouette score of 0.2088. Results show that the proposed extraction from each property document is both feasible and reliable at this scale.

A central goal of mechanistic interpretability is to understand how neural networks work and what each individual component does. Dominant circuit-finding approaches focus on a specific behavior and reverse-engineer the role of components on the associated sub-distribution. However, past work has shown that components can have different functions that are active on different subsets of the input distribution. In this work we ask whether a single weight can be understood globally across the full training distribution by characterizing when it matters (the inputs on which ablating it changes the model's predictions). We introduce an automated LLM pipeline that writes a short, human-readable description of when a weight matters and verifies it on held-out text, crediting a weight only if its description generalizes. Across two sparse and two dense transformers, the fraction of weights that are interpretable (in this sense) is higher in sparse transformers than in dense ones, a gap that widens once unreliable descriptions are discarded. Our results show that a meaningful fraction of a sparse transformer model's weights can be interpreted: 12 to 31% of weights have a single short description that identifies what the weight is used for.

Autonomous-research agents have demonstrated end-to-end LLM automation in machine-learning sandboxes where execution provides calibration. Frontier physical science differs categorically: physical reasoning underlies every methodology choice, toolchains are often underdocumented, and calibration must come from external literature anchors - which unscaffolded agents cite but do not confront, hallucinating plausible, unverifiable results from internal priors. We present a pipeline that runs end-to-end from a corpus of 11,083 recent condensed-matter physics arXiv papers to a publication-grade manuscript with three substantive physics findings (here on altermagnetic piezomagnetism): the agent autonomously conceives a research direction by mapping the corpus, calibrates methodology by reproducing published references, conducts novel first-principles computations, and writes the manuscript - grounded in literature throughout, across 47 fresh-context sessions in six phases sharing only on-disk state, with 2,162 literature-consultation events. Fault tolerance emerges from redundancy: fresh-context isolation, distributed grounding, and adversarial review catch what any single session misses; pre- and post-pilot stages are fully autonomous, and pilot requires bounded human intervention only at reproduction failures - operational knowledge curation, not scientific direction. Two paired failure modes - a pre-architecture baseline and a no-pilot ablation - isolate structurally enforced numerical confrontation at calibration checkpoints as the operative grounding mechanism. The primitives, characterized failure modes, and quantified intervention pattern lay a foundation for autonomous research in high-stakes scientific domains beyond computational physics.

We study inference-time pattern-memory gating in a production-scale clinical natural language processing (NLP) pipeline. The pipeline pairs a generator (Llama-3.3 70B) proposing extractions with a verifier (MMed-Llama-3.1 70B) accepting or rejecting them, over 167,034 PMC-Patients narratives, and adds a lightweight memory that learns at deployment which extractions to filter, so the verifier need not re-examine candidates already seen to fail. We report four findings. First, learning filtering rules directly from the verifier's rejections failed at full scale: the relation-extraction filter stayed empty despite 785,797 logged rejections, because they were spread too thinly across too many distinct forms to accumulate. Second, a simpler rule using a fixed clinical ontology produced the same filtering without the verifier, capturing 49,734 ontology-violating relations on a held-out 5,000-patient set. Third, of five versions of the question-answering filter, four failed for distinct, instructive reasons; the fifth succeeded by checking whether a patient's extracted entities support the question asked, and where it applies was 1.84 times likelier to flag an answer the verifier would reject than one it would accept. Fourth, one pattern held across all five: a filter is selective only when it tests the same evidence the verifier weighs, not when it imitates the verifier's output. Together these give a transferable result for any generator-verifier pipeline: the most natural memory design can fail silently at scale, and whether a pre-generation gate is selective is decided before any engineering effort, by whether its signal probes the question the verifier itself answers. Throughout, the system flags suspect extractions rather than deleting them, so every decision stays visible for clinical review. All code and test artefacts are released openly.

Government documents in India are predominantly issued in regional languages such as Marathi, creating substantial accessibility barriers for non-native readers, interstate administrative bodies, and policy analysts. Although recent advances in neural machine translation have improved sentence-level translation quality, existing systems largely neglect document structure, formatting integrity, and domain-specific terminology, thereby limiting their applicability to official documentation. This paper presents a structure-preserving Marathi-to-English government document translation framework capable of performing end-to-end document transformation while maintaining layout fidelity. The proposed system integrates layout-aware optical character recognition, coordinate-based text extraction, large language model based translation, and structured document reconstruction through HTML representations. By enforcing spatial alignment constraints and preserving hierarchical document elements, the framework ensures structural consistency between the source and translated documents. Experimental evaluation on real-world Marathi government PDFs demonstrates improved structural preservation, translation coherence, and terminological consistency compared to conventional text-only translation pipelines. The proposed framework contributes toward scalable multilingual accessibility solutions for e-governance and administrative document processing.

Data preparation pipelines improve data quality in machine learning by transforming raw tables into learning-ready data through sequential cleaning and feature transformation operators. However, automatically constructing such pipelines is computationally difficult because operator sequences are combinatorial and end-to-end evaluation is expensive. Existing state-of-the-art (SOTA) Multi-DQN methods still face three key limitations: decoupled value estimators weaken long-horizon credit assignment, dataset context is only weakly injected into the policy, and exploration is inefficient in a sparse search space with many invalid states. To address these issues, we propose FlowPipe, a unified framework that formulates pipeline synthesis as conditional probabilistic flow generation over a directed acyclic graph. FlowPipe uses Conditional Generative Flow Networks (C-GFlowNets) with a Trajectory Balance objective to connect terminal validation rewards with early pipeline decisions. It further introduces Deep Semantic Modulation through Feature-wise Linear Modulation (FiLM), allowing LLM-derived logical priors to condition the policy's internal activations according to dataset semantics. In addition, FlowPipe incorporates failure awareness into the flow objective to avoid invalid states and concentrate search on high-potential regions. Experiments on two benchmark suites with 74 real-world datasets show that FlowPipe outperforms SOTA baselines, improving accuracy by 11.96% on average and achieving 12.5x faster training convergence. Source code is available at https://github.com/KunyuNi/FlowPipe.

