The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

As a research community, we are still lacking a systematic understanding of the progress on adversarial robustness, which often makes it hard to identify the most promising ideas in training robust models. A key challenge in benchmarking robustness is that its evaluation is often error-prone, leading to overestimation of the true robustness of models. While adaptive attacks designed for a particular defense are a potential solution, they have to be highly customized for particular models, which makes it difficult to compare different methods. Our goal is to instead establish a standardized benchmark of adversarial robustness, which as accurately as possible reflects the robustness of the considered models within a reasonable computational budget. To evaluate the robustness of models for our benchmark, we consider AutoAttack, an ensemble of white- and black-box attacks which was recently shown in a large-scale study to improve almost all robustness evaluations compared to the original publications. We also impose some restrictions on the admitted models to rule out defenses that only make gradient-based attacks ineffective without improving actual robustness. Our leaderboard, hosted at this https URL, contains evaluations of 90+ models and aims at reflecting the current state of the art on a set of well-defined tasks in $\ell_\infty$- and $\ell_2$-threat models and on common corruptions, with possible extensions in the future. Additionally, we open-source the library this https URL that provides unified access to 60+ robust models to facilitate their downstream applications. Finally, based on the collected models, we analyze the impact of robustness on the performance on distribution shifts, calibration, out-of-distribution detection, fairness, privacy leakage, smoothness, and transferability.

RobustBench: a standardized adversarial robustness benchmark.

The conventional recipe for maximizing model accuracy is to (1) train multiple models with various hyperparameters and (2) pick the individual model which performs best on a held-out validation set, discarding the remainder. In this paper, we revisit the second step of this procedure in the context of fine-tuning large pre-trained models, where fine-tuned models often appear to lie in a single low error basin. We show that averaging the weights of multiple models fine-tuned with different hyperparameter configurations often improves accuracy and robustness. Unlike a conventional ensemble, we may average many models without incurring any additional inference or memory costs -- we call the results"model soups."When fine-tuning large pre-trained models such as CLIP, ALIGN, and a ViT-G pre-trained on JFT, our soup recipe provides significant improvements over the best model in a hyperparameter sweep on ImageNet. The resulting ViT-G model, which attains 90.94% top-1 accuracy on ImageNet, achieved a new state of the art. Furthermore, we show that the model soup approach extends to multiple image classification and natural language processing tasks, improves out-of-distribution performance, and improves zero-shot performance on new downstream tasks. Finally, we analytically relate the performance similarity of weight-averaging and logit-ensembling to flatness of the loss and confidence of the predictions, and validate this relation empirically. Code is available at https://github.com/mlfoundations/model-soups.

Model soups: averaging weights of multiple fine-tuned models improves accuracy without increasing inference time

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).

Fine-Tuning can Distort Pretrained Features and Underperform Out-of-Distribution

We present MSeg, a composite dataset that unifies se- mantic segmentation datasets from different domains. A naive merge of the constituent datasets yields poor performance due to inconsistent taxonomies and annotation practices. We reconcile the taxonomies and bring the pixel-level annotations into alignment by relabeling more than 220,000 object masks in more than 80,000 images. The resulting composite dataset enables training a single semantic segmentation model that functions effectively across domains and generalizes to datasets that were not seen during training. We adopt zero-shot cross-dataset transfer as a benchmark to systematically evaluate a model’s robustness and show that MSeg training yields substantially more robust models in comparison to training on individual datasets or naive mixing of datasets without the presented contributions. A model trained on MSeg ranks first on the WildDash leaderboard for robust semantic segmentation, with no exposure to WildDash data during training.

/pdf/mseg-a-composite-dataset-for-multi-domain-semantic-4ln18ic7cy.pdf

MSeg: A Composite Dataset for Multi-Domain Semantic Segmentation

Distribution shifts -- where the training distribution differs from the test distribution -- can substantially degrade the accuracy of machine learning (ML) systems deployed in the wild. Despite their ubiquity, these real-world distribution shifts are under-represented in the datasets widely used in the ML community today. To address this gap, we present WILDS, a curated collection of 8 benchmark datasets that reflect a diverse range of distribution shifts which naturally arise in real-world applications, such as shifts across hospitals for tumor identification; across camera traps for wildlife monitoring; and across time and location in satellite imaging and poverty mapping. On each dataset, we show that standard training results in substantially lower out-of-distribution than in-distribution performance, and that this gap remains even with models trained by existing methods for handling distribution shifts. This underscores the need for new training methods that produce models which are more robust to the types of distribution shifts that arise in practice. To facilitate method development, we provide an open-source package that automates dataset loading, contains default model architectures and hyperparameters, and standardizes evaluations. Code and leaderboards are available at this https URL.

WILDS: A Benchmark of in-the-Wild Distribution Shifts

/pdf/wilds-a-benchmark-of-in-the-wild-distribution-shifts-2zlb02l5o3.pdf

Irena Gao

Papers

WILDS: A Benchmark of in-the-Wild Distribution Shifts

WILDS: A Benchmark of in-the-Wild Distribution Shifts