Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences.

In the field of artificial intelligence, a combination of scale in data and model capacity enabled by unsupervised learning has led to major advances in representation learning and statistical generation. In the life sciences, the anticipated growth of sequencing promises unprecedented data on natural sequence diversity. Protein language modeling at the scale of evolution is a logical step toward predictive and generative artificial intelligence for biology. To this end, we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. The resulting model contains information about biological properties in its representations. The representations are learned from sequence data alone. The learned representation space has a multiscale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. Information about secondary and tertiary structure is encoded in the representations and can be identified by linear projections. Representation learning produces features that generalize across a range of applications, enabling state-of-the-art supervised prediction of mutational effect and secondary structure and improving state-of-the-art features for long-range contact prediction.

Deep Learning Reconstruction Enables Prospectively Accelerated Clinical Knee MRI.

Background MRI is a powerful diagnostic tool with a long acquisition time. Recently, deep learning (DL) methods have provided accelerated high-quality image reconstructions from undersampled data, but it is unclear if DL image reconstruction can be reliably translated to everyday clinical practice. Purpose To determine the diagnostic equivalence of prospectively accelerated DL-reconstructed knee MRI compared with conventional accelerated MRI for evaluating internal derangement of the knee in a clinical setting. Materials and Methods A DL reconstruction model was trained with images from 298 clinical 3-T knee examinations. In a prospective analysis, patients clinically referred for knee MRI underwent a conventional accelerated knee MRI protocol at 3 T followed by an accelerated DL protocol between January 2020 and February 2021. The equivalence of the DL reconstruction of the images relative to the conventional images for the detection of an abnormality was assessed in terms of interchangeability. Each examination was reviewed by six musculoskeletal radiologists. Analyses pertaining to the detection of meniscal or ligament tears and bone marrow or cartilage abnormalities were based on four-point ordinal scores for the likelihood of an abnormality. Additionally, the protocols were compared with use of four-point ordinal scores for each aspect of image quality: overall image quality, presence of artifacts, sharpness, and signal-to-noise ratio. Results A total of 170 participants (mean age ± SD, 45 years ± 16; 76 men) were evaluated. The DL-reconstructed images were determined to be of diagnostic equivalence with the conventional images for detection of abnormalities. The overall image quality score, averaged over six readers, was significantly better (P < .001) for the DL than for the conventional images. Conclusion In a clinical setting, deep learning reconstruction enabled a nearly twofold reduction in scan time for a knee MRI and was diagnostically equivalent with the conventional protocol. © RSNA, 2023 Supplemental material is available for this article. See also the editorial by Roemer in this issue.

Transfer learning using attentions across atomic systems with graph neural networks (TAAG).

Recent advances in Graph Neural Networks (GNNs) have transformed the space of molecular and catalyst discovery. Despite the fact that the underlying physics across these domains remain the same, most prior work has focused on building domain-specific models either in small molecules or in materials. However, building large datasets across all domains is computationally expensive; therefore, the use of transfer learning (TL) to generalize to different domains is a promising but under-explored approach to this problem. To evaluate this hypothesis, we use a model that is pretrained on the Open Catalyst Dataset (OC20), and we study the model's behavior when fine-tuned for a set of different datasets and tasks. This includes MD17, the *CO adsorbate dataset, and OC20 across different tasks. Through extensive TL experiments, we demonstrate that the initial layers of GNNs learn a more basic representation that is consistent across domains, whereas the final layers learn more task-specific features. Moreover, these well-known strategies show significant improvement over the non-pretrained models for in-domain tasks with improvements of 53% and 17% for the *CO dataset and across the Open Catalyst Project (OCP) task, respectively. TL approaches result in up to 4× speedup in model training depending on the target data and task. However, these do not perform well for the MD17 dataset, resulting in worse performance than the non-pretrained model for few molecules. Based on these observations, we propose transfer learning using attentions across atomic systems with graph Neural Networks (TAAG), an attention-based approach that adapts to prioritize and transfer important features from the interaction layers of GNNs. The proposed method outperforms the best TL approach for out-of-domain datasets, such as MD17, and gives a mean improvement of 6% over a model trained from scratch.

Advancing machine learning for MR image reconstruction with an open competition: Overview of the 2019 fastMRI challenge.

PURPOSE: To advance research in the field of machine learning for MR image reconstruction with an open challenge. METHODS: We provided participants with a dataset of raw k-space data from 1,594 consecutive clinical exams of the knee. The goal of the challenge was to reconstruct images from these data. In order to strike a balance between realistic data and a shallow learning curve for those not already familiar with MR image reconstruction, we ran multiple tracks for multi-coil and single-coil data. We performed a two-stage evaluation based on quantitative image metrics followed by evaluation by a panel of radiologists. The challenge ran from June to December of 2019. RESULTS: We received a total of 33 challenge submissions. All participants chose to submit results from supervised machine learning approaches. CONCLUSIONS: The challenge led to new developments in machine learning for image reconstruction, provided insight into the current state of the art in the field, and highlighted remaining hurdles for clinical adoption.

Using Deep Learning to Accelerate Knee MRI at 3 T: Results of an Interchangeability Study.

