Transductive Active Labeling

We introduce Sharper Transductive Local Complexity (STLC), a localized complexity method for transductive learning under uniform sampling without replacement. The construction starts from a Bernstein-type concentration inequality for the supremum of the test--train empirical process. Its proof uses the modified log-Sobolev inequality for the swap walk and a two-parameter entropy closure. A peeling argument with a surrogate localization functional then gives excess-risk bounds with the same fixed-point and confidence terms as the classical inductive local Rademacher-complexity bounds, without the additional logarithmic confidence factor in earlier transductive results. For realizable learning over a binary class of VC dimension $\dVC$, with training size $m$, test size $u$, and $u\ge m\ge\dVC$, STLC yields $\cO\{\dVC\log(me/\dVC)/m\}$. This matches the standard inductive rate and, when $m\ge9$, is within a logarithmic factor of the transductive minimax lower bound of order $\dVC/m$. For transductive kernel learning, STLC gives a spectrum-adaptive excess-risk bound without the multiplicative imbalance factors appearing in the earlier local-complexity bound.

Test case synthesis is crucial for evaluating and ranking programs generated by large language models (LLMs). However, constructing high-quality test cases remains challenging because reliable expected outputs are often difficult to obtain. We propose Confidence-Gated Transductive Test Generation (CoTT), which first uses an efficient inductive procedure and invokes transductive generation only when inductive confidence is low. This adaptive design improves output reliability while allocating extra computation only when needed. On code reranking benchmarks, CoTT outperforms prior baselines across the reported metrics while reducing cost relative to applying transductive generation to every input. These results show that confidence-based allocation of test-time computation provides a favorable efficiency-effectiveness trade-off with a single efficient LLM.

We continue the study of relatively smart learning, introduced by Dughmi and Pour (2026), which asks a supervised learner to compete, marginal by marginal, with every distribution-fixed error guarantee soundly certifiable from unlabeled data. They showed that the One-Inclusion Graph (OIG) learner is relatively smart with a quadratic sample-complexity blowup, and that no relatively smart learner can do better, leaving open whether ERM or another natural or tractable learner achieves comparable guarantees. They also left open whether the blowup can be restricted to unlabeled data. Our firs results shows that ERM---and in fact any proper consistent learner---is relatively smart for binary classification in the distribution-free setting. We show that a small certifiable error with $m$ samples implies a similarly small error on the uniform distribution over a random sample of size $O(m^2)$, yielding a cover of size at most $2^{m+1}$ on that sample. This suffices to control the error of proper consistent learners with $O(m^2)$ samples. We then show that semi-supervised relatively smart learning is information-theoretically possible with a quadratic blowup only in unlabeled sample complexity and no blowup in labeled sample complexity. The learner uses a natural generalization of OIG to a leave-most-out transductive problem, where labels of part of a finite pool are revealed and the remaining labels are predicted. Finally, this label efficiency comes at a cost in simplicity and tractability. If the hypothesis class is accessed only through an agnostic ERM oracle, any semi-supervised relatively smart learner with substantially sub-quadratic labeled-sample blowup requires super-polynomially many oracle calls. This holds even when the marginal is given explicitly, and thus also yields an intractability result for distribution-fixed learning that may be of independent interest.

Remote sensing scene classification is increasingly relying on foundation models pre-trained on large-scale Earth-observation data. Moreover, transductive inference, which exploits the collective statistical structure of the entire unlabeled query set, appears to naturally match remote sensing pipelines where large images are routinely split into patches and inferred as a batch. In this work, we introduce LC-TIM (Locally Consistent Transductive Information Maximization), which extends the state-of-the-art Transductive Information Maximization for Few-Shot CLIP (TIM++) objective with a local consistency regularizer that enforces prediction agreement between each query sample and its $κ$ nearest feature-space neighbors. The regularizer enters as a single multiplicative factor in the closed-form $q$-update, adding negligible computational overhead. We further propose a multi-source extension that fuses the affinity graph from multiple remote sensing foundation model, further boosting classification accuracy. To assess these methods, we establish the first comprehensive, open-source benchmark for transductive few-shot RS scene classification, evaluating LP++, TransCLIP, TIM++, and LC-TIM across ten diverse datasets, two remote sensing vision-language models, and across various few-shot settings. Our experiments show that transductive methods consistently outperform zero-shot baselines, and that LC-TIM achieves state-of-the-art accuracy, with the largest gains in the low-shot regime where neighborhood cues are most informative. Code is publicly available at: https://github.com/elkhouryk/LC-TIM

