Positive-Unlabeled Learning

Geospatial foundation models (GFMs) are reshaping remote sensing by shifting the field from task-specific modeling toward general-purpose geospatial intelligence. Mapping the damage to buildings stands to benefit substantially from this shift, as GFMs pretrained on large-scale Earth observation data provide generalizable geospatial representations that can facilitate effective responses to sudden-onset disasters. Although parameter-efficient fine-tuning (PEFT) facilitates GFM adaptation, parameter efficiency does not necessarily translate into label efficiency. Building damage mapping remains challenging due to scarce pre-existing labeled data or limited time for annotation. When weak supervision is introduced to alleviate the labeling bottleneck, we identify the difficulty of learning sufficiently discriminative representations as a key challenge for label-efficient GFM adaptation. To address this challenge, we propose a Positive-Unlabeled GFM Adaptation (PUMA) framework that requires annotations for only a small number of damaged buildings. More specifically, PUMA integrates non-contrastive weakly supervised representation refinement to mitigate the impact of noisy supervision on representation learning from a gradient perspective, and latent-state-based label disambiguation to enable reversible supervision refinement without requiring class prior estimation. Extensive experiments on disaster benchmark datasets from around the world demonstrated the effectiveness and robustness of PUMA. A real-world application to the 2025 Los Angeles wildfires further highlighted its potential to accurately map damage under highly limited supervision. More broadly, these findings suggest that weakly supervised PEFT offers a label-efficient pathway from GFMs to real-world applications.

Safety monitors help safeguard language-model agents interacting with external tools and environments, but conservative monitoring can generate many false alarms, consuming extensive review resources and weakening trust in alerts. Because false and genuine alarms often remain interleaved in native monitor scores, obtaining a reliable cutoff still requires substantial manual verification. In practice, a small set of verified-safe non-alarmed trajectories may be available while alarms remain unlabeled, naturally casting false-alarm auditing as a positive-unlabeled (PU) ranking problem. The key challenge is monitor-induced selection, since observed safe references are accepted by the monitor, while the hidden safe alarms of interest are precisely those it incorrectly flags, making the observed positives poorly representative of the positives to be recovered. To address this challenge, we propose a two-stage framework in which Trust-aware PU Supervision adapts safe references toward the alarm domain and protects plausible false alarms from excessive negative pressure, while Reliability-gated Rank Distillation consolidates consistent ordering preferences from multiple PU reference models into a single student. Consensus-guided Structural Refinement then improves the student ranking using hierarchical safe-reference support, alarm relations, and predicted reference consensus. The framework requires no alarm safety labels for fitting and leaves the underlying monitor unchanged. Across mainstream safety monitors, our method achieves a macro AUPRC of $0.6444$, outperforming eight evaluated PU baselines by 5.27--16.98 absolute percentage points; compared with PULDA, the strongest evaluated PU baseline, it recovers 33.3% more false alarms at a 5% review budget.

Critical mineral discovery is a positive-only problem: deposits are observed as sparse locations, while unlabeled regions are not reliable negatives, and similar geophysical signatures can arise from different subsurface states. We therefore model mineral targeting as learning a conditional spatial distribution over occurrence locations, $π(p\mid d)$, given geo-images $d$, rather than predicting a deterministic per-pixel score map. We introduce GeoCFM, a conditional flow-matching model that generates mineral occurrence point sets conditioned on multi-channel geo-images; GeoCFM learns a point-wise transport field in $\mathbb{R}^2$, using UNet features with point-conditioned velocity prediction to bridge dense rasters and sparse supervision without pseudo-negatives. On a synthetic magnetics--geochemistry benchmark with latent activation and on USGS Earth MRI data with a spatially disjoint tile split, GeoCFM improves geometric agreement with observed occurrences over score-map and non-conditional baselines, while representing epistemic uncertainty through conditional sampling.

The partial area under the receiver operating characteristic curve (pAUC) is an important performance metric for binary classification that summarizes true positive rates within a specific range of false positive rates (FPRs). Classifiers that achieve high pAUC need to be obtained in many real-world applications such as cybersecurity, medical care, and advertising. Although many methods for maximizing the pAUC have been proposed, they typically require both labeled positive and negative data for training. However, in practice, labeled negative data are often difficult to collect due to privacy concerns or the need for high expertise to annotate them. In this paper, we propose a method for maximizing the pAUC from positive and unlabeled (PU) data without negative data. Within an empirical risk minimization framework, we show that the pAUC, including its FPR-dependent thresholds, can be represented using only the positive and marginal densities, and derive an empirical estimator from PU data. A classifier is then trained by maximizing the derived smoothed empirical pAUC estimator. We experimentally demonstrate the effectiveness of the proposed method with ten real-world datasets.

