Retrieval-Augmented Classification

Medical time series (MedTS) underpin many clinical classification tasks, yet existing methods usually represent them only as numerical sequences and underuse the morphology that is explicit in waveform inspection. To bridge this gap, we introduce Vision-Informed Retrieval (ViRe), which uses a frozen VLM-derived waveform representation as a morphology-aware Query to guide retrieval from raw numerical MedTS features. Specifically, a Vision Query is extracted using pre-trained vision-language models (VLMs) to obtain morphology-aware priors from waveform plots. A tailored attention-based cross-modal retrieval mechanism then uses the Vision Query to select morphology-relevant temporal and channel evidence from the numerical representation. ViRe demonstrates strong effectiveness against ten established baselines, yielding an overall 6.42% relative improvement over the previous state of the art across six public benchmarks. Code, training scripts, and reproducibility materials are publicly available in the GitHub Repository: https://github.com/Levi-Ackman/ViRe.

Large language models (LLMs) struggle to classify text into taxonomies with many semantically similar labels, as the distinctions are domain-specific and not captured by pre-training. To handle large label spaces, a common approach retrieves top-$K$ candidate labels by embedding similarity and prompt the LLM to choose among them. However, top-$K$ retrieval reduces the number of candidates but does not help the model tell similar ones apart. When two similar labels both appear as candidates, the model lacks the signal to choose correctly between them. We propose a framework that (1) identifies which label pairs the model struggles to distinguish, (2) expands the candidate set to include confusable labels, and (3) generates targeted rules to differentiate between similar candidates. The framework requires no fine-tuning, and the generated rules transfer to smaller, cheaper models. On three benchmarks (WOS, Flipkart, LEDGAR), our approach improves Macro F1 by up to 10.0pp over retrieval baselines, with smaller models (2B--20B) gaining up to 11.5pp via cross-model transfer.

Leukemia cell image classification is challenged by real-world domain shifts from acquisition, staining, illumination, and site protocols, causing single-dataset models to generalize poorly in real clinical scenarios. This work presents a robust framework for leukemia classification across multiple heterogeneous datasets using a two-stage pipeline with a pretrained vision foundation model. Stage 1 performs binary classification (leukemia vs. non-leukemia) and is trained using 122,167 single-cell images. Stage 2 is conditionally applied to Stage 1 positives to perform subtype classification into Acute Lymphoblastic Leukemia (ALL) and Acute Myeloid Leukemia (AML), trained using 69,400 single-cell images. Labels are harmonized across five heterogeneous datasets to enable cross-dataset training, and performance is evaluated on a held-out dataset protocol to assess domain-shift generalization. Within this pipeline, three encoders are benchmarked (DinoBloom, pretrained on single-cell images; BiomedCLIP, pretrained on biomedical data; and CLIP as a general-purpose model) under linear probing, Low-Rank Adaptation (LoRA), and a Retrieval-Augmented Classification (RAC) module that retrieves the top-k most similar cell images to provide cytomorphological grounding. The objective is to quantify how much domain-specific pretraining contributes to performance under domain shift, and whether cost-effective adaptation and retrieval can be a viable alternative to expensive domain-specialized pretraining. The held-out protocol additionally serves as a diagnostic tool, revealing when classification performance is attributable to dataset-specific artifacts rather than to cytomorphological features.

Retrieval-Augmented Generation (RAG) enables large language models to classify network flows and generate human-readable incident reports by retrieving semantically similar historical traffic from a vector knowledge base. However, the retrieval layer introduces vulnerabilities to knowledge poisoning and prompt-injection attacks. We present RAG-IDS, a three-tier multi-agent intrusion detection framework with a retrieval-boundary defense combining soft trust scoring, label-embedding consistency checking (LECC), and prompt sanitization, designed to recover classification quality under retrieval-layer attack. Experiments on CIC-UNSW-NB15 show recovery relative to clean undefended performance ranging from R=1.0 at 1% poisoning to R=0.57 at 30%, with negligible clean-performance overhead. Under prompt injection, multi-document retrieval limits label-flip success to 0.6-2.4%, compared with 35-55% for single-document retrieval. Ablation results show that LECC is the primary contributor to robustness, while soft trust-based demotion outperforms hard filtering. The defended RAG pipeline offers an explainable, attack-resilient foundation for intrusion detection, well suited for hybrid deployment alongside high-throughput classifiers.

