Active Learning Framework for Cost-Effective TCR-Epitope Binding Affinity Prediction

T cell receptors (TCRs) are critical components of adaptive immune systems, responsible for responding to threats by recognizing epitope sequences presented on host cell surface. Computational prediction of binding affinity between TCRs and epitope sequences using machine/deep learning has attracted intense attention recently. However, its success is hindered by the lack of large collections of annotated TCR-epitope pairs. Annotating their binding affinity requires expensive and time-consuming wet-lab evaluation. To reduce annotation cost, we present ActiveTCR, a framework that incorporates active learning and TCR-epitope binding affinity prediction models. Starting with a small set of labeled training pairs, ActiveTCR iteratively searches for unlabeled TCR-epitope pairs that are ''worth'' for annotation. It aims to maximize performance gains while minimizing the cost of annotation. We compared four query strategies with a random sampling baseline and demonstrated that ActiveTCR reduces annotation costs by approximately 40%. Furthermore, we showed that providing ground truth labels of TCR-epitope pairs to query strategies can help identify and reduce more than 40% redundancy among already annotated pairs without compromising model performance, enabling users to train equally powerful prediction models with less training data. Our work is the first systematic investigation of data optimization for TCR-epitope binding affinity prediction.

Zero-Shot Learning by Harnessing Adversarial Samples

Zero-Shot Learning (ZSL) aims to recognize unseen classes by generalizing the knowledge, i.e., visual and semantic relationships, obtained from seen classes, where image augmentation techniques are commonly applied to improve the generalization ability of a model. However, this approach can also cause adverse effects on ZSL since the conventional augmentation techniques that solely depend on single-label supervision is not able to maintain semantic information and result in the semantic distortion issue consequently. In other words, image argumentation may falsify the semantic (e.g., attribute) information of an image. To take the advantage of image augmentations while mitigating the semantic distortion issue, we propose a novel ZSL approach by Harnessing Adversarial Samples (HAS). HAS advances ZSL through adversarial training which takes into account three crucial aspects: (1) robust generation by enforcing augmentations to be similar to negative classes, while maintaining correct labels, (2) reliable generation by introducing a latent space constraint to avert significant deviations from the original data manifold, and (3) diverse generation by incorporating attribute-based perturbation by adjusting images according to each semantic attribute's localization. Through comprehensive experiments on three prominent zero-shot benchmark datasets, we demonstrate the effectiveness of our adversarial samples approach in both ZSL and Generalized Zero-Shot Learning (GZSL) scenarios. Our source code is available at https://github.com/uqzhichen/HASZSL.

Reduce Computational Complexity for Convolutional Layers by Skipping Zeros

Deep neural networks rely on parallel processors for acceleration. To design operators for them, it requires not only good algorithm to reduce complexity, but also sufficient utilization of hardwares. Convolutional layers mainly contain 3 kinds of operators: convolution in forward propagation, deconvolution and dilated-convolution in backward propagation. When executing these operators, 0s are always added to tensors, causing redundant calculations. This paper gives C-K-S algorithm (ConvV2, KS-deconv, Sk-dilated), which skips these 0s in two ways: trim the filters to exclude padded 0s; transform sparse tensors to dense tensors, to avoid inserted 0s in deconvolution and dilated-convolution. In contrast to regular convolution, deconvolution is hard to accelerate due to its complicacy. This paper provides high-performance GPU implementations of C-K-S, and verifies their effectiveness with comparison to PyTorch. According to the experiments, C-K-S has advantages over PyTorch in certain cases, especially in deconvolution on small feature-maps. Further enhancement of C-K-S can be done by making full optimizations oriented at specific GPU architectures.

Dragon-Alpha&cu32: A Java-based Tensor Computing Framework With its High-Performance CUDA Library

Java is very powerful, but in Deep Learning field, its capabilities probably has not been sufficiently exploited. Compared to the Java-based deep-learning-frameworks, the Python-based (PyTorch, TensorFlow, etc) are undoubtedly the mainstream, due to their easy-to-use, flexibility and better ecosystem. Dragon-Alpha is a Java-based Tensor Computing Framework, with easy-to-use, high-scalability and high-performance, trying to break Java's dilemma in deep learning field and make it more effective. Dragon-Alpha supports different levels of APIs, and can be used as a deep-learning-framework through its user-friendly high-level APIs. Dragon-Alpha has potential to aggregate computing-power across heterogeneous platforms and devices, based on its multi-layer architecture and Java's big-data ecosystem. Dragon-Alpha has its asynchronized APIs to improve parallelism, and highly-optimized CUDA library cu32 which adopts unique convolution\deconvolution operators for small feature maps. The experiments show that, compared to PyTorch&cuDNN, Dragon-Alpha&cu32 costs less time and memory (75.38% to 97.32%, 29.2% to 66.4%), to train some typical neural networks (AlexNet, VGG, GoogleNet, ResNet) on Cifar-10.

