2022-10-01 更新
PiFold: Toward effective and efficient protein inverse folding
Authors:Zhangyang Gao, Cheng Tan, Stan Z. Li
How can we design protein sequences folding into the desired structures effectively and efficiently? Structure-based protein design has attracted increasing attention in recent years; however, few methods can simultaneously improve the accuracy and efficiency due to the lack of expressive features and autoregressive sequence decoder. To address these issues, we propose PiFold, which contains a novel residue featurizer and PiGNN layers to generate protein sequences in a one-shot way with improved recovery. Experiments show that PiFold could achieve 51.66\% recovery on CATH 4.2, while the inference speed is 70 times faster than the autoregressive competitors. In addition, PiFold achieves 58.72\% and 60.42\% recovery scores on TS50 and TS500, respectively. We conduct comprehensive ablation studies to reveal the role of different types of protein features and model designs, inspiring further simplification and improvement.
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Active Transfer Prototypical Network: An Efficient Labeling Algorithm for Time-Series Data
Authors:Yuqicheng Zhu, Mohamed-Ali Tnani, Timo Jahnz, Klaus Diepold
The paucity of labeled data is a typical challenge in the automotive industry. Annotating time-series measurements requires solid domain knowledge and in-depth exploratory data analysis, which implies a high labeling effort. Conventional Active Learning (AL) addresses this issue by actively querying the most informative instances based on the estimated classification probability and retraining the model iteratively. However, the learning efficiency strongly relies on the initial model, resulting in the trade-off between the size of the initial dataset and the query number. This paper proposes a novel Few-Shot Learning (FSL)-based AL framework, which addresses the trade-off problem by incorporating a Prototypical Network (ProtoNet) in the AL iterations. The results show an improvement, on the one hand, in the robustness to the initial model and, on the other hand, in the learning efficiency of the ProtoNet through the active selection of the support set in each iteration. This framework was validated on UCI HAR/HAPT dataset and a real-world braking maneuver dataset. The learning performance significantly surpasses traditional AL algorithms on both datasets, achieving 90% classification accuracy with 10% and 5% labeling effort, respectively.
PDF 4th International Conference on Industry 4.0 and Smart Manufacturing
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Less is More: Rethinking Few-Shot Learning and Recurrent Neural Nets
Authors:Deborah Pereg, Martin Villiger, Brett Bouma, Polina Golland
The statistical supervised learning framework assumes an input-output set with a joint probability distribution that is reliably represented by the training dataset. The learner is then required to output a prediction rule learned from the training dataset’s input-output pairs. In this work, we provide meaningful insights into the asymptotic equipartition property (AEP) \citep{Shannon:1948} in the context of machine learning, and illuminate some of its potential ramifications for few-shot learning. We provide theoretical guarantees for reliable learning under the information-theoretic AEP, and for the generalization error with respect to the sample size. We then focus on a highly efficient recurrent neural net (RNN) framework and propose a reduced-entropy algorithm for few-shot learning. We also propose a mathematical intuition for the RNN as an approximation of a sparse coding solver. We verify the applicability, robustness, and computational efficiency of the proposed approach with image deblurring and optical coherence tomography (OCT) speckle suppression. Our experimental results demonstrate significant potential for improving learning models’ sample efficiency, generalization, and time complexity, that can therefore be leveraged for practical real-time applications.
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Promptagator: Few-shot Dense Retrieval From 8 Examples
Authors:Zhuyun Dai, Vincent Y. Zhao, Ji Ma, Yi Luan, Jianmo Ni, Jing Lu, Anton Bakalov, Kelvin Guu, Keith B. Hall, Ming-Wei Chang
Much recent research on information retrieval has focused on how to transfer from one task (typically with abundant supervised data) to various other tasks where supervision is limited, with the implicit assumption that it is possible to generalize from one task to all the rest. However, this overlooks the fact that there are many diverse and unique retrieval tasks, each targeting different search intents, queries, and search domains. In this paper, we suggest to work on Few-shot Dense Retrieval, a setting where each task comes with a short description and a few examples. To amplify the power of a few examples, we propose Prompt-base Query Generation for Retriever (Promptagator), which leverages large language models (LLM) as a few-shot query generator, and creates task-specific retrievers based on the generated data. Powered by LLM’s generalization ability, Promptagator makes it possible to create task-specific end-to-end retrievers solely based on a few examples {without} using Natural Questions or MS MARCO to train %question generators or dual encoders. Surprisingly, LLM prompting with no more than 8 examples allows dual encoders to outperform heavily engineered models trained on MS MARCO like ColBERT v2 by more than 1.2 nDCG on average on 11 retrieval sets. Further training standard-size re-rankers using the same generated data yields another 5.0 point nDCG improvement. Our studies determine that query generation can be far more effective than previously observed, especially when a small amount of task-specific knowledge is given.