This study addresses the PU classification problem under violations of the SCAR assumption. We investigate logistic regression-based approaches, namely the cluster method and its extensions with strict and non-strict Lasso regularization. The primary contribution of this work is the integration of the SMOTE technique to alleviate class imbalance and systematically assess its impact on the performance of the considered algorithms. SMOTE is first applied to rebalance the training dataset. Next, cleaning labels are derived via 2-means clustering. Logistic regression is then trained on the cleaned data, where identified positive instances are augmented with additional true positives and the remaining observations are treated as negative. The experimental evaluation is conducted on 13 real benchmark datasets and one synthetic dataset. For comparison, we include the naive approach and the Spy-EM method. The results demonstrate that incorporating SMOTE improves classification performance when the SCAR condition is violated and indicate moderate robustness of the LassoJoint method in this setting.

Maximizing the area under the receiver operating characteristic curve (AUC) is a standard approach to imbalanced binary classification. Although positive and negative data are required for maximizing the AUC, negative data are often difficult to collect in some real-world applications due to privacy concerns or the need for specialized expertise to annotate them. Thus, AUC maximization from positive and unlabeled (PU) data has been attracting attention. Existing methods assume that labeled positive data are unbiased samples from the true positive distribution. However, this ideal assumption is often violated in practice. In this paper, we propose a method to maximize the AUC from biased PU data. To address the bias, our key idea is to exploit {\it confidence}, i.e., the probability that an instance is positive, associated with the small number of labeled positive data. We derive an estimator of the AUC risk using biased PU data with confidence, enabling AUC maximization under such bias. We further show that the rewritten AUC risk induces a Bayes-optimal AUC ranking even when the available confidence is any strictly increasing transformation of the true posterior probability. We experimentally show the effectiveness of our method on eight real-world datasets.

Vision-Language Models (VLMs) for radiology report generation are typically trained on retrospective clinical reports, which suffer from omission noise: clinically present findings are left unreported due to the omission of subtle findings. For example, prior studies show that cardiomegaly may be omitted from ICU chest X-ray reports when the imaging request is focused on monitoring support device placement. As a result, models trained with standard approaches inherit these omissions, learning to under-report findings themselves. We propose PU-DPO, a preference optimization framework to prevent omission noise from corrupting the preference signal. We reformulate the objective under a positive-unlabeled (PU) learning framework, treating absent mentions as unlabeled rather than truly negative. Our framework provides preference supervision using constructed contrastive pairs, generated using edits to model responses, producing variants that explicitly mention or omit a specific finding. Generated responses that mention the finding are naturally preferred in the context of visual evidence. Across semi-synthetic experiments and analyses on real-world chest radiograph benchmarks where adjudicated labels are available, PU-DPO yields consistent gains in detection rates and recovery of hidden positives across multiple pathologies, and is more robust to omission noise than prior approaches.

Passive acoustic monitoring is an important tool for biodiversity assessment and wildlife conservation because it supports continuous and non-invasive monitoring of species across large spatial and temporal scales. Robust monitoring remains challenging because many datasets contain sparse positive labels, where species presences may be confirmed while unannotated species cannot be assumed absent. In this work, we study transfer learning under sparse positive labels using BirdCLEF+ 2026 as a target benchmark and BirdCLEF 2021, iNatSounds, WABAD, and BirdSet as external bioacoustic sources. We introduce a multi-source reliability framework that models heterogeneous bioacoustic datasets as distinct supervision sources with differing reliability. Our approach achieves 0.584 macro average precision and 0.860 macro AUC on public BirdCLEF+ 2026 validation labels while outperforming naive source pooling strategies. The strongest gains arise from passive acoustic monitoring datasets and biologically informed source selection. Our findings suggest that transfer learning in bioacoustics is fundamentally a weak supervision and negative transfer problem.

Positive-Unlabeled (PU) learning aims to achieve high-accuracy binary classification with limited labeled positive examples and numerous unlabeled ones. Existing cost-sensitive-based methods often rely on strong assumptions that examples with an observed positive label were selected entirely at random. In fact, the uneven distribution of labels is prevalent in real-world PU problems, indicating that most actual positive and unlabeled data are subject to selection bias. Building on the SAR-PU propensity-weighted framework of Bekker et al., we study a PU learning enhancement (PUe) framework using normalized propensity scores and normalized inverse probability weighting (NIPW). PUe's main contributions are a normalized inverse-probability-weighted PU risk formulation; additional theoretical analyses of normalized sample-weight error and common PU estimators under biased labeling; regularized deep propensity-score estimation; integration with modern cost-sensitive PU methods; and support for selectively labeled negative classes. Experiments on MNIST, CIFAR-10, and ADNI demonstrate improvements over several PU baselines under non-uniform label distributions.