Data curation is a critical part of post-training pipelines for large language models, yet existing tools often treat ingestion, deduplication, synthetic generation, and quality filtering as separate stages. This fragmentation makes it difficult to audit pipeline decisions or understand why individual samples are rejected. CuratorKIT is an open-source Python library that covers this full lifecycle in a single configurable pipeline. The framework is composed of six source format readers and automatic schema detection, a pre-generation data hygiene layer for credentials, PII, and toxic content, eight LLM-powered generation tasks, three complementary quality gates with provenance-exact hallucination verification, structured adaptive recovery, and five training-ready export formats compatible with TRL, Unsloth, and AlignTune. Every pipeline decision is recorded in an append-only per-sample provenance chain, and rejected samples carry structured failure reasons rather than being silently discarded. CuratorKIT supports 100+ LLM providers through LiteLLM, exposes both a Python API and a YAML-driven CLI, and is designed for practitioners who need reproducible, auditable data pipelines at scale .

Information extraction from pathology reports is essential for cancer staging, tumor registry population. Yet key data remains embedded in narrative reports, making manual extraction labor-intensive and error-prone. Traditional supervised Natural Language Processing pipelines address this through fully supervised Named Entity Recognition and Relation Extraction, but require expensive manual annotation and suffer cascading failures when upstream entities are missed. In this study, we developed a zero-shot, agentic workflow, and evaluated five open-source generative Large Language Models (LLMs) to populate 13 College of American Pathologists synoptic fields from lung resection pathology reports. We compared them against a state-of-the-art supervised GatorTron NER-RE baseline using a novel, registry-aligned evaluation framework. The baseline achieved Micro-F1of 0.960, while the best zero-shot model (GPT-OSS-20B) achieved Micro-F1 of 0.893 (recall: 0.949), accurately extracting complex relations like Pathologic Stage without task-specific training. These results suggest that open-source, zero-shot agentic LLMs show great potential as a low-cost solution for extracting lung pathology information.

Researchers are interested in learning about Mars so that it may eventually become habitable for humans. To achieve this, there is a need for comprehensive knowledge of the planet's atmosphere, hydrology, surface chemistry, radiation environment, and spatial features through the scientific literature. These contain valuable information and meaningful quantitative constraints that can be used in other models and studies, such as habitability assessment and future terraforming studies. We present TerraMARS, an end-to-end information extraction pipeline that combines a domain-adapted Small Language Model to answer Mars terraforming-related questions and convert unstructured Mars science text into machine-readable structured outputs in JavaScript Object Notation (JSON) format. A corpus of open-access papers is collected and processed using a multistage retrieval and chunking framework. Google Gemma 3 1B was adapted to the domain using Quantized Low-Rank Adaptation (QLoRA) fine-tuning on Mars-specific question-answering and information extraction datasets. The resulting pipeline generates both types of output and provides a foundation for integrating knowledge from scientific literature into downstream applications like digital twins and habitability modeling for Mars. The output from this pipeline looks promising, but further improvements are needed to increase extraction accuracy and factual consistency.

Multi-step LLM pipelines fail through interactions among retrieval, reasoning, and formatting steps, so prompt-only optimization can miss bottlenecks in the chain. We present Fully Automated Prompt Optimization (FAPO), a framework that lets Claude Code optimize an LLM pipeline inside a standardized codebase. FAPO evaluates a pipeline, inspects intermediate steps, diagnoses failures, proposes scoped changes, and validates variants repeatedly to optimize against a score function. It first tries prompt edits and, only when prompt optimization appears insufficient, changes chain structure within the permitted scope when attribution identifies a structural bottleneck. Across six benchmarks and three task models, FAPO beats the baseline GEPA in 15 of 18 model-benchmark comparisons. In 11 model-benchmark comparisons, FAPO wins with non-overlapping mean $\pm$ trial-standard-deviation ranges, and the mean FAPO-GEPA gain is +14.1 pp. In the six HoVer and IFBench comparisons where prompt-first search escalated to structural changes, FAPO wins all six with a mean gain of +33.8 pp. FAPO also improves performance on security tasks: on CTIBench-RCM, a security CVE-to-CWE task, prompt-only FAPO lifts test accuracy by +4.0 pp on GPT-5, +7.1 pp on Foundation-Sec-8B-Instruct, and +2.0 pp on Foundation-Sec-8B-Reasoning. These results position FAPO as a state-of-the-art pipeline optimization technique for both general-purpose and security-focused tasks.

While expert-validated "LLM + script" workflows deliver significant value, they remain static: they encode hard-won domain knowledge yet fail to adapt execution based on feedback. Existing agent research predominantly targets greenfield agents and synthetic benchmarks, leaving the migration of active legacy workflows unresolved. To bridge this gap, we present a reversible, Strangler-Fig migration path that refactors legacy workflows into composable, typed, and auditable stages. Central to this framework is a three-tier convertibility taxonomy (A/B/C), implemented as a routing stage within the system harness, which diagnoses a workflow's readiness and routes it accordingly.

