Machine LearningRead the latest publications from our world-class team of researchers from our Machine Learning team who have been at the forefront of machine learning developments, including deep learning, support vector machines, and semantic analysis, for over a decade. We develop innovative technologies integrated into NEC’s products and services. Machine learning is the critical technology for data analytics and artificial intelligence. Recent progress in this field opens opportunities for various new applications.

Posts

On TCR Binding Predictors Failing to Generalize to Unseen Peptides

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Several recent studies investigate TCR-peptide/-pMHC binding prediction using machine learning or deep learning approaches. Many of these methods achieve impressive results on test sets, which include peptide sequences that are also included in the training set. In this work, we investigate how state of the-art deep learning models for TCR-peptide/-pMHC binding prediction generalize to unseen peptides. We create a dataset including positive samples from IEDB, VDJdb, McPAS-TCR, and the MIRA set, as well as negative samples from both randomization and 10X Genomics assays. We name this collection of samples TChard. We propose the hard split, a simple heuristic for training/test split, which ensures that test samples exclusively present peptides that do not belong to the training set. We investigate the effect of different training/test splitting techniques on the models’ test performance, as well as the effect of training and testing the models using mismatched negative samples generated randomly, in addition to the negative samples derived from assays. Our results show that modern deep learning methods fail to generalize to unseen peptides. We provide an explanation why this happens and verify our hypothesis on the TChard dataset. We then conclude that robust prediction of TCR recognition is still far for being solved.

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Attentive Variational Information Bottleneck for TCR–peptide interaction prediction

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We present a multi-sequence generalization of Variational Information Bottleneck and call the resulting model Attentive Variational Information Bottleneck (AVIB). Our AVIB model leverages multi-head self-attention to implicitly approximate a posterior distribution over latent encodings conditioned on multiple input sequences. We apply AVIB to a fundamental immuno-oncology problem: predicting the interactions between T-cell receptors (TCRs) and peptides.ResultsExperimental results on various datasets show that AVIB significantly outperforms state-of-the-art methods for TCR–peptide interaction prediction. Additionally, we show that the latent posterior distribution learned by AVIB is particularly effective for the unsupervised detection of out-of-distribution amino acid sequences.

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KGxBoard: Explainable and Interactive Leaderboard for Evaluation of Knowledge Graph Completion Models

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Knowledge Graphs (KGs) store information in the form of (head, predicate, tail)-triples. To augment KGs with new knowledge, researchers proposed models for KG Completion (KGC) tasks such as link prediction, i.e., answering (h, p, ?) or (?, p, t) queries. Such models are usually evaluated with averaged metrics on a held-out test set. While useful for tracking progress, averaged single-score metrics cannotreveal what exactly a model has learned — or failed to learn. To address this issue, we propose KGxBoard: an interactive framework for performing fine-grained evaluation on meaningful subsets of the data, each of which tests individual and interpretable capabilities of a KGC model. In our experiments, we highlight the findings that we discovered with the use of KGxBoard, which would have been impossible to detect with standard averaged single-score metrics.

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COMPOSER: Compositional Reasoning of Group Activity in Videos with Keypoint-Only Modality

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Group Activity Recognition detects the activity collectively performed by a group of actors, which requires compositional reasoning of actors and objects. We approach the task by modeling the video as tokens that represent the multi-scale semantic concepts in the video. We propose COMPOSER, a Multiscale Transformer based architecture that performs attention-based reasoning over tokens at each scale and learns group activity compositionally. In addition, prior works suffer from scene biases with privacy and ethical concerns. We only use the keypoint modality which reduces scene biases and prevents acquiring detailed visual data that may contain private or biased information of users. We improve the multiscale representations in COMPOSER by clustering the intermediate scale representations, while maintaining consistent cluster assignments between scales. Finally, we use techniques such as auxiliary prediction and data augmentations tailored to the keypoint signals to aid model training. We demonstrate the model’s strength and interpretability on two widely-used datasets (Volleyball and Collective Activity). COMPOSER achieves up to +5.4% improvement with just the keypoint modality (Code is available at https://github.com/hongluzhou/composer.).

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Unsupervised Anomaly Detection with Self-Training and Knowledge Distillation

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Anomaly Detection (AD) aims to find defective patterns or abnormal samples among data, and has been a hot research topic due to various real-world applications. While various AD methods have been proposed, most of them assume the availability of a clean (anomaly-free) training set, which, however, may be hard to guarantee in many real-world industry applications. This motivates us to investigate Unsupervised Anomaly Detection (UAD) in which the training set includes both normal and abnormal samples. In this paper, we address the UAD problem by proposing a Self-Training and Knowledge Distillation (STKD) model. STKD combats anomalies in the training set by iteratively alternating between excluding samples of high anomaly probabilities and training the model with the purified training set. Despite that the model is trained with a cleaner training set, the inevitably existing anomalies may still cause negative impact. STKD alleviates this by regularizing the model to respond similarly to a teacher model which has not been trained with noisy data. Experiments show that STKD consistently produces more robust performance with different levels of anomalies.

