Shortcut Learning in Language Models

Agentic LLMs increasingly support scientific prediction by grounding decisions in external evidence. In biology, they promise accurate, interpretable predictions for important problems by integrating complex experimental and computational evidence. However, serialized tool results can contain hidden label shortcuts, such as dataset identifiers or template artifacts, that create apparent success without biological reasoning. To address this risk, we introduce a two-stage audit. Stage 1, Per-Tool TF-IDF Decomposition (PT2D), localizes label-predictive patterns to individual tool results while avoiding signal dilution in the concatenated tool trace. Stage 2, Token-Class Redaction, counterfactually tests whether the frozen LLM depends on the localized shortcut. We apply this audit to TCR-pMHC binding, where tool augmentation substantially outperforms a no-evidence baseline. At face value, this suggests that the LLM has learned to use scientific evidence. The audit overturns this interpretation: PT2D localizes the strongest signal to identifiers in one tool result, and redacting them reduces performance to chance. These findings show how hidden label shortcuts can masquerade as scientific reasoning or discovery, motivating source-level audits before benchmark gains are trusted.

Safety alignment of large reasoning models (LRMs) via supervised fine-tuning (SFT) and reinforcement learning (RL) often yields near-perfect safety scores, yet this apparent success comes at the cost of severe over-refusal and degraded general capabilities. Through systematic empirical analysis, we find that these failures are closely associated with the learning of spurious shortcuts rather than robust intent-sensitive safety evaluation. Specifically, we identify two dominant shortcuts: formatting shortcuts, where refusal behaviors are overly bound to structural prompt templates that frequently appear in safety alignment corpora; and lexical shortcuts, where sensitive keywords reflexively trigger refusals on benign queries. To mitigate reliance on these shortcuts, we propose DeShortcut-Align, a shortcut-decoupling alignment framework that reduces dependence on superficial cues. DeShortcut-Align operates across three coordinated stages: (1) Refusal Sensitivity Attribution, which masks input tokens to quantify their impact on the final refusal response distribution; (2) Attribution-Guided Contrastive Augmentation, which constructs benign contrastive samples using high-sensitivity tokens to mitigate lexical shortcuts; and (3) Counterfactual Consistency Regularization, which constructs template-ablated states via attention blinding to enforce decision consistency across SFT and RL, mitigating formatting shortcut dependence. Experiments on 7B and 14B models demonstrate that DeShortcut-Align significantly improves robustness against template-stripping bypass attacks (reducing performance drops by up to 72%), substantially reduces over-refusal by over 58%, and better preserves general-purpose reasoning capabilities, thereby mitigating the alignment tax commonly observed in safety training.

Safety guards are widely used to filter harmful content and are typically trained via supervised fine-tuning on labeled prompt-response pairs. We audit two widely used safety-guard training datasets, WildGuardMix and GR-Train, and find that among responses to harmful prompts, refusal expressions co-occur almost exclusively with unharmful labels. This imbalance motivates what we term the refusal-cue shortcut: inserting a refusal cue into a harmful response could flip the guard's verdict from harmful to unharmful. The shortcut affects not only guards trained on these datasets but also officially released models such as LlamaGuard3 and Qwen3Guard whose training data is undisclosed. It persists across response positions and is generally stronger in smaller variants within a family. To mitigate it, we adapt sparse complementary masking as a lightweight post-hoc intervention that identifies and suppresses a small set of shortcut-associated attention heads and MLP neurons without retraining. On two primary benchmarks, the intervention achieves an approximately 79% relative reduction in response-initial detection failures induced by refusal cues, while preserving standard detection performance. Although optimized using cues at a single response position, the suppression effect transfers to unseen positions and datasets, suggesting that shortcut manifestations across positions are partly mediated by shared internal components. Further analysis provides evidence that shortcut reliance and legitimate refusal recognition are partially functionally separable, as suppressing the shortcut broadly preserves the guard's ability to recognize genuine refusals.