Motivation: Patient-generated text contains critical information on patients' lived experiences, social context, and care engagement, but remains largely unstructured, limiting its use in patient-centered outcomes research. Prior work introduced the PV-Miner benchmark and PVMinerLLM models for structured extraction. However, supervised fine-tuning (SFT) alone struggles with rare, fine-grained, and unevenly distributed errors, particularly in token-critical structured outputs. Results: We present PVminerLLM2, an improved set of LLMs for structured patient voice extraction that applies preference optimization to address token-critical errors beyond the reach of supervised fine-tuning. Our method introduces (i) a preference objective with token-level gated stabilization term that prevents degradation of absolute token likelihood under preference optimization, and (ii) confusion-aware preference pair construction to better capture low-separation distinctions. We further incorporate token-importance weighting and inverse-frequency reweighing to address token imbalance and class skew. Across multiple model sizes, PVMinerLLM2 consistently outperforms strong baselines, achieving gains of up to 4.43% (Code), 3.50% (Sub-code), and 1.55% (Span), and outperforms baseline LLM trained with existing preference optimization methods. Availability and Implementation: The supplementary material, code, evaluation scripts, and trained models for PVminerLLM2 are publicly available at: https://github.com/Data-Mining-Lab-Yale/PVminerLLM2

Electronic prior authorization workflows require FHIR Questionnaire items to carry LOINC codes, yet most items in the HL7 Da Vinci CDS-Library lack these bindings. We treat this as a retrieval problem: given a Questionnaire item's text, find the correct LOINC code in a pool of 97,314 active codes. We compare six methods (TF-IDF, frozen MiniLM, BioBERT, BioLORD, contrastively fine-tuned MiniLM, and a TF-IDF+GPT reranker) on a 54-item evaluation set spanning three query styles (natural question, medium, and terse). No single method wins on every metric. BioLORD, a frozen encoder pre-trained on biomedical ontology definitions, has the best top-rank accuracy (R@1 = 0.185, MRR = 0.246) despite seeing no task-specific data, while a contrastive fine-tune on raw LHC-Forms pairs takes R@5 (0.389) and R@10 (0.426). A distribution-shift ablation shows why the fine-tune in our main table is not the strongest one: adding GPT-generated paraphrases to the raw pairs drops R@5 from 0.389 to 0.296, so the augmented union underperforms raw-only training on every metric except R@1. Performance peaks at 5k training pairs. Error analysis on BioLORD's R@1 failures shows that wrong-specificity and ambiguous-text cases together account for 59% of errors.

Machine learning (ML) pipelines require extensive data preparation, feature engineering, and integration across heterogeneous sources, making them tedious and error-prone to develop. While large language models (LLMs) have recently shown promise for assisting programming tasks, chat-based interfaces provide limited control over pipeline behavior and often produce code that is difficult to optimize or integrate into production systems. We demonstrate SemPipes, a novel programming model that extends ML pipelines with declarative, LLM-powered semantic data operators. SemPipes allows developers to specify high-level natural language instructions for data-centric operations, while seamlessly combining these operators with arbitrary Python code from standard data science libraries. For the semantic operators, it synthesizes specialized implementations at pipeline training time, conditioned on dataset characteristics and pipeline context, enabling the flexible yet controlled integration of LLM capabilities. We demonstrate SemPipes through SemPiper, an interactive interface that visualizes computational graphs of the pipelines, synthesized operator implementations, and optimization trajectories produced by an evolutionary search procedure. Attendees can explore three end-to-end scenarios, modify pipelines, inspect generated code, and observe how semantic operators are synthesized and iteratively optimized. The demonstration highlights how declarative semantic operators enable controllable, optimizable, and practical integration of LLMs into ML pipeline development.

Current cultural alignment approaches focus on inference-time interventions, assuming models already contain sufficient cultural knowledge. We argue modern LLM pipelines suffer from a cultural data funnel. Using a multidimensional tagging framework across pretraining, fine-tuning, alignment, and reasoning datasets, we show explicit cultural signals decline sharply during post-training, while geographically concentrated, task-specialized data dominates. Multilinguality enhances geographic diversity of cultural knowledge but does not ensure balanced representation. Our tags improve downstream cultural benchmark performance, demonstrating that advances require shifting focus in training data pipelines. To facilitate future research, we release our culturally tagged dataset with 5.6M samples at https://huggingface.co/datasets/CohereLabs/CultureMarkers.

The extraction of structured clinical information from unstructured EHR notes is a persistent bottleneck in healthcare informatics. While large language models (LLMs) offer high performance, their deployment in clinical settings is hindered by privacy risks, inference costs, and the tendency to hallucinate beyond textual evidence. We address these challenges for the CL4Health 2026 Case Report Form (CRF) filling task by proposing a fully local, domain-adapted pipeline using the MedGemma-27B model. Our two-stage architecture, which separates binary presence classification from value extraction, enforces strict adherence to textual evidence and ensures deterministic outputs for negated, uncertain, or unknown states. By leveraging item-specific, few-shot in-context learning without external API calls or fine-tuning, our approach achieves a macro-F1 score of 0.55 on the official English test track. This result secures second place among all locally-hosted, open-source submissions. Our work demonstrates that privacy-preserving, on-premise LLM pipelines can achieve near-competitive performance with proprietary frontier models, providing a practical, data-sovereign framework for clinical NLP.

As autonomous research agents and AI co-scientist systems push large language models (LLMs) from drafting toward end-to-end manuscript production, the bottleneck shifts from generation to verification. Fluent LLM output can hide fabricated citations, numbers that drift from source tables, and unmet reporting-guideline items; existing tools generate without verifying, and self-critique inherits the blind spots that produce confident fabrication. We describe an architecture pairing generation with verification, resting on three principles: decompose the workflow into self-contained skills, gate every stage transition with halt-on-failure, and resolve each integrity question with the cheapest sufficient mechanism, a deterministic, re-executable check where one suffices and a prose-level probe only where interpretation is unavoidable. This determinism-where-possible split, organized as an integrity-gate taxonomy, is the core contribution. It is realized as MedSci Skills, an open-source toolkit of 43 skills with a 21-detector deterministic tier, evaluated on three public-dataset pipelines (STARD, PRISMA, STROBE) and a seeded-defect ablation. Across the three pipelines every content-hash manifest verified clean and the gates surfaced real defects; on 27 identical injected defects the deterministic gates detected all 27 with no false positives on the matched clean fixtures, whereas a single-prompt LLM reviewer detected 11, its misses in code, bibliography, and style defects the prose hides. Determinism-where-possible verification yields an auditable, re-executable trail that exposes the evidence a human needs to check an LLM-assisted manuscript: feasibility and reproducibility evidence, not a claim of human-competitive quality, which a separate blinded study addresses. MedSci Skills is MIT-licensed and archived (v3.8.0).