OBJECTIVE. Deep learning (DL) image reconstruction has the potential to disrupt the current state of MRI by significantly decreasing the time required for MRI examinations. Our goal was to use DL to accelerate MRI to allow a 5-minute comprehensive examination of the knee without compromising image quality or diagnostic accuracy. MATERIALS AND METHODS. A DL model for image reconstruction using a variational network was optimized. The model was trained using dedicated multisequence training, in which a single reconstruction model was trained with data from multiple sequences with different contrast and orientations. After training, data from 108 patients were retrospectively undersampled in a manner that would correspond with a net 3.49-fold acceleration of fully sampled data acquisition and a 1.88-fold acceleration compared with our standard twofold accelerated parallel acquisition. An interchangeability study was performed, in which the ability of six readers to detect internal derangement of the knee was compared for clinical and DL-accelerated images. RESULTS. We found a high degree of interchangeability between standard and DL-accelerated images. In particular, results showed that interchanging the sequences would produce discordant clinical opinions no more than 4% of the time for any feature evaluated. Moreover, the accelerated sequence was judged by all six readers to have better quality than the clinical sequence. CONCLUSION. An optimized DL model allowed acceleration of knee images that performed interchangeably with standard images for detection of internal derangement of the knee. Importantly, readers preferred the quality of accelerated images to that of standard clinical images.

fastMRI: A Publicly Available Raw k-Space and DICOM Dataset of Knee Images for Accelerated MR Image Reconstruction Using Machine Learning.

A publicly available dataset containing k-space data as well as Digital Imaging and Communications in Medicine image data of knee images for accelerated MR image reconstruction using machine learning is presented.

Automatic estimation and removal of noise from a single image.

Image denoising algorithms often assume an additive white Gaussian noise (AWGN) process that is independent of the actual RGB values. Such approaches are not fully automatic and cannot effectively remove color noise produced by todays CCD digital camera. In this paper, we propose a unified framework for two tasks: automatic estimation and removal of color noise from a single image using piecewise smooth image models. We introduce the noise level function (NLF), which is a continuous function describing the noise level as a function of image brightness. We then estimate an upper bound of the real noise level function by fitting a lower envelope to the standard deviations of per-segment image variances. For denoising, the chrominance of color noise is significantly removed by projecting pixel values onto a line fit to the RGB values in each segment. Then, a Gaussian conditional random field (GCRF) is constructed to obtain the underlying clean image from the noisy input. Extensive experiments are conducted to test the proposed algorithm, which is shown to outperform state-of-the-art denoising algorithms.

Adopting Abstract Images for Semantic Scene Understanding.

Relating visual information to its linguistic semantic meaning remains an open and challenging area of research. The semantic meaning of images depends on the presence of objects, their attributes and their relations to other objects. But precisely characterizing this dependence requires extracting complex visual information from an image, which is in general a difficult and yet unsolved problem. In this paper, we propose studying semantic information in abstract images created from collections of clip art. Abstract images provide several advantages over real images. They allow for the direct study of how to infer high-level semantic information, since they remove the reliance on noisy low-level object, attribute and relation detectors, or the tedious hand-labeling of real images. Importantly, abstract images also allow the ability to generate sets of semantically similar scenes. Finding analogous sets of real images that are semantically similar would be nearly impossible. We create 1,002 sets of 10 semantically similar abstract images with corresponding written descriptions. We thoroughly analyze this dataset to discover semantically important features, the relations of words to visual features and methods for measuring semantic similarity. Finally, we study the relation between the saliency and memorability of objects and their semantic importance.

Fast Edge Detection Using Structured Forests.

Edge detection is a critical component of many vision systems, including object detectors and image segmentation algorithms. Patches of edges exhibit well-known forms of local structure, such as straight lines or T-junctions. In this paper we take advantage of the structure present in local image patches to learn both an accurate and computationally efficient edge detector. We formulate the problem of predicting local edge masks in a structured learning framework applied to random decision forests. Our novel approach to learning decision trees robustly maps the structured labels to a discrete space on which standard information gain measures may be evaluated. The result is an approach that obtains realtime performance that is orders of magnitude faster than many competing state-of-the-art approaches, while also achieving state-of-the-art edge detection results on the BSDS500 Segmentation dataset and NYU Depth dataset. Finally, we show the potential of our approach as a general purpose edge detector by showing our learned edge models generalize well across datasets.

Exploring tiny images: the roles of appearance and contextual information for machine and human object recognition.

Typically, object recognition is performed based solely on the appearance of the object. However, relevant information also exists in the scene surrounding the object. In this paper, we explore the roles that appearance and contextual information play in object recognition. Through machine experiments and human studies, we show that the importance of contextual information varies with the quality of the appearance information, such as an image's resolution. Our machine experiments explicitly model context between object categories through the use of relative location and relative scale, in addition to co-occurrence. With the use of our context model, our algorithm achieves state-of-the-art performance on the MSRC and Corel data sets. We perform recognition tests for machines and human subjects on low and high resolution images, which vary significantly in the amount of appearance information present, using just the object appearance information, the combination of appearance and context, as well as just context without object appearance information (blind recognition). We also explore the impact of the different sources of context (co-occurrence, relative-location, and relative-scale). We find that the importance of different types of contextual information varies significantly across data sets such as MSRC and PASCAL.

Image restoration by matching gradient distributions.

The restoration of a blurry or noisy image is commonly performed with a MAP estimator, which maximizes a posterior probability to reconstruct a clean image from a degraded image. A MAP estimator, when used with a sparse gradient image prior, reconstructs piecewise smooth images and typically removes textures that are important for visual realism. We present an alternative deconvolution method called iterative distribution reweighting (IDR) which imposes a global constraint on gradients so that a reconstructed image should have a gradient distribution similar to a reference distribution. In natural images, a reference distribution not only varies from one image to another, but also within an image depending on texture. We estimate a reference distribution directly from an input image for each texture segment. Our algorithm is able to restore rich mid-frequency textures. A large-scale user study supports the conclusion that our algorithm improves the visual realism of reconstructed images compared to those of MAP estimators.