Large Language Models (LLMs) are increasingly used as judges for scalable evaluation, yet such LLM--as--a--Judge systems exhibit systematic biases that are decoupled from semantic quality, most notably verbosity bias. Meanwhile, human supervision is costly and typically selective, yielding reliable positive judgments but leaving most outputs unlabelled and potentially mixed in quality. We formulate LLM evaluation under selective human supervision as a positive--unlabelled learning problem and propose a geometric auditing framework based on Partial Optimal Transport. By aligning a small set of human--verified positives with a reliable subset of unlabelled outputs in a fixed embedding space, our method identifies human--consistent preferences and corrects biased judges without retraining. Experiments demonstrate improved alignment with human preferences, increased robustness to presentation biases, and interpretable confidence estimates, offering a scalable and statistically grounded alternative to existing LLM--as--a--judge pipelines.

Detecting covariate shift is critical for building reliable vision systems. While most prior work focuses on improving robustness to shift, explicitly detecting covariate shift remains underexplored. Existing approaches typically rely on fully supervised training, requiring labeled examples from both original and shifted distributions, which is often impractical. In this paper, we show that covariate shift detection can be effectively addressed with weaker supervision using Positive Unlabeled (PU) learning. However, under covariate shift, in distribution and shifted data overlap significantly, making classical PU methods unstable and sensitive to noise. To overcome this challenge, we introduce Spectral PU Neighborhood Annotation (SPUNA), a geometry aware framework that progressively discovers shifted data by leveraging the local manifold structure of visual features. Extensive experiments show that SPUNA achieves state of the art performance in PU settings and remarkably matches the performances of fully supervised methods. Moreover, our approach transfers robustly across different types of shifts, demonstrating strong generalization capabilities.

Music streaming fraud, where bad actors artificially inflate stream counts to manipulate chart rankings and royalty payments, poses a significant threat to streaming services and legitimate content creators. Traditional fraud detection approaches struggle with a critical challenge: many legitimate edge cases, including super-fans and sleep-music sessions, exhibit activity patterns that closely mimic those of coordinated fraud. We present SAGE, a novel counterfactual-aware negative harvesting approach that combines SimHash-based stratified sampling with a modular gating ensemble for confident negative identification from unlabeled data. Our ensemble architecture employs pluggable statistical gates (currently instantiated with Mahalanobis distance and k-NN density) with configurable voting thresholds enabling adaptive precision-recall trade-offs. This addresses the representation bias problem in Positive-Unlabeled learning by ensuring comprehensive coverage of rare behavioral cohorts through floor-constrained sampling. Evaluation demonstrates strong precision and recall on held-out data. The approach generalizes across fraud detection domains, achieving strong performance on both customer-level and artist-level fraud without modification to the core methodology.

We propose a new method of learning from positive and unlabeled (PU) examples in highly imbalanced datasets. Many real-world problems, such as disease gene identification, targeted marketing, fraud detection, and recommender systems, are hard to address with machine learning methods, due to limited labeled data. Often, training data comprises positive and unlabeled instances, the latter typically being dominated by negative, but including also several positive instances. While PU learning is well-studied, few methods address imbalanced settings or hard-to-detect positive examples that resemble negative ones. Our approach uses a focused empirical risk estimator, incorporating both positive and unlabeled examples to train binary classifiers. Empirical evaluations demonstrate state-of-the-art performance on imbalanced datasets under two labeling mechanisms - selecting positives completely at random (SCAR) and selecting at random (SAR). Beyond these controlled experiments, we demonstrate the value of the proposed method in the real-world application of financial misstatement detection.

Large Language Model (LLM) personalization aims to align model behaviors with individual user preferences. Existing methods often focus on isolated user histories, neglecting the essential role of inter-user differences. We propose C-BPO, a framework that personalizes LLMs via preference-calibrated binary signals. By treating target user data as positive feedback and other users' data as an auxiliary set of implicit negative signals, C-BPO captures distinct inter-user differences. To mitigate the preference overlap issue, where shared task knowledge is erroneously penalized, we derive an objective grounded in Positive-Unlabeled (PU) learning theory. This approach purifies negative signals by subtracting ``positive bias'', ensuring alignment with unique idiosyncrasies without compromising general helpfulness. Empirical experiments across various personalization tasks and backbone LLMs show C-BPO consistently outperforms baselines, demonstrating the efficacy of preference-calibrated binary signals in modeling inter-user differences.