Researchers organize the papers they collect into personal folder hierarchies in reference managers, and route each new paper into the folder where it belongs. This task differs from standard hierarchical text classification. A user's folder hierarchy is not a fixed, shared taxonomy but a private and evolving folksonomy whose folder meanings may be topical, shorthand, venue-based, or process-oriented, and are often defined by the papers already stored inside them. We formalize this setting as personalized hierarchical paper routing (PHPR): assigning an incoming paper to folders in a user-specific hierarchy without per-user training. We propose PaperRouter-Agent, a training-free LLM agent that grounds routing decisions in folder members rather than folder names alone. The agent first narrows the candidate hierarchy, retrieves folder-specific evidence, verifies fit by inspecting member papers, and incorporates similarity-gated feedback from past user rejections. A formative study on real personal libraries shows that PaperRouter-Agent raises overall Recall@1 from 0.39 to 0.61 and Recall@3 from 0.57 to 0.83, with the largest gains on organizational folders defined by metadata such as venue or year, where single-shot methods collapses (Recall@1 0.09 to 0.50). On the public LaMP-2 benchmark, the same approach improves accuracy from 44.5% to 51.5% (+9.0 macro-F1) over a single-shot baseline, while remaining low-cost for practical use.

Tasks such as customs tariff classification, export control categorization, and standards-based equipment coding require assigning an input instance to a fine-grained class under an explicit regulatory hierarchy. Unlike standard text classification, the correct label in these tasks is not determined by semantic similarity alone, but by rule-defined boundaries, threshold conditions, exclusion clauses, definitions, and local exceptions. As a result, two highly similar inputs may require different labels, while a retrieved passage that appears relevant may still be inapplicable under the governing rules. Existing flat classifiers, hierarchical text classification methods, and retrieval-augmented LLM systems are not designed to jointly enforce hierarchical validity, rule consistency, and fine-grained boundary reasoning. In this paper, we formulate this setting as regulation-driven fine-grained hierarchical classification, where an external instance must be assigned to a fine-grained class through a valid path in a regulatory hierarchy and supported by auditable evidence. We construct four benchmark datasets from representative regulation-intensive scenarios and validate the annotations through an expert-in-the-loop process. We further propose a constraint-aware hierarchical search framework that converts regulatory documents into a searchable tree, retrieves only valid local candidate nodes, and uses structured regulatory fields with evidence snippets to guide each next-hop decision. Experiments show that our method achieves the best mean accuracy on all four datasets and provides interpretable decision paths, with the largest gains on cases involving fine-grained neighboring categories and rule-based boundary conditions.

Exact-match retrieval recall is often used as a proxy for whether a retriever supplies useful policy context to a downstream decision model. We test this proxy for pre-action policy classification in $τ$-bench using Qwen2.5-3B/7B classifiers. Under gold-policy conditioning, a compact structured state improves macro-F1 over raw trajectories by $0.20$ after tuning at 3B, with the same ordering at 7B under shared hyperparameters. We then replace the benchmark-designated governing rule with the top-ranked benchmark assertion retrieved from decision-time context. Although the exact governing rule is retrieved at rank 1 for only $7\%$ of airline states, the primary 3B classifier obtains macro-F1 $0.58$ with retrieved assertions versus $0.60$ with the gold rule ($Δ=-0.02$, task-cluster 95% CI $[-0.23,+0.21]$); random non-gold and no-assertion controls score $0.32$ and $0.21$. We do not detect a macro-F1 difference between retrieved assertions and the gold rule in this configuration, although the interval remains too wide to establish non-inferiority. The same qualitative pattern appears with a second retriever and at 7B, while varying across fine-tuning configurations. These results show that exact-match recovery of the benchmark-designated rule can underestimate the downstream utility of retrieved benchmark assertions in this setting. Retrieval should therefore be evaluated inside the classification loop rather than by exact-match recall alone.

Automatic dysarthria severity assessment is limited by the scarcity of labeled pathological speech data. To address this, we propose Cross-lingual Retrieval-Augmented Classification (CRAC), which leverages speech from a different language via an align-retrieve-fuse pipeline. Supervised contrastive learning first shapes a severity-focused embedding space, then a vector database is built from the opposite-language corpus. During both training and inference, the classifier retrieves top-k references from the aligned space and fuses them with the input via cross-attention. Evaluated on Korean post-stroke and Italian ALS dysarthria datasets under a speaker-independent three-class protocol, CRAC achieves balanced accuracies of 87.3% on Korean and 86.7% on Italian, improving over monolingual baselines by 8.4 and 20.0 percentage points, respectively.