While reinforcement learning (RL) significantly enhances LLM reasoning, its efficacy is severely undermined by Pre-RL data overlap, where RL datasets overlap with pretraining or SFT corpora, causing models to exploit shortcuts by memorizing correct answers and fabricating post-hoc reasoning. To address this, we introduce HIPPO, a novel RL framework that integrates hint-injected aggregation with a tailored pairwise reward model. By utilizing hint injection to deliberately trigger overlap-induced behaviors, the resulting traces naturally serve as explicit anchors for pairwise comparison. This provides highly discriminable preference signals, enabling a lightweight judge model to reliably distinguish genuine reasoning deduction from shortcut-driven rationalization, while the pairwise formulation ensures stable and robust optimization compared to standard PRMs. Extensive experiments demonstrate that HIPPO yields substantial improvements over standard baselines and generalizes effectively to out-of-distribution general tasks, showing it extracts authentic, transferable reasoning skills rather than superficial shortcut patterns.

The morphological form of a word can often give cues to its meaning, but purely relying on these mappings can lead to overgeneralization in high-stakes domains. In the medical domain, for instance, LLMs can confidently reason about fictitious drugs from their affixes alone (e.g., wugcillin) and generate plausible-looking clinical content. We present a behavioral and mechanistic study of LLM "affix heuristics" in pharmacology. Using fictitious drug names built from real affixes, we show that affix signals alone elicit class-level pharmacological responses. We introduce a framework for identifying whether a model's drug semantics are driven mainly by the affix, the stem, or the drug name as a whole. Applied across 653 drugs, our framework reveals that models often induce drug meaning primarily through affix cues, yet rarely explicitly indicate this reliance, and sometimes incorrectly conflate properties among affix-sharing drugs. Activation patching across models further localizes this behavior to early-mid layers. These findings show that morphological shortcuts pose a subtle but measurable risk to safety.

Large language models reach 50 to 70% accuracy on causal reasoning benchmarks such as CLadder, but it is unclear whether this reflects structural reasoning or lexical pattern matching. We introduce Caliper, a controlled perturbation that replaces semantic variable names with placeholder tokens while preserving the causal graph and probabilistic specification of each question. Across nine instruction-tuned LLMs from 3.8B to 671B and three causal reasoning benchmarks, lexical anonymization yields robust accuracy drops of +7.6, +27.0, and +11.1 pp on a local 3.8B-14B set, rising to +29.6 and +18.0 pp on CRASS and e-CARE across nine frontier models spanning the 2024-2026 generations. Of 40 engaged model-by-benchmark cells, 39 show a positive gap, and the gap collapses by 17x on CLadder's pseudoword subset. Structured scaffolding and few-shot in-context learning each narrow the gap, but mainly by lowering P0 accuracy on smaller models rather than recovering P1. Current instruction-tuned LLMs, evaluated zero-shot, show little evidence of structural causal reasoning once lexical anchors are removed.

Large Language Models (LLMs) aligned via outcome-based Reinforcement Learning (RL) frequently exhibit a critical failure mode: they achieve high performance on in-distribution benchmarks while demonstrating brittle reasoning capabilities on out-of-distribution (OOD) tasks. We term this phenomenon Reward-Induced Manifold Collapse. We establish a theoretical framework bridging Structural Causal Models (SCM) and the Information Bottleneck (IB) principle to explain this paradox. We define reasoning as a high-complexity causal process and shortcut learning as the exploitation of low-complexity spurious correlations. Under the implicit inductive bias of Stochastic Gradient Descent (SGD), models optimized for outcome rewards are biased toward shortcut solutions whenever the training distribution allows for a ``Markovian Screening'' of the true causal mechanism. We derive a new generalization bound based on Semantic Coverage Measure ($η$) rather than sample size, showing why data scaling on homogeneous distributions may fail to correct reasoning flaws. We also show that Process Reward Models (PRMs) function as Topological Filters, enforcing step-wise mutual information constraints that render the low-complexity shortcut manifold inadmissible. These results provide a mathematical grounding for the role of process supervision beyond simple credit assignment.