Effective "all-team" summarization in high-complexity settings like the Neonatal Intensive Care Unit (NICU) requires aggregating insights from diverse disciplines (physicians, nurses, therapists) spread across hundreds of clinical free-text notes. Simply pooling heterogeneous text often leads to incoherent outputs. Structured summarization therefore first requires accurate categorization of sentence-level provenance across multi-source notes. This pilot study introduces a clinical provenance categorization pipeline using supervised fine-tuning (SFT) of large language models (LLMs). We adapted two Llama-3 models (8B and 70B) to MedSecId, a corpus of 2,002 MIMIC-III (Adult ICU) notes annotated with clinical provenance headers, achieving in-domain Macro F1 scores above 92% for both models. To evaluate cross-domain generalization, we assessed model capacity (8B vs. 70B) and quantization on a gold-standard dataset of 227 sentence-level spans derived from three multi-disciplinary NICU summaries. Experimental results demonstrate a scale-dependent transfer effect: while SFT produced only marginal changes for the 8B model, it substantially improved the 70B model, increasing Macro F1 by 7%. Notably, the quantized fine-tuned 70B model outperformed its full-precision baseline while substantially reducing computational requirements. These findings suggest that sufficient model capacity is critical for preserving semantic flexibility during cross-domain clinical transfer and that efficient quantized adaptation can enable structured provenance modeling for downstream summarization.

We describe a registry-bound large-language-model extraction pipeline producing evidence-grounded structured trait records at scale, on cultivated tropical plant, aquatic, and pet species. Four mechanisms render LLM-derived rows auditable: a versioned 39-key closed-vocabulary trait registry constraining every admitted value to a typed schema; a per-row verbatim evidence quote tying each value to source text; a per-row confidence label (high or medium; low dropped pre-persist); and multi-version preservation. Applied to 409,880 publishable species from the Tropical Species Encyclopedia, the pipeline executed 706,220 runs and persisted 5,489,881 trait records across 409,820 species (99.985%), 81.57% at high confidence. We report three validation layers in descending evidentiary strength: at full population, 90.12% of 5,427,588 evidence-bearing rows have their quote as a verbatim source substring (93.49% excluding one compliance meta-trait); a quote-supports-value audit on n=100 stratified non-red-zone rows yielded 100/100 (lower bound 96.30%); face-validity on n=50 red-zone rows yielded 50/50 Accept (lower bound 92.86%). Per-record correctness is not claimed; 100% pending human curation. The contribution is the four-mechanism framework.

Public consultations generate large volumes of data in the form of stakeholder submissions that are practically unfeasible to analyse manually. We present an end-to-end LLM-based pipeline and interactive dashboard for structured topic extraction from regulatory consultation submissions, demonstrated on the European Commission's Digital Fairness Act (DFA) public call for evidence as a case study. The system processes raw PDF attachments and web-form responses, extracts topic annotations, and grounds every extraction in a verbatim quote from the source text. Applied to 4,322 DFA submissions, the pipeline produced 15,368 topic annotations supported by 20,951 verbatim evidence quotes. Three principles govern the proposed design: verbatim grounding, full traceability, and transparency by design. The dashboard exposes the full extraction dataset through five analytical views, from dataset-level topic overviews to individual paragraph drill-downs, with every result traceable to its source. Beyond the predefined DFA topic categories, the pipeline generated certain stakeholder concerns, such as Age Verification, Payment Processor Censorship, and Digital Ownership, that a fixed-taxonomy approach would have missed. The pipeline is domain-generic; adapting it to a new consultation requires only a prompt update and a new dataset. A live demo is available at https://dfa-dashboard.thalesbertaglia.com/. The code and processed data are publicly available at https://github.com/thalesbertaglia/dfa-dashboard.

We propose a novel algorithm for incremental Byte Pair Encoding (BPE) tokenization. The algorithm processes each input byte in worst-case $\mathcal{O}(\log^2 t)$ time, leading to an overall complexity of $\mathcal{O}(n \log^2 t)$, where $n$ is the input length and $t$ is the maximum token length. The algorithm incrementally maintains BPE tokenization results for every prefix of the input text, implementing the standard BPE merge procedure defined by a fixed set of merge rules. This enables efficient partial tokenization in streaming settings. Functioning as a drop-in replacement for standard BPE, our approach achieves a speedup of up to ${\sim}3\times$ over Hugging Face's tokenizers, and demonstrates significant latency reductions over OpenAI's tiktoken on pathological inputs. We further introduce an eager output algorithm that enables streaming output, emitting tokens as soon as token boundaries are determined during incremental tokenization. Overall, our results demonstrate that BPE tokenization can be performed incrementally with strong worst-case guarantees, while providing practical latency benefits in modern large language model pipelines. Code: https://github.com/ModelTC/mtc-inc-bpe

In this paper, we introduce LLMBridge, a new LLM based system for the task of end-to-end referential bridging resolution in English. Our bridging resolution pipeline combines heuristic pre/post-processing with the natural language inference ability that comes from LLMs. We evaluate our bridging resolution pipeline on three datasets which have been used for referential bridging resolution evaluation in English: ISNotes, BASHI, and GUMBridge. Comparison to previous bridging resolution systems shows that the performance of LLMBridge surpasses previous state-of-the-art (SoTA) systems for all 3 datasets in the challenging End-to-end Evaluation Setting, as well as the Basic Bridging Resolution Evaluation Setting (gold bridging anaphor given). We also conduct a thorough error analysis of the LLMBridge performance, examining what varieties of bridging remain difficult for LLM based systems to identify. With this paper, we release the code for the LLMBridge pipeline.