Protein sequence data from nature exhibits survivorship bias: we only observe data from those organisms that survive and reproduce, while non-functional protein mutations are eliminated by natural selection. Thus, predicting whether a protein sequence is functional often requires learning from positive examples alone. While positive-unlabeled (PU) learning frameworks offer a generic solution to this problem, existing PU methods ignore the evolutionary processes that shape sequence observability and cause survivorship bias. Consider a sequence that is one mutation away from a commonly-observed protein variant in a well-surveilled organism. If the sequence were functional, it would likely be observed. If it is not observed, this suggests non-functionality. In contrast, sequences that are unlikely to arise through mutation may be missing simply because they never arose. Thus, these two kinds of missing sequences should be treated differently when training models. In this work, we propose Evo-PU, a PU learning framework that uses a scientific understanding of nucleotide mutation to model survivorship bias for well-surveilled single-organism sequence data. On three prediction tasks using single-organism uniform-coverage surveillance data -- predicting results from held-out influenza and respiratory syncytial virus (RSV) mutagenesis studies, and predicting future SARS-CoV-2 variants -- Evo-PU outperforms standard PU learning, one-class classification (OCC), and protein language models (PLMs). On prediction tasks from multi-organism ProteinGym datasets with more heterogeneous surveillance coverage, we identify opportunities to generalize our approach.

Positive-unlabeled (PU) learning addresses binary classification when only a set of labeled positives is available alongside a pool of unlabeled samples drawn from a mixture of positives and negatives. Existing PU methods typically require dataset-specific training or iterative optimization, which limits their applicability when many tasks must be solved quickly or with little tuning. We introduce PUICL, a pretrained transformer that solves PU classification entirely through in-context learning. PUICL is pretrained on synthetic PU datasets generated from randomly instantiated structural causal models, exposing it to a wide range of feature-label relationships and class-prior configurations. At inference time, PUICL receives the labeled positives and the unlabeled samples as a single input and returns class probabilities for the unlabeled rows in one forward pass, with no gradient updates or per-task fitting. On 20 semi-synthetic PU benchmarks derived from the UCI Machine Learning Repository, OpenML, and scikit-learn, PUICL outperforms four standard PU learning baselines in average AUC and accuracy, and is competitive on F1-score. These results show that the in-context learning paradigm extends naturally beyond fully supervised tabular prediction to the semi-supervised PU setting.

Open-vocabulary scene graph generation (SGG) aims to describe visual scenes with flexible relation phrases beyond a fixed predicate set. Existing methods usually treat annotated triplets as positives and all unannotated object-pair relations as negatives. However, scene graph annotations are inherently incomplete: many valid relations are missing, and the same interaction can be described at different granularities, e.g., on, standing on, resting on, and supported by. This issue becomes more severe in open-vocabulary SGG due to the much larger relation space. We propose ReLIC-SGG, a relation-incompleteness-aware framework that treats unannotated relations as latent variables rather than definite negatives. ReLIC-SGG builds a semantic relation lattice to model similarity, entailment, and contradiction among open-vocabulary predicates, and uses it to infer missing positive relations from visual-language compatibility, graph context, and semantic consistency. A positive-unlabeled graph learning objective further reduces false-negative supervision, while lattice-guided decoding produces compact and semantically consistent scene graphs. Experiments on conventional, open-vocabulary, and panoptic SGG benchmarks show that ReLIC-SGG improves rare and unseen predicate recognition and better recovers missing relations.

Scalable synthesis remains the gate between MOF discovery and industrial deployment, as scale-up know-how is fragmented across disparate reports. We introduce ScaleMOF, a literature-mined dataset and a positive-unlabeled learning strategy that fine-tunes large language models. Achieving 93.5% accuracy, this proof-of-concept serves as a literature-grounded ranking tool prioritizing plausible scale-up candidates.

The present study aims to investigate a cluster cleaning algorithm that is both computationally simple and capable of solving the PU classification when the SCAR condition is unsatisfied. A secondary objective of this study is to determine the robustness of the LassoJoint method to perturbations of the SCAR condition. In the first step of our algorithm, we obtain cleaning labels from 2-means clustering. Subsequently, we perform logistic regression on the cleaned data, assigning positive labels from the cleaning algorithm with additional true positive observations. The remaining observations are assigned the negative label. The proposed algorithm is evaluated by comparing 11 real data sets from machine learning repositories and a synthetic set. The findings obtained from this study demonstrate the efficacy of the clustering algorithm in scenarios where the SCAR condition is violated and further underscore the moderate robustness of the LassoJoint algorithm in this context.