Machine unlearning aims to remove the influence of specific training data from a model while preserving reliable behavior on the remaining data, making reliable prediction and uncertainty estimation essential for evaluation. Calibration is commonly used as a proxy for reliability in language models, but low calibration error does not necessarily imply reliable decision rules, as models may rely on spurious correlations while remaining well calibrated. We investigate this gap in generative language models using the multiple-choice question-answering evaluation protocol on the TOFU benchmark, measuring probabilistic reliability with calibration metrics (ECE, MCE, Brier) and decision-rule reliability via attribution-based shortcut detection with Integrated Gradients and Local Mutual Information. We find that fine-tuned models achieve low calibration error (ECE ~ 0.04) compared to pretrained models (ECE > 0.5), and models after unlearning retain similarly low calibration despite reduced accuracy on the forget split, while attribution analysis shows increased reliance on correlation-based tokens. These results demonstrate that good calibration can coexist with shortcut-based decision rules after unlearning, extending the reliability paradox to the machine unlearning setting.

Large Language Models (LLMs) have achieved impressive results on public benchmarks, often leading to claims of advanced reasoning and understanding. However, recent research in cognitive science reveals that these models sometimes rely on shallow heuristics and memorization, taking shortcuts rather than demonstrating genuine cognitive abilities. This paper investigates LLM behavior in automated test generation for software, contrasting performance on an open-source system (LevelDB) with SAP HANA, one of the most widely deployed commercial database systems worldwide, whose proprietary codebase is guaranteed to be absent from training data. We combine cognitive evaluation principles, drawing on Mitchell's mechanism-focused assessment methodology, with empirical software testing, employing mutation score and iterative compiler-feedback repair loops to assess both accuracy and underlying reasoning strategies. Results show that LLMs excel on familiar, open-source benchmarks but struggle with unseen, complex domains, often prioritizing compilability over semantic effectiveness. These findings provide independent software engineering evidence for the broader claim that current LLMs lack robust reasoning, and highlight the need for evaluation frameworks that penalize trivial shortcuts and reward true generalization.

Large language models exhibit strong reasoning capabilities, yet often rely on shortcuts such as surface pattern matching and answer memorization rather than genuine logical inference. We propose Shortcut-Aware Reasoning Training (SART), a gradient-aware framework that detects and mitigates shortcut-promoting samples via ShortcutScore and gradient surgery. Our method identifies shortcut signals through gradient misalignment with validation objectives and answer-token concentration, and modifies training dynamics accordingly. Experiments on controlled reasoning benchmarks show that SART achieves +16.5% accuracy and +40.2% robustness over the strongest baseline, significantly improving generalization under distribution shifts. Code is available at: https://github.com/fuyanjie/short-cut-aware-data-centric-reasoning.

While Large Language Models (LLMs) achieve expert-level performance on standard medical benchmarks through single-hop factual recall, they severely struggle with the complex, multi-hop diagnostic reasoning required in real-world clinical settings. A primary obstacle is "shortcut learning", where models exploit highly connected, generic hub nodes (e.g., "inflammation") in knowledge graphs to bypass authentic micro-pathological cascades. To address this, we introduce ShatterMed-QA, a bilingual benchmark of 10,558 multi-hop clinical questions designed to rigorously evaluate deep diagnostic reasoning. Our framework constructs a topology-regularized medical Knowledge Graph using a novel $k$-Shattering algorithm, which physically prunes generic hubs to explicitly sever logical shortcuts. We synthesize the evaluation vignettes by applying implicit bridge entity masking and topology-driven hard negative sampling, forcing models to navigate biologically plausible distractors without relying on superficial elimination. Comprehensive evaluations of 21 LLMs reveal massive performance degradation on our multi-hop tasks, particularly among domain-specific models. Crucially, restoring the masked evidence via Retrieval-Augmented Generation (RAG) triggers near-universal performance recovery, validating ShatterMed-QA's structural fidelity and proving its efficacy in diagnosing the fundamental reasoning deficits of current medical AI. Explore the dataset, interactive examples, and full leaderboards at our project website: https://shattermed-qa-web.vercel.app/