Few-shot Open-set audio classification requires classifying query samples from known classes with a few labeled support samples while rejecting query samples from unknown classes. Transductive inference jointly observes the full unlabeled query set to improve prototype estimation, yet standard transductive updates do not distinguish known from unknown query samples, leaving prototypes vulnerable to open-set contamination. Drawing on latent-inlierness weighting and decoupled scoring for unknown-class samples, we propose a two-phase transductive method operating over a frozen audio encoder. First, each query sample is assigned a latent inlierness score that down-weights likely unknown-class samples, so that prototype refinement is driven primarily by known-class evidence. The refined prototypes are then directly optimized on a transductive loss combining support cross-entropy, inlierness-weighted conditional entropy minimization, and inlierness-weighted marginal entropy maximization, while open-set rejection uses a prior-adaptive free-energy score that adjusts its threshold with the prior proportion of unknown-class samples, decoupling detection from classification. Experiments on three audio datasets show our method achieves state-of-the-art results for few-shot open-set audio classification under multiple experimental conditions.

Plant biosynthetic gene clusters (BGCs) encode specialized-metabolite pathways, yet curated plant BGC labels remain scarce, hindering supervised discovery at genome scale. Existing plant BGC mining tools are largely signature- and rule-driven and do not fully leverage recent advances in contextual representation learning for modeling long-range domain context and controlling false positives under strong domain shift. We seek an AI-assisted workflow that narrows experimental search space by transferring supervision from well-annotated microbial BGCs to plant genomes. We present PlantBGC, representing genomes as ordered Pfam-domain sequences and learning BGC-likeness with an encoder-only Transformer trained on MIBiG microbial BGCs and adapted to plants via label-free masked language modeling. On microbial benchmarks, PlantBGC achieves token-level AUC = 0.988 (10-fold CV) and 0.979 (leave-class-out). On plants, adaptation improves known-BGC recovery on n = 34 curated loci under strict 100% coverage, increasing recovery from 29.4% to 67.6% and indicating more complete boundaries. GO/KEGG-derived weak supervision reduces proxy primary-like ratio by 48.40% (GO) and 45.20% (KEGG), with consistent per-species reductions (paired Wilcoxon p = 1.53e-5). Compared to plantiSMASH, PlantBGC yields more compact loci on matched regions (median length ratio = 0.278; 93.8% of pairs are shorter).

A range of methods aim to enhance the performance of vision-language models (VLMs) at test time. Among them, transduction has emerged as a promising paradigm due to its strong compatibility and efficiency. However, realistic evaluations often involve highly imbalanced class distributions, which cause performance degradation or even collapse. In this work, we systematically revisit transduction from the perspective of penalized likelihood estimation (PLE), showing that PLE with a KL-divergence anchor term naturally yields an adaptive shrinkage behavior between prior anchors and empirical estimates. From this viewpoint, the brittleness of transductive methods can be attributed to the absence of anchoring mechanism and static modeling of the shrinkage strength. Therefore, we propose Mixture of Von Mises-Fisher Models with Dynamic Shrinkage (MOON). MOON is built upon a mixture of von Mises-Fisher distributions to model feature representations on the unit hypersphere. To handle imbalance, MOON dynamically adjusts the shrinkage strength using zero-shot priors at both instance and class levels. Thus, it suppresses unreliable assignments and prevents harmful updates from outlier classes, thereby mitigating negative transfer. MOON is model-agnostic, training-free, and requires no task-specific hyperparameter tuning. Extensive experiments further validate the advantage of MOON in both performance and efficiency. Our code is available at https://github.com/walawalagoose/MOON

Inferring gene regulatory networks (GRNs) from single-cell transcriptomic data is crucial for biological discovery, yet existing approaches suffer from a fundamental misalignment with real-world needs. Researchers typically seek a small set of high-confidence regulatory interactions for experimental validation, often involving previously unseen genes. However, current benchmarks rely on transductive splits with global classification metrics, while prevailing models struggle to generalize under inductive settings. To bridge this gap, we reformulate GRN inference as an inductive, ranking-centric graph completion problem and introduce \textbf{\benchmark}, a new benchmark that incorporates an inductive gene-holdout split together with knowledge graph completion metrics to better evaluate top-ranked predictions. Building on this, we propose \textbf{\method}, the first co-evolutionary discrete diffusion framework that jointly models biologically coherent discretized gene expression states and regulatory interactions for robust inductive generalization and improved top-ranked regulatory discovery. We further introduce TF-ALL Subgraph Sampling (TASS) for scalable training. Extensive experiments on {\benchmark} show that {\method} establishes new state-of-the-art performance, significantly outperforming existing methods in novel regulatory discovery, and ablation studies further verify the effectiveness of our design.