We formulate curator-in-the-loop duplicate discovery in the AtticPOT repository as a Positive-Unlabeled (PU) learning problem. Given a single anchor per artefact, we train a lightweight per-query Clone Encoder on augmented views of the anchor and score the unlabeled repository with an interpretable threshold on the latent l_2 norm. The system proposes candidates for curator verification, uncovering cross-record duplicates that were not verified a priori. On CIFAR-10 we obtain F1=96.37 (AUROC=97.97); on AtticPOT we reach F1=90.79 (AUROC=98.99), improving F1 by +7.70 points over the best baseline (SVDD) under the same lightweight backbone. Qualitative "find-similar" panels show stable neighbourhoods across viewpoint and condition. The method avoids explicit negatives, offers a transparent operating point, and fits de-duplication, record linkage, and curator-in-the-loop workflows.

Weakly supervised learning has emerged as a practical alternative to fully supervised learning when complete and accurate labels are costly or infeasible to acquire. However, many existing methods are tailored to specific supervision patterns -- such as positive-unlabeled (PU), unlabeled-unlabeled (UU), complementary-label (CLL), partial-label (PLL), or similarity-unlabeled annotations -- and rely on post-hoc corrections to mitigate instability induced by indirect supervision. We propose a principled, unified framework that bypasses such post-hoc adjustments by directly formulating a stable surrogate risk grounded in the structure of weakly supervised data. The formulation naturally subsumes diverse settings -- including PU, UU, CLL, PLL, multi-class unlabeled, and tuple-based learning -- under a single optimization objective. We further establish a non-asymptotic generalization bound via Rademacher complexity that clarifies how supervision structure, model capacity, and sample size jointly govern performance. Beyond this, we analyze the effect of class-prior misspecification on the bound, deriving explicit terms that quantify its impact, and we study identifiability, giving sufficient conditions -- most notably via supervision stratification across groups -- under which the target risk is recoverable. Extensive experiments show consistent gains across class priors, dataset scales, and class counts -- without heuristic stabilization -- while exhibiting robustness to overfitting.

Predicting which hypothetical inorganic crystals can be experimentally realized remains a central challenge in accelerating materials discovery. SyntheFormer is a positive-unlabeled framework that learns synthesizability directly from crystal structure, combining Fourier-transformed crystal properties (FTCP) representation with structure-aware feature extraction, Random-Forest feature selection, and a compact deep MLP classifier. The model is trained on historical data from 2011 through 2018 and evaluated prospectively on future years from 2019 to 2025, where the positive class constitutes only 1.02 percent of samples. Under this temporally separated evaluation, SyntheFormer achieves a test AUC of 0.735, AUPRC of 0.099 and 97.6 percent recall at 94.2 percent coverage with dual-threshold calibration. Direct prospective validation supports this result as two materials that were unlabeled at the time of data curation, Y6Fe(SiS7)2 and BaYb2F8, were assigned high SyntheFormer scores (0.961 and 0.753, respectively) and were subsequently reported experimentally. Crucially, the model recovers experimentally confirmed metastable compounds that lie far from the convex hull and simultaneously assigns low scores to many thermodynamically stable yet unsynthesized candidates, demonstrating that stability alone is insufficient to predict experimental attainability.

Semi-supervised anomaly detection, which aims to improve the anomaly detection performance by using a small amount of labeled anomaly data in addition to unlabeled data, has attracted attention. Existing semi-supervised approaches assume that most unlabeled data are normal, and train anomaly detectors by minimizing the anomaly scores for the unlabeled data while maximizing those for the labeled anomaly data. However, in practice, the unlabeled data are often contaminated with anomalies. This weakens the effect of maximizing the anomaly scores for anomalies, and prevents us from improving the detection performance. To solve this, we propose the deep positive-unlabeled anomaly detection framework, which integrates positive-unlabeled learning with deep anomaly detection models such as autoencoders and deep support vector data descriptions. Our approach enables the approximation of anomaly scores for normal data using the unlabeled data and the labeled anomaly data. Therefore, without labeled normal data, our approach can train anomaly detectors by minimizing the anomaly scores for normal data while maximizing those for the labeled anomaly data. We also provide a theoretical analysis establishing a generalization error bound for the proposed objective, guaranteeing that the empirical minimizer converges asymptotically to the ideal minimizer. Our approach achieves better detection performance than existing approaches on various datasets.