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In-context learning is the ability of a pretrained model to adapt to novel and diverse downstream tasks by conditioning on prompt examples, without optimizing any parameters. While large language models have demonstrated this ability, how in-context learning could be performed over graphs is unexplored. In this paper, we develop Pretraining Over Diverse In-Context Graph Systems (PRODIGY), the first pretraining framework that enables in-context learning over graphs. The key idea of our framework is to formulate in-context learning over graphs with a novel prompt graph representation, which connects prompt examples and queries. We then propose a graph neural network architecture over the prompt graph and a corresponding family of in-context pretraining objectives. With PRODIGY, the pre- trained model can directly perform novel downstream classification tasks on unseen graphs via in-context learning. We provide empirical evidence of the effectiveness of our framework by showcasing its strong in-context learning performance on tasks involving citation networks and knowledge graphs. Our approach outperforms the in-context learning accuracy of contrastive pretraining baselines with hard-coded adaptation by 18% on average across all setups. Moreover, it also outperforms standard finetuning with limited data by 33% on average with in-context learning. 

Adversarial training augments the training set with perturbations to improve the robust error (over worst-case perturbations), but it often leads to an increase in the standard error (on unperturbed test inputs). Previous explanations for this tradeoff rely on the assumption that no predictor in the hypothesis class has low standard and robust error. In this work, we precisely characterize the effect of augmentation on the standard error in linear regression when the optimal linear predictor has zero standard and robust error. In particular, we show that the standard error could increase even when the augmented perturbations have noiseless observations from the optimal linear predictor. We then prove that the recently proposed robust self-training (RST) estimator improves robust error without sacrificing standard error for noiseless linear regression. Empirically, for neural networks, we find that RST with different adversarial training methods improves both standard and robust error for random and adversarial rotations and adversarial l_infty perturbations in CIFAR-10. 

Language model (LM) pretraining can learn various knowledge from text corpora, helping downstream tasks. However, existing methods such as BERT model a single document, and do not capture dependencies or knowledge that span across documents. In this work, we propose LinkBERT, an LM pretraining method that leverages links between documents, e.g., hyperlinks. Given a text corpus, we view it as a graph of documents and create LM inputs by placing linked documents in the same context. We then pretrain the LM with two joint self-supervised objectives: masked language modeling and our new proposal, document relation prediction. We show that LinkBERT outperforms BERT on various downstream tasks across two domains: the general domain (pretrained on Wikipedia with hyperlinks) and biomedical domain (pretrained on PubMed with citation links). LinkBERT is especially effective for multi-hop reasoning and few-shot QA (+5% absolute improvement on HotpotQA and TriviaQA), and our biomedical LinkBERT sets new states of the art on various BioNLP tasks (+7% on BioASQ and USMLE). 

A common approach to transfer learning under distribution shift is to fine-tune the last few layers of a pre-trained model, preserving learned features while also adapting to the new task. This paper shows that in such settings, selectively fine-tuning a subset of layers (which we term surgical fine-tuning) matches or outperforms commonly used fine-tuning approaches. Moreover, the type of distribution shift influences which subset is more effective to tune: for example, for image corruptions, fine-tuning only the first few layers works best. We validate our findings systematically across seven real-world data tasks spanning three types of distribution shifts. Theoretically, we prove that for two-layer neural networks in an idealized setting, first-layer tuning can outperform fine-tuning all layers. Intuitively, fine-tuning more parameters on a small target dataset can cause information learned during pre-training to be forgotten, and the relevant information depends on the type of shift. 

When transferring a pretrained model to a downstream task, two popular methods are full fine-tuning (updating all the model parameters) and linear probing (updating only the last linear layer—the “head”). It is well known that fine-tuning leads to better accuracy in-distribution (ID). However, in this paper, we find that fine-tuning can achieve worse accuracy than linear probing out-of-distribution (OOD) when the pretrained features are good and the distribution shift is large. On 10 distribution shift datasets (Breeds-Living17, Breeds-Entity30, DomainNet, CIFAR → STL, CIFAR10.1, FMoW, ImageNetV2, ImageNet-R, ImageNet-A, ImageNet-Sketch), fine-tuning obtains on average 2% higher accuracy ID but 7% lower accuracy OOD than linear probing. We show theoretically that this tradeoff between ID and OOD accuracy arises even in a simple setting: fine-tuning overparameterized two-layer linear networks. We prove that the OOD error of fine-tuning is high when we initialize with a fixed or random head—this is because while fine-tuning learns the head, the lower layers of the neural network change simultaneously and distort the pretrained features. Our analysis suggests that the easy two-step strategy of linear probing then full fine-tuning (LP-FT), sometimes used as a fine-tuning heuristic, combines the benefits of both fine-tuning and linear probing. Empirically, LP-FT outperforms both fine-tuning and linear probing on the above datasets (1% better ID, 10% better OOD than full fine-tuning). 

When transferring a pretrained model to a downstream task, two popular methods are full fine-tuning (updating all the model parameters) and linear probing (updating only the last linear layer -- the "head"). It is well known that fine-tuning leads to better accuracy in-distribution (ID). However, in this paper, we find that fine-tuning can achieve worse accuracy than linear probing out-of-distribution (OOD) when the pretrained features are good and the distribution shift is large. On 10 distribution shift datasets (Breeds-Living17, Breeds-Entity30, DomainNet, CIFAR → STL, CIFAR10.1, FMoW, ImageNetV2, ImageNet-R, ImageNet-A, ImageNet-Sketch), fine-tuning obtains on average 2% higher accuracy ID but 7% lower accuracy OOD than linear probing. We show theoretically that this tradeoff between ID and OOD accuracy arises even in a simple setting: fine-tuning overparameterized two-layer linear networks. We prove that the OOD error of fine-tuning is high when we initialize with a fixed or random head -- this is because while fine-tuning learns the head, the lower layers of the neural network change simultaneously and distort the pretrained features. Our analysis suggests that the easy two-step strategy of linear probing then full fine-tuning (LP-FT), sometimes used as a fine-tuning heuristic, combines the benefits of both fine-tuning and linear probing. Empirically, LP-FT outperforms both fine-tuning and linear probing on the above datasets (1% better ID, 10% better OOD than full fine-tuning).