martin renqiang min Archives | Page 3 of 5

Attentive Variational Information Bottleneck for TCR–peptide interaction prediction

December 26, 2022/in Publications/by NEC Labs America

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.

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

August 14, 2022/in Publications/by NEC Labs America

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.

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

June 21, 2022/in Publications/by NEC Labs America

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

Learning Transferable Reward for Query Object Localization with Policy Adaptation

April 25, 2022/in Publications/by NEC Labs America

We propose a reinforcement learning-based approach to query object localization, for which an agent is trained to localize objects of interest specified by a small exemplary set. We learn a transferable reward signal formulated using the exemplary set by ordinal metric learning. Our proposed method enables test-time policy adaptation to new environments where the reward signals are not readily available and outperforms fine-tuning approaches that are limited to annotated images. In addition, the transferable reward allows repurposing the trained agent from one specific class to another class. Experiments on corrupted MNIST, CU-Birds, and COCO datasets demonstrate the effectiveness of our approach.

AE-StyleGAN: Improved Training of Style-Based Auto-Encoders

January 4, 2022/in Publications/by NEC Labs America

StyleGANs have shown impressive results on data generation and manipulation in recent years, thanks to its disentangled style latent space. A lot of efforts have been made in inverting a pretrained generator, where an encoder is trained ad hoc after the generator is trained in a two-stage fashion. In this paper, we focus on style-based generators asking a scientific question: Does forcing such a generator to reconstruct real data lead to more disentangled latent space and make the inversion process from image to latent space easy? We describe a new methodology to train a style-based autoencoder where the encoder and generator are optimized end-to-end. We show that our proposed model consistently outperforms baselines in terms of image inversion and generation quality. Supplementary, code, and pretrained models are available on the project website.

A Deep Generative Model for Molecule Optimization via One Fragment Modification

January 1, 2022/in Publications/by NEC Labs America

Molecule optimization is a critical step in drug development to improve the desired properties of drug candidates through chemical modification. We have developed a novel deep generative model, Modof, over molecular graphs for molecule optimization. Modof modifies a given molecule through the prediction of a single site of disconnection at the molecule and the removal and/or addition of fragments at that site. A pipeline of multiple, identical Modof models is implemented into Modof-pipe to modify an input molecule at multiple disconnection sites. Here we show that Modof-pipe is able to retain major molecular scaffolds, allow controls over intermediate optimization steps and better constrain molecule similarities. Modof-pipe outperforms the state-of-the-art methods on benchmark datasets. Without molecular similarity constraints, Modof-pipe achieves 81.2% improvement in the octanol–water partition coefficient, penalized by synthetic accessibility and ring size, and 51.2%, 25.6% and 9.2% improvement if the optimized molecules are at least 0.2, 0.4 and 0.6 similar to those before optimization, respectively. Modof-pipe is further enhanced into Modof-pipem to allow modification of one molecule to multiple optimized ones. Modof-pipem achieves additional performance improvement, at least 17.8% better than Modof-pipe.

Retrieval, Analogy, and Composition: A framework for Compositional Generalization in Image Captioning

November 7, 2021/in Publications/by NEC Labs America

Image captioning systems are expected to have the ability to combine individual concepts when describing scenes with concept combinations that are not observed during training. In spite of significant progress in image captioning with the help of the autoregressive generation framework, current approaches fail to generalize well to novel concept combinations. We propose a new framework that revolves around probing several similar image caption training instances (retrieval), performing analogical reasoning over relevant entities in retrieved prototypes (analogy), and enhancing the generation process with reasoning outcomes (composition). Our method augments the generation model by referring to the neighboring instances in the training set to produce novel concept combinations in generated captions. We perform experiments on the widely used image captioning benchmarks. The proposed models achieve substantial improvement over the compared baselines on both composition-related evaluation metrics and conventional image captioning metrics.

Dual Projection Generative Adversarial Networks for Conditional Image Generation

October 11, 2021/in Publications/by NEC Labs America

Conditional Generative Adversarial Networks (cGANs) extend the standard unconditional GAN framework to learning joint data-label distributions from samples, and have been established as powerful generative models capable of generating high-fidelity imagery. A challenge of training such a model lies in properly infusing class information into its generator and discriminator. For the discriminator, class conditioning can be achieved by either (1) directly incorporating labels as input or (2) involving labels in an auxiliary classification loss. In this paper, we show that the former directly aligns the class-conditioned fake-and-real data distributions P (image|class) (data matching), while the latter aligns data-conditioned class distributions P (class|image) (label matching). Although class separability does not directly translate to sample quality and becomes a burden if classification itself is intrinsically difficult, the discriminator cannot provide useful guidance for the generator if features of distinct classes are mapped to the same point and thus become inseparable. Motivated by this intuition, we propose a Dual Projection GAN (P2GAN) model that learns to balance between data matching and label matching. We then propose an improved cGAN model with Auxiliary Classification that directly aligns the fake and real conditionals P (class|image) by minimizing their f-divergence. Experiments on a synthetic Mixture of Gaussian (MoG) dataset and a variety of real-world datasets including CIFAR100, ImageNet, and VGGFace2 demonstrate the efficacy of our proposed models.

Towards Robustness of Deep Neural Networks via Networks via Regularization

October 11, 2021/in Publications/by NEC Labs America

Recent studies have demonstrated the vulnerability of deep neural networks against adversarial examples. In-spired by the observation that adversarial examples often lie outside the natural image data manifold and the intrinsic dimension of image data is much smaller than its pixel space dimension, we propose to embed high-dimensional input images into a low-dimensional space and apply regularization on the embedding space to push the adversarial examples back to the manifold. The proposed framework is called Embedding Regularized Classifier (ER-Classifier), which improves the adversarial robustness of the classifier through embedding regularization. Besides improving classification accuracy against adversarial examples, the framework can be combined with detection methods to detect adversarial examples. Experimental results on several benchmark datasets show that, our proposed framework achieves good performance against strong adversarial at-tack methods.

DECODE: A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays

July 25, 2021/in Publications/by NEC Labs America

MotivationMapping distal regulatory elements, such as enhancers, is a cornerstone for elucidating how genetic variations may influence diseases. Previous enhancer-prediction methods have used either unsupervised approaches or supervised methods with limited training data. Moreover, past approaches have implemented enhancer discovery as a binary classification problem without accurate boundary detection, producing low-resolution annotations with superfluous regions and reducing the statistical power for downstream analyses (e.g. causal variant mapping and functional validations). Here, we addressed these challenges via a two-step model called Deep-learning framework for Condensing enhancers and refining boundaries with large-scale functional assays (DECODE). First, we employed direct enhancer-activity readouts from novel functional characterization assays, such as STARR-seq, to train a deep neural network for accurate cell-type-specific enhancer prediction. Second, to improve the annotation resolution, we implemented a weakly supervised object detection framework for enhancer localization with precise boundary detection (to a 10 bp resolution) using Gradient-weighted Class Activation Mapping.ResultsOur DECODE binary classifier outperformed a state-of-the-art enhancer prediction method by 24% in transgenic mouse validation. Furthermore, the object detection framework can condense enhancer annotations to only 13% of their original size, and these compact annotations have significantly higher conservation scores and genome-wide association study variant enrichments than the original predictions. Overall, DECODE is an effective tool for enhancer classification and precise localization.