Background Invariance Testing According to Semantic Proximity

In many applications, machine learned (ML) models are required to hold some invariance qualities, such as rotation, size, intensity, and background invariance. Unlike many types of variance, the variants of background scenes cannot be ordered easily, which makes it difficult to analyze the robustness and biases of the models concerned. In this work, we present a technical solution for ordering background scenes according to their semantic proximity to a target image that contains a foreground object being tested. We make use of the results of object recognition as the semantic description of each image, and construct an ontology for storing knowledge about relationships among different objects using association analysis. This ontology enables (i) efficient and meaningful search for background scenes of different semantic distances to a target image, (ii) quantitative control of the distribution and sparsity of the sampled background scenes, and (iii) quality assurance using visual representations of invariance testing results (referred to as variance matrices). In this paper, we also report the training of an ML4ML assessor to evaluate the invariance quality of ML models automatically.

MME-CRS: Multi-Metric Evaluation Based on Correlation Re-Scaling for Evaluating Open-Domain Dialogue

Automatic open-domain dialogue evaluation is a crucial component of dialogue systems. Recently, learning-based evaluation metrics have achieved state-of-the-art performance in open-domain dialogue evaluation. However, these metrics, which only focus on a few qualities, are hard to evaluate dialogue comprehensively. Furthermore, these metrics lack an effective score composition approach for diverse evaluation qualities. To address the above problems, we propose a Multi-Metric Evaluation based on Correlation Re-Scaling (MME-CRS) for evaluating open-domain dialogue. Firstly, we build an evaluation metric composed of 5 groups of parallel sub-metrics called Multi-Metric Evaluation (MME) to evaluate the quality of dialogue comprehensively. Furthermore, we propose a novel score composition method called Correlation Re-Scaling (CRS) to model the relationship between sub-metrics and diverse qualities. Our approach MME-CRS ranks first on the final test data of DSTC10 track5 subtask1 Automatic Open-domain Dialogue Evaluation Challenge with a large margin, which proved the effectiveness of our proposed approach.

Adaptive Prompt Learning-based Few-Shot Sentiment Analysis

In the field of natural language processing, sentiment analysis via deep learning has a excellent performance by using large labeled datasets. Meanwhile, labeled data are insufficient in many sentiment analysis, and obtaining these data is time-consuming and laborious. Prompt learning devotes to resolving the data deficiency by reformulating downstream tasks with the help of prompt. In this way, the appropriate prompt is very important for the performance of the model. This paper proposes an adaptive prompting(AP) construction strategy using seq2seq-attention structure to acquire the semantic information of the input sequence. Then dynamically construct adaptive prompt which can not only improve the quality of the prompt, but also can effectively generalize to other fields by pre-trained prompt which is constructed by existing public labeled data. The experimental results on FewCLUE datasets demonstrate that the proposed method AP can effectively construct appropriate adaptive prompt regardless of the quality of hand-crafted prompt and outperform the state-of-the-art baselines.

Experimental quantum adversarial learning with programmable superconducting qubits

Quantum computing promises to enhance machine learning and artificial intelligence. Different quantum algorithms have been proposed to improve a wide spectrum of machine learning tasks. Yet, recent theoretical works show that, similar to traditional classifiers based on deep classical neural networks, quantum classifiers would suffer from the vulnerability problem: adding tiny carefully-crafted perturbations to the legitimate original data samples would facilitate incorrect predictions at a notably high confidence level. This will pose serious problems for future quantum machine learning applications in safety and security-critical scenarios. Here, we report the first experimental demonstration of quantum adversarial learning with programmable superconducting qubits. We train quantum classifiers, which are built upon variational quantum circuits consisting of ten transmon qubits featuring average lifetimes of 150 $\mu$s, and average fidelities of simultaneous single- and two-qubit gates above 99.94% and 99.4% respectively, with both real-life images (e.g., medical magnetic resonance imaging scans) and quantum data. We demonstrate that these well-trained classifiers (with testing accuracy up to 99%) can be practically deceived by small adversarial perturbations, whereas an adversarial training process would significantly enhance their robustness to such perturbations. Our results reveal experimentally a crucial vulnerability aspect of quantum learning systems under adversarial scenarios and demonstrate an effective defense strategy against adversarial attacks, which provide a valuable guide for quantum artificial intelligence applications with both near-term and future quantum devices.