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Proc. 2023 Int. Conf. on Machine Learning (Ed.)Recent studies have revealed the intriguing fewshot learning ability of pretrained language models (PLMs): They can quickly adapt to a new task when fine-tuned on a small amount of labeled data formulated as prompts, without requiring abundant task-specific annotations. Despite their promising performance, most existing few-shot approaches that only learn from the small training set still underperform fully supervised training by nontrivial margins. In this work, we study few-shot learning with PLMs from a different perspective: We first tune an autoregressive PLM on the few-shot samples and then use it as a generator to synthesize a large amount of novel training samples which augment the original training set. To encourage the generator to produce label discriminative samples, we train it via weighted maximum likelihood where the weight of each token is automatically adjusted based on a discriminative meta-learning objective. A classification PLM can then be fine-tuned on both the few-shot and the synthetic samples with regularization for better generalization and stability. Our approach FewGen achieves an overall better result across seven classification tasks of the GLUE benchmark than existing few-shot learning methods, improving no-augmentation methods by 5+ average points, and outperforming augmentation methods by 3+ average points.more » « less
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Supervised machine learning approaches have been increasingly used in accelerating electronic structure prediction as surrogates of first-principle computational methods, such as density functional theory (DFT). While numerous quantum chemistry datasets focus on chemical properties and atomic forces, the ability to achieve accurate and efficient prediction of the Hamiltonian matrix is highly desired, as it is the most important and fundamental physical quantity that determines the quantum states of physical systems and chemical properties. In this work, we generate a new Quantum Hamiltonian dataset, named as QH9, to provide precise Hamiltonian matrices for 2,399 molecular dynamics trajectories and 130,831 stable molecular geometries, based on the QM9 dataset. By designing benchmark tasks with various molecules, we show that current machine learning models have the capacity to predict Hamiltonian matrices for arbitrary molecules. Both the QH9 dataset and the baseline models are provided to the community through an open-source benchmark, which can be highly valuable for developing machine learning methods and accelerating molecular and materials design for scientific and technological applications.more » « less
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null (Ed.)We report two highly fluorinated Cu-based imaging agents, CuL1 and CuL2 , for detecting cellular hypoxia as nanoemulsion formulations. Both complexes retained their initial quenched 19 F MR signals due to paramagnetic Cu 2+ ; however, both complexes displayed a large signal increase when the complex was reduced. DLS studies showed that the CuL1 nanoemulsion ( NE CuL1 ) had a hydrodiameter of approximately 100 nm and that it was stable for four weeks post-preparation. Hypoxic cells incubated with NE CuL1 showed that 40% of the Cu 2+ taken up was reduced in low oxygen environments.more » « less
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Malik, Harmit S. (Ed.)The sequence space accessible to evolving proteins can be enhanced by cellular chaperones that assist biophysically defective clients in navigating complex folding landscapes. It is also possible, at least in theory, for proteostasis mechanisms that promote strict quality control to greatly constrain accessible protein sequence space. Unfortunately, most efforts to understand how proteostasis mechanisms influence evolution rely on artificial inhibition or genetic knockdown of specific chaperones. The few experiments that perturb quality control pathways also generally modulate the levels of only individual quality control factors. Here, we use chemical genetic strategies to tune proteostasis networks via natural stress response pathways that regulate the levels of entire suites of chaperones and quality control mechanisms. Specifically, we upregulate the unfolded protein response (UPR) to test the hypothesis that the host endoplasmic reticulum (ER) proteostasis network shapes the sequence space accessible to human immunodeficiency virus-1 (HIV-1) envelope (Env) protein. Elucidating factors that enhance or constrain Env sequence space is critical because Env evolves extremely rapidly, yielding HIV strains with antibody- and drug-escape mutations. We find that UPR-mediated upregulation of ER proteostasis factors, particularly those controlled by the IRE1-XBP1s UPR arm, globally reduces Env mutational tolerance. Conserved, functionally important Env regions exhibit the largest decreases in mutational tolerance upon XBP1s induction. Our data indicate that this phenomenon likely reflects strict quality control endowed by XBP1s-mediated remodeling of the ER proteostasis environment. Intriguingly, and in contrast, specific regions of Env, including regions targeted by broadly neutralizing antibodies, display enhanced mutational tolerance when XBP1s is induced, hinting at a role for host proteostasis network hijacking in potentiating antibody escape. These observations reveal a key function for proteostasis networks in decreasing instead of expanding the sequence space accessible to client proteins, while also demonstrating that the host ER proteostasis network profoundly shapes the mutational tolerance of Env in ways that could have important consequences for HIV adaptation.more » « less
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