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Analyzing Coreference and Bridging in Product Reviews

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Product reviews may have complex discourse including coreference and bridging relations to a main product, competing products, and interacting products. Current approaches to aspect-based sentiment analysis (ABSA) and opinion summarization largely ignore this complexity. On the other hand, existing systems for coreference and bridging were trained in a different domain. We collect mention type annotations relevant to coreference and bridging for 498 product reviews. Using these annotations, we show that a state-of-the-art factuality score fails to catch coreference errors in product reviews, and that a state-of-the-art coreference system trained on OntoNotes does not perform nearly as well on product mentions. As our dataset grows, we expect it to help ABSA and opinion summarization systems to avoid entity reference errors.

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T-Cell Receptor-Peptide Interaction Prediction with Physical Model Augmented Pseudo-Labeling

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Predicting the interactions between T-cell receptors (TCRs) and peptides is crucial for the development of personalized medicine and targeted vaccine in immunotherapy. Current datasets for training deep learning models of this purpose remain constrained without diverse TCRs and peptides. To combat the data scarcity issue presented in the current datasets, we propose to extend the training dataset by physical modeling of TCR-peptide pairs. Specifically, we compute the docking energies between auxiliary unknown TCR-peptide pairs as surrogate training labels. Then, we use these extended example-label pairs to train our model in a supervised fashion. Finally, we find that the AUC score for the prediction of the model can be further improved by pseudo-labeling of such unknown TCR-peptide pairs (by a trained teacher model), and re-training the model with those pseudo-labeled TCR-peptide pairs. Our proposed method that trains the deep neural network with physical modeling and data-augmented pseudo-labeling improves over baselines in the available two datasets. We also introduce a new dataset that contains over 80,000 unknown TCR-peptide pairs with docking energy scores.

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StyleT2I: Towards Compositional and High-Fidelity Text-to-Image Synthesis

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Although progress has been made for text-to-image synthesis, previous methods fall short of generalizing to unseen or underrepresented attribute compositions in the input text. Lacking compositionality could have severe implications for robustness and fairness, e.g., inability to synthesize the face images of underrepresented demographic groups. In this paper, we introduce a new framework, StyleT2I, to improve the compositionality of text-to-image synthesis. Specifically, we propose a CLIP-guided Contrastive Loss to better distinguish different compositions among different sentences. To further improve the compositionality, we design a novel Semantic Matching Loss and a Spatial Constraint to identify attributes’ latent directions for intended spatial region manipulations, leading to better disentangled latent representations of attributes. Based on the identified latent directions of attributes, we propose Compositional Attribute Adjustment to adjust the latent code, resulting in better compositionality of image synthesis. In addition, we leverage the l2 -norm regularization of identified latent directions (norm penalty) to strike a nice balance between image-text alignment and image fidelity. In the experiments, we devise a new dataset split and an evaluation metric to evaluate the compositionality of text-to-image synthesis models. The results show that StyleT2I outperforms previous approaches in terms of the consistency between the input text and synthesized images and achieves higher fidelity

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Self-supervised Video Representation Learning with Cascade Positive Retrieval

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Self-supervised video representation learning has been shown to effectively improve downstream tasks such as video retrieval and action recognition. In this paper, we present the Cascade Positive Retrieval (CPR) that successively mines positive examples w.r.t. the query for contrastive learning in a cascade of stages. Specifically, CPR exploits multiple views of a query example in different modalities, where an alternative view may help find another positive example dissimilar in the query view. We explore the effects of possible CPR configurations in ablations including the number of mining stages, the top similar example selection ratio in each stage, and progressive training with an incremental number of the final Top-k selection. The overall mining quality is measured to reflect the recall across training set classes. CPR reaches a median class mining recall of 83.3%, outperforming previous work by 5.5%. Implementation-wise, CPR is complementary to pretext tasks and can be easily applied to previous work. In the evaluation of pretraining on UCF101, CPR consistently improves existing work and even achieves state-of-the-art R@1 of 56.7% and 24.4% in video retrieval as well as 83.8% and 54.8% in action recognition on UCF101 and HMDB51. The code is available at https://github.com/necla-ml/CPR.

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Fast Few-shot Debugging for NLU Test Suites

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We study few-shot debugging of transformer based natural language understanding models, using recently popularized test suites to not just diagnose but correct a problem. Given a few debugging examples of a certain phenomenon, and a held-out test set of the same phenomenon, we aim to maximize accuracy on the phenomenon at a minimal cost of accuracy on the original test set. We examine several methods that are faster than full epoch retraining. We introduce a new fast method, which samples a few in-danger examples from the original training set. Compared to fast methods using parameter distance constraints or Kullback-Leibler divergence, we achieve superior original accuracy for comparable debugging accuracy.

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