Logical Multi-Hop Query Answering over Knowledge Graphs (KGs) can be formulated as querying, with an implicit completeness assumption. Current works mainly focus on Existential First Order Logic (EFO) queries. These EFO queries contain conjunction, disjunction, and negation operators. Most existing works employ transductive reasoning, meaning they are not capable of reasoning over entities unseen during training. In the real world, there is a resource scarcity, and we cannot train a model with all the nodes of a large KG. Hence, we propose InductWave, a wavelet-based inductive embedding method for logical query answering on large KGs. Here, the training graph consists of fewer nodes than the test graph. Our model performs on par with the baseline models while having half the number of message-passing layers. It outperforms all of them in most cases, with 75% of the layers. These fewer resource requirements enable us to evaluate InductWave on massive graphs, such as Wiki-KG. We test our model using extensive experiments across varying train-test graph proportions of the FB15k-(237) dataset, comparing it with the state-of-the-art models. The code and datasets for the model are available at https://github.com/kracr/inductwave/.

Predicting transcriptional responses to genetic perturbations could reduce the experimental burden of functional genomics, but extrapolation to genes that were never perturbed during training remains difficult. We present Stable-Shift, a structured method for estimating unseen-gene responses. Stable-Shift aggregates single-cell measurements into perturbation-level expression shifts, fits a low-rank response basis using training perturbations only, and predicts an unseen gene's coordinates in that basis from biological context. The context combines STRING interactions, network structure, control-cell expression statistics, and Gene Ontology annotations; the evaluated implementation uses graph convolution to integrate these inputs. On the supplied K562 Perturb-seq benchmark, Stable-Shift obtained 0.592 cosine similarity, compared with 0.569 for GEARS, together with higher Spearman correlation and top-gene precision among the evaluated methods. Its mean cosine similarity over five unseen-gene splits was 0.589 +/- 0.008. The same ordering was observed in the supplied graph-aware, residualized, gene-space, and Norman-dataset comparisons. These results support further study of biologically structured latent-response prediction, while the lower gene-space accuracy and sensitivity to sparse graph neighborhoods limit the scope of the present conclusions.

Contrastive language-audio pretraining (CLAP) enables zero-shot audio classification, but standard inference classifies each clip in isolation and ignores the structure of the unlabeled test set. We present the first systematic study of TransCLIP-style transductive inference for CLAP: a text-anchored spherical Gaussian-mixture EM that refines zero-shot posteriors using the audio-embedding statistics of the test batch, with no labels, no gradients, and negligible compute (about 15 ms on one CPU core for 2,000 clips). Across ESC-50, UrbanSound8K, and VocalSound, this consistently improves top-1 accuracy by +4.6 to +9.2 points over the zero-shot baseline (e.g., 89.1 -> 94.8% on ESC-50, 73.8 -> 81.8% on UrbanSound8K). We further show that the gain (i) is governed by a simple operating boundary -- roughly 2.5 test samples per class per batch are required, with diminishing returns beyond ~5; (ii) is complementary to entropy-guided prompt weighting, with the combination reaching 96.2% on ESC-50; and (iii) attenuates but remains positive under long-tailed batches (+4.9 -> +3.1 points at a 20:1 imbalance), which we report as an explicit limitation. We also document a negative result: on TUT Urban Acoustic Scenes 2018, where zero-shot CLAP is near chance, transduction has no signal to amplify.

We present a recipe-controlled decoder audit (RCDA) for structural transductive knowledge-graph completion (KGC). The audit asks a simple reporting question: before attributing gains to an encoder or training recipe, what changes when the decoder is swapped under the same recipe? Using ComplEx and DistMult as the primary controlled pair, with targeted RotatE/TransE spot-checks, we evaluate seven benchmarks. On five standard KGs, ComplEx-vs-DistMult differences are modest but consistent under our recipe (+0.005 to +0.012 MRR), whereas CompGCN-style encoder effects vary more by dataset. On small KGs, decoder effects become the main diagnostic: Kinship shows a stable ComplEx advantage of +0.143 MRR (6 seeds), while UMLS favours ComplEx by +0.022 MRR in a clean 6-seed server rerun but reverses in an earlier provenance variant. We therefore treat small-KG decoder choice as recipe- and provenance-sensitive rather than as a fixed dataset winner. We further show that decoder choice interacts with encoder depth on WN18RR, and that under our recipe L=0 ComplEx on YAGO3-10 reaches 0.6971 +/- 0.0048 MRR at d=128. The result is a compact audit protocol: report matched decoder rows, log small-KG provenance, and sweep decoder x depth before making encoder-level claims.