Multi-stage LLM pipelines that perform multi-agent debate, intrinsic self-correction, or retrieval-augmented verification exhibit puzzling aggregate behaviors: accuracy plateaus and reversals across rounds, non-replication of debate gains on contemporary frontier models, intrinsic self-correction degradation, and qualitative cross-provider divergence in debate dynamics. Downstream agent response can be operationalized as two coupled decisions: detection (whether to treat upstream content as authoritative) and conditional generation (what to produce if not). This decomposition yields four observable response regimes, of which detection-without-correction is the load-bearing failure mode. Across a nine-cell empirical grid spanning four model families, four benchmarks (GSM8K, MATH-500, GPQA-Diamond, AIME), and two methods (multi-agent debate, intrinsic self-correction), we find that the conditional miscorrection rate is consistently dominant (53-94% across cohorts) while detection rate varies contextually by more than an order of magnitude. The framework unifies the four phenomena above as signatures of a common mechanism and characterizes detection threshold as a stable model/protocol-level regularity that persists across methods at matched benchmark difficulty.

When a multi-module LLM agent fails, the module most responsible for the failure is not necessarily the best place to intervene. We demonstrate this Diagnostic Paradox empirically: causal analysis consistently identifies the routing module -- which selects which tool to call next -- as the primary bottleneck across three independent agent families. Yet injecting prompt-level correction examples into this module consistently degrades performance, sometimes severely. Patching an upstream query-rewriting module instead reliably improves outcomes. The effect holds with statistical significance on two agent families and directional consistency on a third; alternative repair strategies at the routing module (instruction rewriting, model upgrade) are neutral, confirming that the harm is specific to correction-injection patching. We explain this asymmetry through the Linguistic Contract hypothesis: each downstream module implicitly adapts to its upstream's characteristic error distribution, so correcting the bottleneck breaks this implicit alignment in a way that upstream corrections do not. We operationalize this via a per-agent co-adaptation measure, derived from diagnosis alone, and show it is consistently associated with patching harm across agent families: higher co-adaptation co-occurs with harm, lower with safety. This trend holds across all three agent families, providing preliminary support for the hypothesis beyond a single-agent observation.

Pipeline parallelism is a key technique for distributed training of large language models because it reduces per-device parameter and activation memory. However, comparing pipeline schedules is difficult: analytical models expose structural quantities such as bubble ratios, while end-to-end hardware experiments are costly and system-specific. In this work, we introduce a tabular schedule abstraction and a unified multi-abstraction methodology that connects formula-based reasoning, idealized schedule tables, and communication-aware execution simulation. Using this framework, we compare GPipe, 1F1B, Chimera, and Hanayo in its restricted regime across multiple modeled system configurations. Our results show that schedule rankings are not abstraction-invariant: communication can negate structural advantages suggested by bubble analysis alone. Under the assumptions considered here, GPipe and 1F1B are runtime-equivalent, but 1F1B achieves a lower activation-memory peak. Chimera is advantageous mainly at low microbatch counts and in communication-favorable regimes, while Hanayo is effective in its intended restricted operating point but remains sensitive to network bottlenecks. We further study an asymmetric Chimera-style placement, which does not reduce the global peak memory requirement but reveals limited runtime gains in shallow pipelines. Overall, pipeline schedule quality is meaningful only in the context of the modeled execution environment.

We tackle the question of how to scale more efficiently across the many, ever-growing stages of current LLM training pipelines. Our guiding intuition stems from the fact that the dynamics of later stages of the pipeline, e.g. post-training, can be used to inform earlier stages such as pre-training. To this end, we propose Introspective Training (or IXT), inspired by offline reward-conditioned reinforcement learning and applicable to any stage of training. IXT uses a thinking reward model to annotate data with natural language critique based feedback, enabling quality aware training from the earliest stages of the pipeline. Models are then trained by prefix-conditioning the data with the generated feedback -- ensuring that not all tokens are treated equally starting much earlier in training than usual. Comprehensive experiments on 7.5-12B transformer-based dense LLMs trained from scratch all the way up to 18 Trillion tokens seen show that our method: bends scaling curves resulting in up to 2.8x more compute efficiency generally; and reaches performance levels unachievable for models trained otherwise in domains such as math and code.

We propose last-mile fine-tuning, or Lift, a pipeline in which a pre-trained large language model extracts an initial table from unstructured clipboard text, and a fine-tuned small language model (1B-24B parameters SLM) repairs errors in the extracted table. On a benchmark of 2,596 tables from three datasets, Lift matches or exceeds end-to-end SLM fine-tuning on tree-edit-distance-based similarity (TEDS) metric while requiring as little as 1,000 training examples - where it outperforms end-to-end fine-tuning by up to 0.144 TEDS points. We term this approach last-mile fine-tuning and show it also more robust to input format variability. Comparisons with self-debug and end-to-end fine-tuning approaches show that last-mile fine-tuning provides an attractive option when training data is limited or when robustness to input variation is sought without compromising on accuracy.

