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Machine Learning
In protein biophysics, the separation between the functionally important residues (forming the active site or binding surface) and those that create the overall structure (the fold) is a well-established and fundamental concept. Identifying and modifying those functional sites is critical for protein
Recent few-shot video classification (FSVC) works achieve promising performance by capturing similarity across support and query samples with different temporal alignment strategies or learning discriminative features via Transformer block within each episode. However, they ignore two important issues:
Conditional image-to-video (cI2V) generation aims to synthesize a new plausible video starting from an image (e.g., a person’s face) and a condition (e.g., an action class label like smile). The key challenge of the cI2V task lies in the simultaneous generation of realistic spatial appearance and temporal
Source-free domain adaptation (SFDA) is an emerging research topic that studies how to adapt a pretrained source model using unlabeled target data. It is derived from unsupervised domain adaptation but has the advantage of not requiring labeled source data to learn adaptive models. This makes it particularly
Diffusion probabilistic models have achieved enormous success in the field of image generation and manipulation. In this paper, we explore a novel paradigm of using the diffusion model and classifier guidance in the latent semantic space for compositional visual tasks. Specifically, we train latent diffusion
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
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
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
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
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
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
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
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
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
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
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
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
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
This paper considers the problem of spatiotemporal object-centric reasoning in videos. Central to our approach is the notion of object permanence, i.e., the ability to reason about the location of objects as they move through the video while being occluded, contained or carried by other objects. Existing
Learning disentangled representations leads to interpretable models and facilitates data generation with style transfer, which has been extensively studied on static data such as images in an unsupervised learning framework. However, only a few works have explored unsupervised disentangled sequential
T-cell receptors can recognize foreign peptides bound to major histocompatibility complex (MHC) class-I proteins, and thus trigger the adaptive immune response. Therefore, identifying peptides that can bind to MHC class-I molecules plays a vital role in the design of peptide vaccines. Many computational
Deep neural networks have been widely applied for missing data imputation. However, most existing studies have been focused on imputing continuous data, while discrete data imputation is under-explored. Discrete data is common in real world, especially in research areas of bioinformatics, genetics, and
Learning disentangled representations of natural language is essential for many NLP tasks, e.g., conditional text generation, style transfer, personalized dialogue systems, etc. Similar problems have been studied extensively for other forms of data, such as images and videos. However, the discrete nature
We propose a sequential variational autoencoder to learn disentangled representations of sequential data (e.g., videos and audios) under self-supervision. Specifically, we exploit the benefits of some readily accessible supervision signals from input data itself or some off-the-shelf functional models
Recent developments in discovering dynamic treatment regimes (DTRs) have heightened the importance of deep reinforcement learning (DRL) which are used to recover the doctor’s treatment policies. However, existing DRL-based methods expose the following limitations: 1) supervised methods based on behavior
The rich and accessible labeled data fueled the revolutionary successes of deep learning in object recognition. However, recognizing objects of novel classes with limited supervision information provided, i.e., Novel Object Recognition (NOR), remains a challenging task. We identify in this paper two
Zero-shot learning (ZSL) aims to recognize instances of unseen classes solely based on the semantic descriptions of the classes. Existing algorithms usually formulate it as a semantic-visual correspondence problem, by learning mappings from one feature space to the other. Despite being reasonable, previous
Developing conditional generative models for text-to-video synthesis is an extremely challenging yet an important topic of research in machine learning. In this work, we address this problem by introducing Text-Filter conditioning Generative Adversarial Network (TFGAN), a conditional GAN model with a
Traditional embedding approaches associate a real-valued embedding vector with each symbol or data point, which is equivalent to applying a linear transformation to “one-hot” encoding of discrete symbols or data objects. Despite simplicity, these methods generate storage-inefficient representations
In spite of its importance, passenger demand prediction is a highly challenging problem, because the demand is simultaneously influenced by the complex interactions among many spatial and temporal factors and other external factors such as weather. To address this problem, we propose a Spatio-TEmporal
Recent studies have demonstrated the vulnerability of deep convolutional neural networks against adversarial examples. Inspired by the observation that the intrinsic dimension of image data is much smaller than its pixel space dimension and the vulnerability of neural networks grows with the input dimension,
Convolutional neural networks (CNNs) have recently emerged as a popular building block for natural language processing (NLP). Despite their success, most existing CNN models employed in NLP share the same learned (and static) set of filters for all input sentences. In this paper, we consider an approach
Parametric embedding methods such as parametric t-distributed Stochastic Neighbor Embedding (pt-SNE) enables out-of-sample data visualization without further computationally expensive optimization or approximation. However, pt-SNE favors small mini-batches to train a deep neural network but large mini-batches
Many deep learning architectures have been proposed to model the compositionality in text sequences, requiring substantial number of parameters and expensive computations. However, there has not been a rigorous evaluation regarding the added value of sophisticated compositional functions. In this paper,
Conventional embedding methods directly associate each symbol with a continuous embedding vector, which is equivalent to applying a linear transformation based on a one-hot encoding of the discrete symbols. Despite its simplicity, such approach yields the number of parameters that grows linearly
Unsupervised anomaly detection on multi- or high-dimensional data is of great importance in both fundamental machine learning research and industrial applications, for which density estimation lies at the core. Although previous approaches based on dimensionality reduction followed by density estimation
Previous models for video captioning often use the output from a specific layer of a Convolutional Neural Network (CNN) as video features. However, the variable context-dependent semantics in the video may make it more appropriate to adaptively select features from the multiple CNN layers. We propose
Generating videos from text has proven to be a significant challenge for existing generative models. We tackle this problem by training a conditional generative model to extract both static and dynamic information from text. This is manifested in a hybrid framework, employing a Variational Autoencoder