Predicting the effect of an unseen gene knockout perturbation on transcriptomic gene expression remains a highly challenging problem for virtual cell models. Recent progress has been made by leveraging biological knowledge graphs to provide a notion of similar perturbation, allowing for improved extrapolation beyond the set of training perturbations. In this work, we demonstrate that the simplest model to leverage these assumptions - a K-nearest neighbour from the knowledge graph - achieves highly competitive performance on this task, and that this can be improved further using LLMs optimised via reinforcement learning (RL) for predictive performance. Specifically, we find that the K-nearest neighbour approach beats almost all methods on out-of-distribution perturbation prediction, and when a reasoning LLM is trained via RL to make changes to the neighbourhood, it obtains equivalent performance to current state of the art methods on the cell lines from Replogle et al. (2022). We also demonstrate that the RL training improves the LLM's performance on the downstream task of differential expression prediction, despite not being trained on this directly. Overall, these findings demonstrate the efficacy of knowledge graphs as model priors, and show early signs that RL can refine LLMs into generalizable tools for predicting complex biological responses.

Network dynamics - including spreading, influence maximisation, and epidemic modelling - remain largely confined to the transductive paradigm, where models are trained on a single network and cannot be reused on unseen graphs without retraining. We argue that inductive cross-network generalisation is a necessary prerequisite for Graph Foundation Models (GFMs) in this domain and propose four design properties towards this goal. As a proof of concept, ts-net (TopSpreadersNetwork), trained solely on synthetic multilayer networks (MLNs), demonstrates zero-shot generalisation to real-world MLNs of varying size and layer count, outperforming classical heuristics and transductive baselines on three of four metrics. Based on ts-net's performance, we further outline five open challenges towards building GFMs for network dynamics: scale, many-layer generalisation, self-supervised pretraining, cross-task transfer, and node-attribute integration.

We show every multi-group learner in the transductive setting may incur a multiplicative penalty in its error rate on some group relative to the error rate achievable in the single-group setting, and the penalty can increasing linearly with the number of groups, up to roughly the square-root of the sample size. This stands in stark contrast to optimal multi-group learners in an analogous (group-realizable) statistical setting, where the penalty is always at most logarithmic in the sample size and independent of the number of groups.

Active learning is now standard practice in labeling ecological data, enabling ecologists to quickly process large volumes of field data to understand and monitor natural environments. Current practices evaluate active learning inductively, estimating predictive performance on a held-out test set. We argue that this evaluation is misaligned with most ecological tasks, where the goal is to transductively label an entire pool of data as efficiently as possible. We demonstrate that ignoring the human-in-the-loop underestimates the importance of continuing to label, particularly for classes in the long tail which may be of disproportionate ecological importance (rare species, uncommon behaviors, etc.). Our analysis shows that, for this long tail, the transductive objective shifts importance from prediction to discovery: the true challenge becomes finding "needles in the haystack," examples of rare classes that are embedded within dense regions of abundant classes in the latent geometry, which we quantify with a novel metric of sampling difficulty. Finally, to translate these insights to practical ecological workflows, we propose a conservative hybrid stopping criterion inspired by ecological rarefaction curves, and show that combining predictive performance with discovery criteria reduces premature stopping on long-tailed pools, improving rare-class recovery when discovery, not classification, is the limiting factor.

RNA sequencing produces rich and diverse datasets of gene expression, offering compelling insights into cellular state and function that have many applications in drug discovery. Modeling such data is challenging due to inherent technical noise and experimental batch effects, as evidenced by many existing transcriptomic foundation models (FMs) underperforming relative to linear baselines. Such results raise the question of whether deep representation learning provides a distinct advantage over the direct use of raw transcript counts. Our work explores this by developing a new self-supervised model, TxFM, with a focus on inductive representation learning evaluations. TxFM employs a masked autoencoding approach tailored to diverse RNA-seq count data, and our ablation study empirically identifies crucial architecture configurations required for strong transfer performance. Additionally, we curate a public training corpus, DiverseRNA-1.4M, and find that TxFM trained on this curated dataset yields high-fidelity gene representations that outperform FMs trained on atlas-scale corpora over 100x larger. Overall, our results indicate that inductive self-supervised learning is a viable modeling approach for transcriptomics representation, provided a careful synthesis of model architecture and training data curation.