We present a framework for verifying the deterministic structured computations surrounding a large language model rather than the model itself, extending a Lean 4 trust-boundary architecture to the generic interfaces of modern LLM pipelines. Certificate validity is a Lean 4 kernel type-check plus a sorry-free transitive axiom audit against the trusted set {propext, Classical.choice, Quot.sound}; other assumptions are declared and partitioned by tier (mathematical placeholders, cryptographic assumptions, ML/human oracles). The technical contribution comprises three local certificate families and two operators. The families are conflict-aware bilattice grounding (with an emission-gate soundness lemma), embedding sensitivity and paraphrase stability, and Hoare-style agent action. The operators are a Maximal Certifiable Residue, which turns abstention into the maximum-weight certifiable residue with audit-logged dropped claims, and a Compositional Stability theorem, which yields a closed-form pipeline-wide perturbation budget from per-layer gains and margins. The three families plus a Universal Assurance Card consolidator form the per-call deliverable for high-stakes deployments: patent and legal retrieval, regulated finance, clinical decision support, and agentic systems with irreversible side effects. A compiled Lean 4 reference artifact (Lean v4.30.0-rc2, Mathlib) covers all 22 certificate types, with 17 of 46 kernel-audited declarations axiom-free, the rest depending only on the trusted set and declared assumptions, and zero uses of sorryAx or Lean.ofReduceBool. The three families are empirically tested through four registered pilots: bilattice grounding on adversarially perturbed HotpotQA, embedding sensitivity in short- and long-form settings, and Hoare-style agent action on a filesystem sandbox with adversarial prompt injection.

Mental health disorders affect millions worldwide, and healthcare systems are increasingly overwhelmed by the volume of clinical data generated from electronic records, telemedicine platforms, and population-level screening programs. At the same time, the emergence of novel AI-based approaches in healthcare calls for intelligent frameworks capable of processing domain-specific unstructured clinical information while adapting to patient-specific needs. This paper proposes an agentic framework for building robust LLM-based pipelines, where each stage is encapsulated as a LangChain agent governed by explicit policies and proxy-guided evaluation. Stages are incrementally locked once validated, ensuring that later adaptations cannot overwrite configurations without demonstrated improvement. The proposed framework evolves from feature-level exploration, through proxy-based tuning and freeze/rollback mechanisms, to full orchestration by an Orchestrator Agent that coordinates preprocessing, retrieval, selection, diversity, threshold optimization, and decoding. A proof-of-concept in transcript-based depression detection demonstrates that the framework converges to stable configurations, such as cosine similarity, dynamic Top-k, and threshold 0.75, while controlling evaluation costs and avoiding regressions. These results highlight the potential of agentic AI to enable population-level mental health screening over large clinical datasets, addressing critical challenges in trustworthiness, reproducibility, and adaptability required in healthcare environments.

The power distribution engineering workforce faces a projected shortage of up to 1.5 million engineers by 2030, creating urgent demand for more accessible analysis tools. This paper introduces Grid-Orch, a framework that bridges Large Language Models (LLMs) and power system simulation through the Model Context Protocol (MCP), enabling engineers to perform complex distribution analyses via natural language. Using OpenDSS as the reference implementation, Grid-Orch provides 36 domain-specific tools across eleven categories, covering power flow, voltage analysis, quasi-static time series (QSTS) simulation, and automated optimization. A provider-agnostic LLM layer supports both cloud-hosted (Gemini, Claude) and locally deployed (Ollama, llama-cpp) models, enabling air-gapped operation for security-sensitive utility environments. Three optimization skills, capacitor placement, voltage violation analysis, and overvoltage mitigation, extend the platform beyond single-tool queries to multi-step engineering workflows. Grid-Orch is delivered as an interactive web platform with chat-based interaction, a QSTS dashboard, and feeder topology visualization, and renders simulation results inline. Workflow demonstrations show that distribution analyses formerly requiring hours of scripting, such as distributed energy resource (DER) interconnection screening, complete in under two minutes through natural language, producing numerically identical results to direct OpenDSS scripting.

Academic research tends to focus on new models for document understanding creating a wide gap in the literature between model definition and running models at production scale. To close that gap, we present a microservice architecture that encapsulates pipelines of multiple models for classification, optical character recognition (OCR), and large language model structured field extraction as well as our experience running this pipeline on thousands of multi-page documents per hour. We describe our primary design decisions, including a hybrid classification, separation of GPU-bound inference from CPU-bound orchestration, use of asynchronous processing for the many IO-bound operations in the pipeline, and an independent, horizontal scaling strategy. Using batch profiling, we identified two surprising qualitative findings that shape production deployments: OCR, not language-model parsing, dominates end-to-end latency, and the system saturates at a concurrency determined by shared GPU-inference capacity rather than worker count. Our goal is to provide practitioners with concrete architectural patterns for building document understanding systems that work beyond the benchmark; effectively operationalizing models in production.

Modern NLP and LLM systems are pipelines: named entity recognition (NER) -> entity disambiguation (NED) -> entity typing, retrieval-augmented generation (retriever -> reader), and agentic chains of planner -> tool -> critic. Errors compound across stages, but existing uncertainty quantification methods either calibrate each stage independently (no joint coverage) or apply a Bonferroni union bound (joint coverage, but conservative). We present PASC (Pipeline-Aware Split Conformal), which reduces multi-stage joint coverage to a single scalar conformal prediction problem on the joint maximum nonconformity score. PASC provides a finite-sample distribution-free guarantee that all K stages are simultaneously covered with probability at least 1 - alpha, and is nearly tight up to a 1/(n+1) factor. On a three-stage NER -> NED -> entity-typing pipeline over CoNLL-2003, PASC achieves 96.4% end-to-end coverage versus 93.4% for Bonferroni and 86.5% for independent CP, at identical average prediction set size (1.083). Under distribution shift to WNUT-17 Twitter and WikiNEuRal Wikipedia data, PASC empirically maintains the target coverage in the tested shift settings while independent CP collapses to 59%. PASC requires a single quantile computation, runs 1.7x faster than Bonferroni, and scales to K = 6 stages where independent CP drops to 0.53 end-to-end coverage. The same joint-maximum-score reduction applies directly to compound LLM systems and agent pipelines.

