Shortcut Learning

Classifying the topology of closed curves is a central problem in low dimensional topology with applications beyond mathematics spanning protein folding, polymer physics and even magnetohydrodynamics. The central problem is how to determine whether two embeddings of a closed arc are equivalent under ambient isotopy. Given the striking ability of neural networks to solve complex classification tasks, it is therefore natural to ask if the knot classification problem can be tackled using Machine Learning (ML). In this paper, we investigate generic shortcut methods employed by ML to solve the knot classification challenge and specifically discover hidden non-topological features in training data generated through Molecular Dynamics simulations of polygonal knots that are used by ML to arrive to positive classifications results. We then provide a rigorous foundation for future attempts to tackle the knot classification challenge using ML by developing a publicly-available (i) dataset, that aims to remove the potential of non-topological feature classification and (ii) code, that can generate knot embeddings that faithfully explore chosen geometric state space with fixed knot topology. We expect that our work will accelerate the development of ML models that can solve complex geometric knot classification challenges.

Machine learning can accelerate materials discovery. Models perform impressively on many benchmarks. However, strong benchmark performance does not imply that a model learned chemistry. I test a concrete alternative hypothesis: that property prediction can be driven by bibliographic confounding. Across five tasks spanning MOFs (thermal and solvent stability), perovskite solar cells (efficiency), batteries (capacity), and TADF emitters (emission wavelength), models trained on standard chemical descriptors predict author, journal, and publication year well above chance. When these predicted metadata ("bibliographic fingerprints") are used as the sole input to a second model, performance is sometimes competitive with conventional descriptor-based predictors. These results show that many datasets do not rule out non-chemical explanations of success. Progress requires routine falsification tests (e.g., group/time splits and metadata ablations), datasets designed to resist spurious correlations, and explicit separation of two goals: predictive utility versus evidence of chemical understanding.

Although deep learning models in medical imaging often achieve excellent classification performance, they can rely on shortcut learning, exploiting spurious correlations or confounding factors that are not causally related to the target task. This poses risks in clinical settings, where models must generalize across institutions, populations, and acquisition conditions. Feature disentanglement is a promising approach to mitigate shortcut learning by separating task-relevant information from confounder-related features in latent representations. In this study, we systematically evaluated feature disentanglement methods for mitigating shortcuts in medical imaging, including adversarial learning and latent space splitting based on dependence minimization. We assessed classification performance and disentanglement quality using latent space analyses across one artificial and two medical datasets with natural and synthetic confounders. We also examined robustness under varying levels of confounding and compared computational efficiency across methods. We found that shortcut mitigation methods improved classification performance under strong spurious correlations during training. Latent space analyses revealed differences in representation quality not captured by classification metrics, highlighting the strengths and limitations of each method. Model reliance on shortcuts depended on the degree of confounding in the training data. The best-performing models combine data-centric rebalancing with model-centric disentanglement, achieving stronger and more robust shortcut mitigation than rebalancing alone while maintaining similar computational efficiency. The project code is publicly available at https://github.com/berenslab/medical-shortcut-mitigation.

Vision Language Models (VLMs) are designed to extend Large Language Models (LLMs) with visual capabilities, yet in this work we observe a surprising phenomenon: VLMs can outperform their underlying LLMs on purely text-only tasks, particularly in long-context information retrieval. To investigate this effect, we build a controlled synthetic retrieval task and find that a transformer trained only on text achieves perfect in-distribution accuracy but fails to generalize out of distribution, while subsequent training on an image-tokenized version of the same task nearly doubles text-only OOD performance. Mechanistic interpretability reveals that visual training changes the model's internal binding strategy: text-only training encourages positional shortcuts, whereas image-based training disrupts them through spatial translation invariance, forcing the model to adopt a more robust symbolic binding mechanism that persists even after text-only examples are reintroduced. We further characterize how binding strategies vary across training regimes, visual encoders, and initializations, and show that analogous shifts occur during pretrained LLM-to-VLM transitions. Our findings suggest that cross-modal training can enhance reasoning and generalization even for tasks grounded in a single modality.

Temporal knowledge graph (TKG) forecasting has advanced remarkably in recent years. Yet we found existing benchmarks inadvertently introduce a shortcut: For a subset of test queries, models can achieve optimal evaluation metrics without using any time information. We trace this to two pieces of evidence: inherent dataset biases and an overly simplistic task formulation that allows models to exploit biases, revealing fundamental flaws in current evaluation protocols for differentiating true forecasting ability. Moreover, existing datasets rely on fixed history that poorly reflects real-world dynamics, lack semantic context, and fail to explicitly mitigate shortcut, preventing thorough assessment of forecasting abilities. To address these, we propose TKGB, a comprehensive benchmark for evaluating the capability of TKG forecasting models. By integrating four complementary tasks with an automatic pipeline for constructing up-to-date and context-enriched TKG datasets with controllable shortcuts, TKGB reveals capability differences and failure modes hidden under conventional evaluation.