Multi-label legal annotation requires assigning multiple labels from large, evolving taxonomies to long, fact-intensive documents, often under limited supervision. Parametric encoders typically require task-specific training and retraining when the label set changes, while prompting generative large language models becomes costly and degrades as the label space grows. We cast legal annotation as retrieval: we embed documents and label descriptions with a frozen retrieval model and predict labels via k-nearest neighbors in the embedding space, enabling updates by re-embedding and re-indexing rather than gradient-based backpropagation. Across three legal datasets (ECtHR-A, ECtHR-B, and Eurlex with 100 labels), retrieval achieves competitive accuracy and strong data efficiency; on Eurlex, Qwen-8B retrieval improves Macro-F1 from 40.41 (GPT-5.2, zero-shot) to 49.12 while reducing estimated compute by 20-30 times compared to fine-tuning. With only (N=100) training samples, retrieval nearly doubles Micro-F1 over hierarchical Legal-BERT on ECtHR-A (48.29 vs. 27.87). We also quantify a reliability failure mode of generative inference: GPT-5.2 hallucinates labels outside the provided taxonomy in 0.12-0.9% of test samples under deterministic decoding. In contrast, retrieval strictly respects defined label sets, eliminating hallucination by design. These results suggest retrieval-model-based annotators are a practical, deployable alternative for high-cardinality and rapidly changing legal label spaces.

Industrial multi-label document understanding pipelines score candidate labels and threshold or rank them to form a label set per document. This early selection step directly affects the accuracy of downstream information extraction from the document, as well as the associated verification effort. In practice, OCR noise, label imbalance, instance-dependent label cardinality, and asymmetric error costs make global score thresholds brittle and hard to maintain as document formats evolve. We present RAPT, a deployment-oriented retrieval-augmented score thresholding wrapper, applied post-hoc to improve label set selection without retraining the underlying classifier. RAPT is a model-agnostic wrapper: any predictor that provides document representations for similarity search and per label confidence scores can be used, including metric learning encoders and fine-tuned transformer classifiers. For each query document, given a classifier's score vector, RAPT retrieves similar document thresholding situations (cases) and adapts the query's label set selection threshold using their outcomes. The adaptation selects the final label set by locally aggregating neighbour solutions (e.g. average label count, cutoff calibration). Evaluation compared multi-label classifiers (metric learners and transformers) combined with RAPT against global and label-wise thresholding baselines, and against few-shot LLMs. Across an industrial dataset and six public benchmarks, RAPT consistently outperformed global and label-wise static thresholding baselines. In the industrial setting, RAPT achieved its best predictive performance with metric learners, reaching 0.87 Macro-F1, while fine-tuned transformer variants on average achieved 0.775 Macro-F1, outperforming fewshot LLM baselines (K = 5) by 2x and requiring at least 115x less inference time and 13.5x less GPU memory.

Identifying species in biology among tens of thousands of visually similar taxa while discovering unknown species in open-world environments remains a fundamental challenge in biodiversity research. Current methods treat identification and discovery as separate problems, with classification models assuming closed sets and discovery relying on threshold-based rejection. Here we present DeepTaxon, a retrieval-augmented multimodal framework that unifies species identification and discovery through interpretable reasoning over retrieved visual evidence. Given a query image, DeepTaxon retrieves the top-$k$ candidate species with $n$ exemplar images each from a retrieval index and performs chain-of-thought comparative reasoning. Critically, we redefine discovery as an explicit, retrieval-based decision problem rather than an implicit parametric memory problem. A sample is novel if and only if the retrieval index lacks sufficient evidence for identification, so each retrieval naturally yields a classification or discovery label without manual annotation, thereby providing automatic supervision for both tasks. We train the framework via supervised fine-tuning on synthetic retrieval-augmented data, followed by reinforcement learning on hard samples, converting high-recall retrieval into high-precision decisions that scale to massive taxonomic vocabularies. Extensive experiments on a large-scale in-distribution benchmark and six out-of-distribution datasets demonstrate consistent improvements in both identification and discovery. Ablation studies further reveal effective test-time scaling with candidate count $k$ and exemplar count $n$, strong zero-shot transfer to unseen domains, and consistent performance across retrieval encoders, establishing an interpretable solution for biodiversity research.