Predictive models in biomedicine depend on structured assay data locked in the text, tables, and supplements of primary publications. This bottleneck is especially acute in targeted protein degradation (TPD), where each assay record must combine compound identity, degradation target, recruiter, assay context, and endpoint values reported across sections, tables, and supplementary files. Inconsistent compound identifiers and incomplete or implicit assay context further demand domain-specific logic that generic LLM pipelines do not provide. Existing molecular glue and PROTAC databases are manually curated and often lack the experimental context required for downstream modeling. We formulate TPD database extraction as a domain-specific curation task and present an expert-in-the-loop LLM workflow, evaluated through a triangular comparison among LLM predictions, standardized baseline records, and expert-annotated ground truth. A lightweight cross-validated prompt-refinement module adapts extraction instructions from scarce expert annotations. With only seven annotated molecular glue publications, the workflow achieved record-level $F_1 = 0.98$ and transferred to PROTACs by terminology substitution alone, maintaining record-level $F_1 > 0.93$. Applied at scale, it expanded molecular glue and PROTAC databases by 81% and 92% records, respectively, with 92% and 82.5% of newly recovered records validated as correct upon expert review. The workflow also recovered kinetic and assay-context information essential for cross-study potency comparison and condition-aware degradation modeling. We release the workflow, prompts, evaluation code, and extracted datasets as resources for TPD data curation and AI-assisted scientific curation more broadly.

Compound AI systems that chain multiple LLM calls into directed computation graphs are now the dominant architecture for production AI. Although these architectures leverage heterogeneous nodes with mixed-mode outputs, no existing framework quantifies how perturbations propagate through such pipelines, where nodes are stochastic and execution paths can diverge structurally. We introduce QUIVER, a formal framework for measuring perturbation propagation in graph-structured LLM pipelines. The framework defines: (1) a sensitivity matrix with type-dispatched distance metrics that classifies edges as amplifiers, absorbers, or threshold-sensitive, complemented by occurrence-lift; (2) trajectory divergence decomposing variation into value drift, structural path divergence, and iteration count divergence; (3) bifurcation thresholds identifying the smallest perturbation that causes structural execution path changes; and (4) distribution faithfulness, quantifying when per node evaluation datasets diverge from production distributions. We validate on two production enterprise pipelines and a public DSPy multihop QA pipeline, three structurally distinct architectures. Across 8,200+ instrumented traces (32,000+ pair comparisons), we demonstrate that QUIVER reveals distinct sensitivity profiles across architectures, distinguishes mechanistically different cascade patterns producing identical divergence rates, predicts nodes prone to trajectory bifurcation from observational data alone, and localizes stale evaluation artifacts to specific node-field categories that aggregate metrics cannot surface.

Automated privacy audits of web and mobile applications often analyse outbound HTTP traffic to detect Personally Identifiable Information (PII) leakage. However, existing learning-based detectors typically depend on scarce, manually labelled traffic and are tightly coupled to fixed label taxonomies, limiting transferability across domains and evolving definitions of PII. This paper investigates whether Large Language Models (LLMs) can support taxonomy-agnostic annotation of explicitly transmitted PII values in HTTP message bodies when the taxonomy is provided at runtime. We introduce a multi-stage LLM-based pipeline that combines deterministic pre-processing with label-level classification, targeted instance-level value annotation, and output validation. To enable controlled evaluation and exemplar-based prompting without relying on sensitive real-user captures, we further propose an LLM-based generator for synthetic HTTP traffic with manually validated, taxonomy-derived PII annotations. We evaluate the approach across three taxonomies spanning different PII domains and granularity levels. Results show that the pipeline accurately detects PII types and extracts corresponding values for concrete PII taxonomies. Overall, our findings position LLMs as a promising foundation for flexible, taxonomy-agnostic traffic annotation and for creating labelled data under evolving privacy taxonomies.

The large-scale digitization of historical archives has created a paradox: "dark data"-digital objects lacking metadata for retrieval. Manual archival description is slow and expensive, limiting discovery and reuse. We propose Vidya, a modular pipeline that orchestrates Large Language Models (LLMs) and FOSS tools to automate semantic enrichment and archival ingestion at scale. Vidya constrains generations using YAML-defined ontologies and Pydantic validation, producing deterministic, structured JSON outputs from probabilistic models. Developed at Laboratory for Digital Humanities and Innovation (LAMUHDI) of the State University of Ponta Grossa (UEPG), Vidya applies Maker principles and open-source practices to enable low-cost deployment in memory institutions using modest hardware. We compare LLM performance and present a cost-benefit analysis showing major gains, reducing processing time from decades to days while complying with NOBRADE and ISAD(G).

Extracting structured data from unstructured text using large language models (LLMs) becomes challenging when target schemas are large and complex. In such cases, including the full schema in the prompt increases cost and latency, risks lost-in-the-middle performance degradation, and can exceed context length limits. We propose SchemaRAG, a retrieval-augmented generation (RAG) framework that dynamically prunes the output schema space for schema-conditioned information extraction tasks by leveraging schema metadata and few-shot examples when available. We evaluate SchemaRAG on real-world healthcare and e-commerce datasets. Our results show that SchemaRAG can achieve up to an 8.8% increase in micro-F1, a 47% reduction in latency, and a 48% reduction in token costs, demonstrating its practicality for large-schema extraction.

