Towards Realizing the Value of Labeled Target Samples: a Two-Stage Approach for Semi-Supervised Domain Adaptation Semi-Supervised Domain Adaptation (SSDA) is a recently emerging research topic that extends from the widely-investigated Unsupervised Domain Adaptation (UDA) by further having a few target samples labeled, i.e., the model is trained with labeled source samples, unlabeled target samples as well as a few labeled target samples. Compared with UDA, the key to SSDA lies how to most effectively utilize the few labeled target samples. Existing SSDA approaches simply merge the few precious labeled target samples into vast labeled source samples or further align them, which dilutes the value of labeled target samples and thus still obtains a biased model. To remedy this, in this paper, we propose to decouple SSDA as an UDA problem and a semi-supervised learning problem where we first learn an UDA model using labeled source and unlabeled target samples and then adapt the learned UDA model in a semi-supervised way using labeled and unlabeled target samples. By utilizing the labeled source samples and target samples separately, the bias problem can be well mitigated. We further propose a consistency learning based mean teacher model to effectively adapt the learned UDA model using labeled and unlabeled target samples. Experiments show our approach outperforms existing methods.
T-Cell Receptor Optimization with Reinforcement Learning and Mutation Polices for Precision Immunotherapy T cells monitor the health status of cells by identifying foreign peptides displayed on their surface. T-cell receptors (TCRs), which are protein complexes found on the surface of T cells, are able to bind to these peptides. This process is known as TCR recognition and constitutes a key step for immune response. Optimizing TCR sequences for TCR recognition represents a fundamental step towards the development of personalized treatments to trigger immune responses killing cancerous or virus-infected cells. In this paper, we formulated the search for these optimized TCRs as a reinforcement learning (RL) problem and presented a framework TCRPPO with a mutation policy using proximal policy optimization. TCRPPO mutates TCRs into effective ones that can recognize given peptides. TCRPPO leverages a reward function that combines the likelihoods of mutated sequences being valid TCRs measured by a new scoring function based on deep autoencoders, with the probabilities of mutated sequences recognizing peptides from a peptide-TCR interaction predictor. We compared TCRPPO with multiple baseline methods and demonstrated that TCRPPO significantly outperforms all the baseline methods to generate positive binding and valid TCRs. These results demonstrate the potential of TCRPPO for both precision immunotherapy and peptide-recognizing TCR motif discovery.
Adversarial Alignment for Source Free Object Detection Source-free object detection (SFOD) aims to transfer a detector pre-trained on a label-rich source domain to an unlabeled target domain without seeing source data. While most existing SFOD methods generate pseudo labels via a source-pretrained model to guide training, these pseudo labels usually contain high noises due to heavy domain discrepancy. In order to obtain better pseudo supervisions, we divide the target domain into source-similar and source-dissimilar parts and align them in the feature space by adversarial learning. Specifically, we design a detection variance-based criterion to divide the target domain. This criterion is motivated by a finding that larger detection variances denote higher recall and larger similarity to the source domain. Then we incorporate an adversarial module into a mean teacher framework to drive the feature spaces of these two subsets indistinguishable. Extensive experiments on multiple cross-domain object detection datasets demonstrate that our proposed method consistently outperforms the compared SFOD methods. Our implementation is available at https://github.com/ChuQiaosong
Binding Peptide Generation for MHC Class I Proteins with Deep Reinforcement Learning Motivation: MHC Class I protein plays an important role in immunotherapy by presenting immunogenic peptides to anti-tumor immune cells. The repertoires of peptides for various MHC Class I proteins are distinct, which can be reflected by their diverse binding motifs. To characterize binding motifs for MHC Class I proteins, in vitro experiments have been conducted to screen peptides with high binding affinities to hundreds of given MHC Class I proteins. However, considering tens of thousands of known MHC Class I proteins, conducting in vitro experiments for extensive MHC proteins is infeasible, and thus a more efficient and scalable way to characterize binding motifs is needed.Results: We presented a de novo generation framework, coined PepPPO, to characterize binding motif for any given MHC Class I proteins via generating repertoires of peptides presented by them. PepPPO leverages a reinforcement learning agent with a mutation policy to mutate random input peptides into positive presented ones. Using PepPPO, we characterized binding motifs for around 10 000 known human MHC Class I proteins with and without experimental for the rapid screening of neoantigens at a much lower time cost than previous deep-learning methods.
Real-time ConcealedWeapon Detection on 3D Radar Images forWalk-through Screening System This paper presents a framework for real-time concealed weapon detection (CWD) on 3D radar images for walk-through screening systems. The walk-through screening system aims to ensure security in crowded areas by performing CWD on walking persons, hence it requires an accurate and real-time detection approach. To ensure accuracy, a weapon needs to be detected irrespective of its 3D orientation, thus we use the 3D radar images as detection input. For achieving real-time, we reformulate classic U-Net based segmentation networks to perform 3D detection tasks. Our 3D segmentation network predicts peak-shaped probability map, instead of voxel-wise masks, to enable position inference by elementary peak detection operation on the predicted map. In the peak-shaped probability map, the peak marks the weapon’s position. So, weapon detection task translates to peak detection on the probability map. A Gaussian function is used to model weapons in the probability map. We experimentally validate our approach on realistic 3D radar images obtained from a walk-through weapon screening system prototype. Extensive ablation studies verify the effectiveness of our proposed approach over existing conventional approaches. The experimental results demonstrate that our proposed approach can perform accurate and real-time CWD, thus making it suitable for practical applications of walk-through screening.
On TCR Binding Predictors Failing to Generalize to Unseen Peptides 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.
Attentive Variational Information Bottleneck for TCR–peptide interaction prediction MotivationWe 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.
KGxBoard: Explainable and Interactive Leaderboard for Evaluation of Knowledge Graph Completion Models 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.
COMPOSER: Compositional Reasoning of Group Activity in Videos with Keypoint-Only Modality 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.).
Unsupervised Anomaly Detection with Self-Training and Knowledge Distillation 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.