Reliable models should not only predict correctly, but also justify decisions with acceptable evidence. Yet conventional supervised learning typically provides only class-level labels, allowing models to achieve high accuracy through shortcut correlations rather than the intended evidence. Human priors can help constrain such behavior, but aligning models to these priors remains challenging because learned representations often diverge from human perception. To address this challenge, we propose an attribution-based human prior alignment method. We encode human priors as input regions that the model is expected to rely on (e.g., bounding boxes), and leverage a highly faithful subset-selection-based attribution approach to expose the model's decision evidence during training. When the attribution region deviates substantially from the prior regions, we penalize reliance on off-prior evidence, encouraging the model to shift its attribution toward the intended regions. This is achieved through a training objective that imposes attribution constraints induced by the human prior. We validate our method on both image classification and click decision tasks in MLLM-based GUI agent models. Across conventional classification and autoregressive generation settings, human prior alignment consistently improves task accuracy while also enhancing the model's decision reasonability.

Zero-Shot Compositional Action Recognition (ZS-CAR) requires recognizing novel verb-object combinations composed of previously observed primitives. In this work, we tackle a key failure mode: models predict verbs via object-driven shortcuts (i.e., relying on the labeled object class) rather than temporal evidence. We argue that sparse compositional supervision and verb-object learning asymmetry can promote object-driven shortcut learning. Our analysis with proposed diagnostic metrics shows that existing methods overfit to training co-occurrence patterns and underuse temporal verb cues, resulting in weak generalization to unseen compositions. To address object-driven shortcuts, we propose Robust COmpositional REpresentations (RCORE) with two components. Co-occurrence Prior Regularization (CPR) adds explicit supervision for unseen compositions and regularizes the model against frequent co-occurrence priors by treating them as hard negatives. Temporal Order Regularization for Composition (TORC) enforces temporal-order sensitivity to learn temporally grounded verb representations. Across Sth-com and EK100-com, RCORE reduces shortcut diagnostics and consequently improves compositional generalization.

Large-scale image classification datasets exhibit strong compositional biases: objects tend to be centered, appear at characteristic scales, and co-occur with class-specific context. By exploiting such biases, models attain high in-distribution accuracy but remain fragile under distribution shifts. To address this issue, we introduce ForAug, a controlled composition augmentation scheme that factorizes each training image into a foreground object and a background and recombines them to explicitly manipulate object position, object scale, and background identity. ForAug uses off-the-shelf segmentation and inpainting models to (i) extract the foreground and synthesize a neutral background, and (ii) paste the foreground onto diverse neutral backgrounds before applying standard strong augmentation policies. Compared to conventional augmentations and content-mixing methods, our factorization provides direct control knobs that break foreground-background correlations. Across 10 architectures, ForAug improves ImageNet top-1 accuracy by up to 6 percentage points (p.p.) and yields gains of up to 7.3 p.p. on fine-grained downstream datasets. Moreover, the same control knobs enable targeted diagnostic tests: we quantify background reliance, foreground focus, center bias, and size bias via controlled background swaps and position/scale sweeps, and show that training with ForAug substantially reduces these shortcut behaviors and significantly increases accuracy on standard distribution-shift benchmarks by up to $19$ p.p. Our code and dataset are publicly available at https://github.com/tobna/ForAug.

Background: Neurosymbolic (NeSy) artificial intelligence describes the combination of logic or rule-based techniques with neural networks. Compared to neural approaches, NeSy methods often possess enhanced interpretability, which is particularly promising for biomedical applications like drug discovery. However, no clear guidelines exist to assess the biological plausibility of model interpretations. Methods: To assess interpretability in the context of drug discovery, we devise a novel prediction task, called drug mechanism-of-action (MoA) deconvolution, with an associated, tailored knowledge graph (KG), MoA-net. We then develop the MoA Retrieval System (MARS), a NeSy approach for drug discovery which leverages logical rules with learned rule weights. Results: Using MARS' interpretable features alongside domain knowledge, we find that MARS and other NeSy approaches on KGs are susceptible to reasoning shortcuts, in which the prediction of true labels is driven by ``degree-bias'' rather than the domain-based rules. Subsequently, we demonstrate ways to identify and mitigate this. Thereafter, MARS achieves performance on par with current state-of-the-art models while producing model interpretations aligned with known MoAs. Conclusion: Through MARS, we showcase the novel task of computational MoA deconvolution. Our results emphasize the importance of using interpretable models, like NeSy ones, for applications in drug discovery. Specifically, by identifying and mitigating reasoning shortcuts, MARS MoA predictions which are biologically meaningful and, therefore, more reliable for downstream drug discovery research.