Patient portals now give individuals direct access to their electronic health records (EHRs), yet access alone does not ensure patients understand or act on the complex clinical information contained in these records. The ArchEHR-QA 2026 shared task addresses this challenge by focusing on grounded question answering over EHRs, and this paper presents the system developed by the HealthNLP_Retrievers team for this task. The proposed approach uses a multi-stage cascaded pipeline powered by the Gemini 2.5 Pro large language model to interpret patient-authored questions and retrieve relevant evidence from lengthy clinical notes. Our architecture comprises four integrated modules: (1) a few-shot query reformulation unit which summarizes verbose patient queries; (2) a heuristic-based evidence scorer which ranks clinical sentences to prioritize recall; (3) a grounded response generator which synthesizes professional-caliber answers restricted strictly to identified evidence; and (4) a high-precision many-to-many alignment framework which links generated answers to supporting clinical sentences. This cascaded approach achieved competitive results. Across the individual tracks, the system ranked 1st in question interpretation, 5th in answer generation, 7th in evidence identification, and 9th in answer-evidence alignment. These results show that integrating large language models within a structured multi-stage pipeline improves grounding, precision, and the professional quality of patient-oriented health communication. To support reproducibility, our source code is publicly available in our GitHub repository

Most enterprise document AI today is a pipeline. Parse, index, retrieve, generate. Each of those stages has been studied to death on its own -- what's still hard is evaluating the system as a whole. We built EnterpriseDocBench to take a swing at it: parsing fidelity, indexing efficiency, retrieval relevance, and generation groundedness, all on the same corpus. The corpus is built from public, permissively licensed documents across six enterprise domains (five represented in the current pilot). We ran three pipelines through it -- BM25, dense embedding, and a hybrid -- all with the same GPT-5 generator. The headline numbers: hybrid retrieval narrowly beats BM25 (nDCG@5 of 0.92 vs. 0.91), and both beat dense embedding (0.83). Hallucination doesn't grow monotonically with document length -- short documents and very long ones both hallucinate more than medium ones (28.1% and 23.8% vs. 9.2%). Cross-stage correlations are very weak: parsing->retrieval r=0.14, parsing->generation r=0.17, retrieval->generation 0.02. If quality were cascading the way most of us assume, those numbers would be much higher; they aren't. Design caveats are real (parsing fixed, generator shared, automated proxy metrics) and we don't oversell the result. One result that genuinely surprised us: factual accuracy on stated claims is 85.5%, but answer completeness averages 0.40. The system is right when it answers -- it just leaves things out. That gap matters more for real deployments than the headline accuracy number does. We also describe three reference architectures (ColPali, ColQwen2, agentic complexity-based routing) which are not yet integrated end-to-end. Framework, metrics, baselines, and collection scripts will be released open-source on acceptance.

Clinical framing -- the linguistic manner in which clinical information is presented -- can influence patient understanding and decision-making, with important implications for healthcare outcomes. Obstetrics is a high-stakes domain in which physicians counsel patients on delivery mode choices such as vaginal birth after cesarean (VBAC) and repeat cesarean section (RCS), yet counseling language remains underexplored in large-scale clinical text analysis. In this work, we analyze physician counseling language in 2,024 obstetric history and physical narratives for a rigorously defined cohort of patients for whom both VBAC and RCS were clinically viable options. To control for confounding due to medical contraindications, we first construct a VBAC-eligible cohort using structured clinical data supplemented by a large language model (LLM)-based extraction pipeline constrained to grounded, verbatim evidence from free-text narratives. We then apply a zero-shot LLM framework to categorize counseling segments into predefined framing categories capturing how physicians linguistically present delivery options. Our analysis reveals a significant difference in counseling framing distributions between VBAC and RCS notes; risk-focused language accounts for a substantially larger share of counseling segments in RCS documentation than in VBAC, with category-level differences confirmed by statistical testing, highlighting the value of controlled LLM-based framing analysis in obstetric care.

The promise of data-driven materials discovery remains constrained by the scarcity of large, high-quality, and accessible experimental datasets. Here, we introduce a generalizable large language model (LLM)-powered pipeline for automated extraction and structuring of materials data from unstructured scientific literature, using concrete materials as a representative and particularly challenging example. The pipeline exhibits robust performance across a broad range of LLMs and achieves an $F_1$ score of up to 0.98 for diverse composition--process--property attributes. Within one hour, it extracts nearly 9,000 high-quality records with over 100 attributes from a corpus screened from more than 27,000 publications, enabling the construction of the largest open laboratory database for blended cement concrete. Machine learning analyses underscore the importance of large, diverse, and information-rich datasets for enhancing both in-distribution accuracy and out-of-distribution generalization to unseen materials. The proposed pipeline is readily adaptable to other materials domains and accelerates the development of scalable data infrastructures for materials informatics.

Patient-trial matching requires reasoning over long, heterogeneous electronic health records (EHRs) and complex eligibility criteria, posing significant challenges for scalability, generalization, and computational efficiency. Existing approaches either rely on full-document processing with large language models (LLMs), which is computationally expensive, or use traditional machine learning methods that struggle to capture unstructured clinical narratives. In this work, we propose a lightweight framework that combines retrieval-augmented generation and large language model-based modeling for scalable patient-trial matching. The framework explicitly separates two key components: retrieval-augmented generation is used to identify clinically relevant segments from long EHRs, reducing input complexity, while large language models are used to encode these selected segments into informative representations. These representations are further refined through dimensionality reduction and modeled using lightweight predictors, enabling efficient and scalable downstream classification. We evaluate the proposed approach on multiple public benchmarks (n2c2, SIGIR, TREC 2021/2022) and a real-world multimodal dataset from Mayo Clinic (MCPMD). Results show that retrieval-based information selection significantly reduces computational burden while preserving clinically meaningful signals. We further demonstrate that frozen LLMs provide strong representations for structured clinical data, whereas fine-tuning is essential for modeling unstructured clinical narratives. Importantly, the proposed lightweight pipeline achieves performance comparable to end-to-end LLM approaches with substantially lower computational cost.