We consider the problem of universal transductive online classification with a possibly unbounded label space. This setting considers online learning, with the sequence of instances (without labels) known to the learner in advance. We say a concept class $\mathcal{H}$ is learnable if there is a learning algorithm $\mathcal{A}$, such that for every realizable sequence, the number of mistakes made by $\mathcal{A}$ grows at most sublinearly with the number of predictions. We characterize the learnability of this setting and show that there are only two possible optimal rates for the learnable classes: either bounded or increasing logarithmically. We introduce a new combinatorial structure, called ``Level-Constrained-Littlestone-Littlestone (LCLL) tree'', which, along with the indifference property, characterizes the learnability. We also extend the learnability result to the agnostic case and the case where only the stochastic process that generates the instance sequence is known.

In the transductive setting, where the full graph is observed but node labels are only partially available, progress in semi-supervised node classification has largely focused on architectural innovation. In this paper, we revisit an orthogonal axis: the training objective. We start from a simple observation: transductive models produce predictions for every node during training, including nodes without labels. These unlabeled-node predictions may contain useful training signal, but standard supervised objectives discard them because no ground-truth labels are available. Inspired by the decomposition of cross-entropy into a label-dependent alignment term and a label-independent entropy term, we propose prediction confidence as a natural way to extract this signal in the absence of labels. This motivates Transductive Sharpening (TS): a loss-level modification that minimizes prediction entropy on unlabeled nodes while counterbalancing this effect on labeled nodes. We evaluate Transductive Sharpening across a wide range of node-classification benchmarks and observe consistent performance improvements without requiring any changes to the backbone architecture. Code is available at https://github.com/transductive-sharpening/tunedGNN.

The consensus that GCN, GraphSAGE, GAT, and EvolveGCN outperform feature-only baselines on the Elliptic Bitcoin Dataset is widely cited but has not been rigorously stress-tested under a leakage-free evaluation protocol. We perform a seed-matched inductive-versus-transductive comparison and find that this consensus does not hold. Under a strictly inductive protocol, Random Forest on raw features achieves F1 = 0.821 and outperforms all evaluated GNNs, while GraphSAGE reaches F1 = 0.689 +/- 0.017. A paired controlled experiment reveals a 39.5-point F1 gap attributable to training-time exposure to test-period adjacency. Additionally, edge-shuffle ablations show that randomly wired graphs outperform the real transaction graph, indicating that the dataset's topology can be misleading under temporal distribution shift. Hybrid models combining GNN embeddings with raw features provide only marginal gains and remain substantially below feature-only baselines. We release code, checkpoints, and a strict-inductive protocol to enable reproducible, leakage-free evaluation.

We revisit transductive learning where predictions are made with the set of all covariates known in advance. In the leave-one-out (LOO) setting, the prediction is made with labels of the remaining sample points and evaluated by the average error. In particular, we study multiplicative oracle inequalities for agnostic transductive LOO prediction for a variety of tasks, including classification with 0-1 loss, squared loss regression, density estimation, and logistic regression. Specifically, we introduce \emph{Median of Level-Set Aggregation} (MLSA), an aggregation procedure built on near-ERM level sets (i.e., empirical-risk level sets around the ERM). We prove a general multiplicative oracle inequality for the LOO error of the form $$LOO_S(MLSA) \;\le\; C \left( \frac{1}{n} \min_{h\in H} L_S(h) \;+\; \frac{\log |H|}{n}\right), \qquad C>1,$$ where $H$ is the hypothesis/function class. This inequality holds for hypothesis classes under a local level-set growth condition together with losses satisfying a mild monotonicity assumption. For classification with VC classes under the $0$--$1$ loss, the $\log |H|$ factor can be improved to be $d\log n$, where $d$ is the VC dimension, recovering Long (1998) up to a $\log n$ factor. For logistic regression with bounded covariates and parameters, the $\log |H|$ factor can be improved to be $d\log n$ up to problem-dependent factors, where $d$ is the ambient dimension.