Time introduces fundamental challenges in model development and deployment: models are usually trained on historical data while deployed on future data where semantic distributions and domain knowledge may evolve. Unfortunately, existing studies either overlook temporal shifts or hardly capture rich shifting patterns of both semantic and knowledge. We develop Knowledge-driven Augmentation and Retrieval for Integrative Temporal Adaptation (KARITA) to capture diverse temporal shifts (e.g., uncertainty and feature shift), construct and integrate rich knowledge sources (e.g., medical ontology like MeSH), and leverage shifting insights for selecting-retrieval augmented learning. We evaluate KARITA on classification tasks across multiple domains, clinical, legal, and scientific corpora, demonstrating consistent improvements across multiple domains with temporal adaptation. Our results show that knowledge integration can be more critical and effective in temporal augmentation and learning.

Fine-grained medical image classification is challenged by subtle inter-class variations and visually ambiguous cases, where confidence estimates often exhibit uncertainty rather than being overconfident. In such scenarios, purely discriminative classifiers may achieve high overall accuracy yet still fail to distinguish between highly similar categories, leading to miscalibrated predictions. We propose T-DuMpRa, a teacher-guided dual-path multi-prototype retrieval-augmented framework, where discriminative classification and multi-prototype retrieval jointly drive both training and prediction. During training, we jointly optimize cross-entropy and supervised contrastive objectives to learn a cosine-compatible embedding geometry for reliable prototype matching. We further employ an exponential moving average (EMA) teacher to obtain smoother representations and build a multi-prototype memory bank by clustering teacher embeddings in the teacher embedding space. Our framework is plug-and-play: it can be easily integrated into existing classification models by constructing a compact prototype bank, thereby improving performance on visually ambiguous cases. At inference, we combine the classifier's predicted distribution with a similarity-based distribution computed via cosine matching to prototypes, and apply a conservative confidence-gated fusion that activates retrieval only when the classifier's prediction is uncertain and the retrieval evidence is decisive and conflicting, otherwise keeping confident predictions unchanged. On HAM10000 and ISIC2019, our method yields 0.68%-0.21% and 0.44%-2.69% improvements on 5 different backbones. And visualization analysis proves our model can enhance the model's ability to handle visually ambiguous cases.

Clinical value set authoring -- the task of identifying all codes in a standardized vocabulary that define a clinical concept -- is a recurring bottleneck in clinical quality measurement and phenotyping. A natural approach is to prompt a large language model (LLM) to generate the required codes directly, but structured clinical vocabularies are large, version-controlled, and not reliably memorized during pretraining. We propose Retrieval-Augmented Set Completion (RASC): retrieve the $K$ most similar existing value sets from a curated corpus to form a candidate pool, then apply a classifier to each candidate code. Theoretically, retrieve-and-select can reduce statistical complexity by shrinking the effective output space from the full vocabulary to a much smaller retrieved candidate pool. We demonstrate the utility of RASC on 11,803 publicly available VSAC value sets, constructing the first large-scale benchmark for this task. A cross-encoder fine-tuned on SAPBert achieves AUROC0.852 and value-set-level F10.298, outperforming a simpler three-layer Multilayer Perceptron (AUROC0.799, F10.250) and both reduce the number of irrelevant candidates per true positive from 12.3 (retrieval-only) to approximately 3.2 and 4.4 respectively. Zero-shot GPT-4o achieves value-set-level F1~0.105, with 48.6% of returned codes absent from VSAC entirely. This performance gap widens with increasing value set size, consistent with RASC's theoretical advantage. We observe similar performance gains across two other classifier model types, namely a cross-encoder initialized from pre-trained SAPBert and a LightGBM model, demonstrating that RASC's benefits extend beyond a single model class. The code to download and create the benchmark dataset, as well as the model training code is available at: https://github.com/mukhes3/RASC.

Structured radiology reporting promises faster, more consistent communication than free text, but automation remains difficult as models must make many fine-grained, discrete decisions about rare findings and attributes from limited structured supervision. In contrast, free-text reports are produced at scale in routine care and implicitly encode fine-grained, image-linked information through detailed descriptions. To leverage this unstructured knowledge, we propose ProtoSR, an approach for injecting free-text information into structured report population. First, we introduce an automatic extraction pipeline that uses an instruction-tuned LLM to mine 80k+ MIMIC-CXR studies and build a multimodal knowledge base aligned with a structured reporting template, representing each answer option with a visual prototype. Using this knowledge base, ProtoSR is trained to retrieve prototypes relevant for the current image-question pair and augment the model predictions through a prototype-conditioned residual, providing a data-driven second opinion that selectively corrects predictions. On the Rad-ReStruct benchmark, ProtoSR achieves state-of-the-art results, with the largest improvements on detailed attribute questions, demonstrating the value of integrating free-text derived signal for fine-grained image understanding.