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Few-Shot Object Detection with Fully Cross-Transformer
Authors:Guangxing Han, Jiawei Ma, Shiyuan Huang, Long Chen, Shih-Fu Chang
Few-shot object detection (FSOD), with the aim to detect novel objects using very few training examples, has recently attracted great research interest in the community. Metric-learning based methods have been demonstrated to be effective for this task using a two-branch based siamese network, and calculate the similarity between image regions and few-shot examples for detection. However, in previous works, the interaction between the two branches is only restricted in the detection head, while leaving the remaining hundreds of layers for separate feature extraction. Inspired by the recent work on vision transformers and vision-language transformers, we propose a novel Fully Cross-Transformer based model (FCT) for FSOD by incorporating cross-transformer into both the feature backbone and detection head. The asymmetric-batched cross-attention is proposed to aggregate the key information from the two branches with different batch sizes. Our model can improve the few-shot similarity learning between the two branches by introducing the multi-level interactions. Comprehensive experiments on both PASCAL VOC and MSCOCO FSOD benchmarks demonstrate the effectiveness of our model.
PDF CVPR 2022 (Oral). Code is available at https://github.com/GuangxingHan/FCT
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Hyperseed: Unsupervised Learning with Vector Symbolic Architectures
Authors:Evgeny Osipov, Sachin Kahawala, Dilantha Haputhanthri, Thimal Kempitiya, Daswin De Silva, Damminda Alahakoon, Denis Kleyko
Motivated by recent innovations in biologically-inspired neuromorphic hardware, this article presents a novel unsupervised machine learning algorithm named Hyperseed that draws on the principles of Vector Symbolic Architectures (VSA) for fast learning of a topology preserving feature map of unlabelled data. It relies on two major operations of VSA, binding and bundling. The algorithmic part of Hyperseed is expressed within Fourier Holographic Reduced Representations model, which is specifically suited for implementation on spiking neuromorphic hardware. The two primary contributions of the Hyperseed algorithm are, few-shot learning and a learning rule based on single vector operation. These properties are empirically evaluated on synthetic datasets as well as on illustrative benchmark use-cases, IRIS classification, and a language identification task using n-gram statistics. The results of these experiments confirm the capabilities of Hyperseed and its applications in neuromorphic hardware.
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Bidirectional Language Models Are Also Few-shot Learners
Authors:Ajay Patel, Bryan Li, Mohammad Sadegh Rasooli, Noah Constant, Colin Raffel, Chris Callison-Burch
Large language models such as GPT-3 (Brown et al., 2020) can perform arbitrary tasks without undergoing fine-tuning after being prompted with only a few labeled examples. An arbitrary task can be reformulated as a natural language prompt, and a language model can be asked to generate the completion, indirectly performing the task in a paradigm known as prompt-based learning. To date, emergent prompt-based learning capabilities have mainly been demonstrated for unidirectional language models. However, bidirectional language models pre-trained on denoising objectives such as masked language modeling produce stronger learned representations for transfer learning. This motivates the possibility of prompting bidirectional models, but their pre-training objectives have made them largely incompatible with the existing prompting paradigm. We present SAP (Sequential Autoregressive Prompting), a technique that enables the prompting of bidirectional models. Utilizing the machine translation task as a case study, we prompt the bidirectional mT5 model (Xue et al., 2021) with SAP and demonstrate its few-shot and zero-shot translations outperform the few-shot translations of unidirectional models like GPT-3 and XGLM (Lin et al., 2021), despite mT5’s approximately 50% fewer parameters. We further show SAP is effective on question answering and summarization. For the first time, our results demonstrate prompt-based learning is an emergent property of a broader class of language models, rather than only unidirectional models.
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Meta-Learning a Cross-lingual Manifold for Semantic Parsing
Authors:Tom Sherborne, Mirella Lapata
Localizing a semantic parser to support new languages requires effective cross-lingual generalization. Recent work has found success with machine-translation or zero-shot methods although these approaches can struggle to model how native speakers ask questions. We consider how to effectively leverage minimal annotated examples in new languages for few-shot cross-lingual semantic parsing. We introduce a first-order meta-learning algorithm to train a semantic parser with maximal sample efficiency during cross-lingual transfer. Our algorithm uses high-resource languages to train the parser and simultaneously optimizes for cross-lingual generalization for lower-resource languages. Results across six languages on ATIS demonstrate that our combination of generalization steps yields accurate semantic parsers sampling $\le$10% of source training data in each new language. Our approach also trains a competitive model on Spider using English with generalization to Chinese similarly sampling $\le$10% of training data.
PDF Accepted to TACL 2022. Pre-MIT Press publication
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