31 accepted papers
Recent advances in $\textit{de novo}$ protein binder design have enabled increasing experimental validation, yet reported $\textit{in silico}$ metrics remain difficult to interpret or compare across studies due to non-standardized evaluation protocols. We introduce $\textbf{ProtDBench}$, a standardi…
Protein language (or sequence) models, like the popular ESM2, are now widely used tools for extracting evolution-based protein representations and have achieved significant success on core downstream biological tasks. A major open problem is how to obtain representations that best capture both the s…
Flow-based generative models have shown promise in various machine learning applications, but they often face challenges in handling noise and ensuring robustness in trajectory estimation. In this work, we propose NRFlow, a novel extension to flow-based generative modeling that incorporates second-o
AI-based frameworks for protein engineering use self-supervised learning (SSL) to obtain representations for downstream mutation effect predictions. The most common training objective for these methods is wildtype accuracy: given a sequence or structure where a wildtype residue has been masked, pred…
Recent works have demonstrated success in controlling sentence attributes (e.g., sentiment) and structure (e.g., syntactic structure) based on the diffusion language model. A key component that drives theimpressive performance for generating high-quality samples from noise is iteratively denoise for…
Very deep neural networks lead to significantly better performance on various real tasks. However, it usually causes slow inference and is hard to be deployed on real-world devices. How to reduce the number of layers to save memory and to accelerate the inference is an eye-catching topic. In thi…
Auto-regressive generation models achieve competitive performance across many different NLP tasks such as summarization, question answering, and classifications. However, they are also known for being slow in inference, which makes them challenging to deploy in real-time applications. We propose a s…
Diffusion models have emerged as a powerful tool for point cloud generation. A key component that drives the impressive performance for generating high-quality samples from noise is iteratively denoise for thousands of steps. While beneficial, the complexity of learning steps has limited its applica…
We present rectified flow, a simple approach to learning (neural) ordinary differential equation (ODE) models to transport between two empirically observed distributions $\pi_0$ and $\pi_1$, hence providing a unified solution to generative modeling and domain transfer, among various other tasks invo…
Generative modeling with ordinary differential equations (ODEs) has achieved fantastic results on a variety of applications. Yet, few works have focused on controlling the generated content of a pre-trained ODE-based generative model. In this paper, we propose to optimize the output of ODE models ac…
The molecular basis of protein thermal stability is only partially understood and has major significance for drug and vaccine discovery. The lack of datasets and standardized benchmarks considerably limits learning-based discovery methods. We present \texttt{HotProtein}, a large-scale protein datas…
Active learning, which effectively collects informative unlabeled data for annotation, reduces the demand for labeled data. In this work, we propose to retrieve unlabeled samples with a local sensitivity and hardness-aware acquisition function. The proposed method generates data copies through local…
AI-based molecule generation provides a promising approach to a large area of biomedical sciences and engineering, such as antibody design, hydrolase engineering, or vaccine development. Because the molecules are governed by physical laws, a key challenge is to incorporate prior information into the…
Learning embedding layers (for classes, words, items, etc.) is a key component of lots of applications, ranging from natural language processing, recommendation systems to electronic health records, etc. However, the frequency of real-world items follows a long-tail distribution in these application…
Although traditional optimization methods focus on finding a single optimal solution, most objective functions in modern machine learning problems, especially those in deep learning, often have multiple or infinite number of optimal points. Therefore, it is useful to consider the problem of finding…
Designing accurate and efficient vision transformers (ViTs) is a highly important but challenging task. Supernet-based one-shot neural architecture search (NAS) enables fast architecture optimization and has achieved state-of-the-art (SOTA) results on convolutional neural networks (CNNs). However, d…
Retriever-reader models achieve competitive performance across many different NLP tasks such as open question answering and dialogue conversations. In this work, we notice these models easily overfit the top-rank retrieval passages and standard training fails to reason over the entire retrieval pass…
Semi-supervised learning (SSL) is a key approach toward more data-efficient machine learning by jointly leverage both labeled and unlabeled data. We propose AlphaMatch, an efficient SSL method that leverages data augmentations, by efficiently enforcing the label consistency between the data points a…
Weight-sharing neural architecture search (NAS) is an effective technique for automating efficient neural architecture design. Weight-sharing NAS builds a supernet that assembles all the architectures as its sub-networks and jointly trains the supernet with the sub-networks. The success of weight-sh…
Neural architecture search (NAS) has shown great promise in designing state-of-the-art (SOTA) models that are both accurate and efficient. Recently, two-stage NAS, e.g. BigNAS, decouples the model training and searching process and achieves remarkable search efficiency and accuracy. Two-stage NAS re…
Many machine learning tasks have to make a trade-off between two loss functions, typically the main data-fitness loss and an auxiliary loss. The most widely used approach is to optimize the linear combination of the objectives, which, however, requires manual tuning of the combination coefficient a…
Data augmentation (DA) is an essential technique for training state-of-the-art deep learning systems. In this paper, we empirically show data augmentation might introduce noisy augmented examples and consequently hurt the performance on unaugmented data during inference. To alleviate this issue, we…
Training NLP systems typically assumes access to annotated data that has a single human label per example. Given imperfect labeling from annotators and inherent ambiguity of language, we hypothesize that single label is not sufficient to learn the spectrum of language interpretation. We explore new…
We propose MaxUp, an embarrassingly simple, highly effective technique for improving the generalization performance of machine learning models, especially deep neural networks. The idea is to generate a set of augmented data with some random perturbations or transforms, and minimize the maximum, or…
We propose a general method to construct centroid approximation for the distribution of maximum points of a random function (a.k.a. argmax distribution), which finds broad applications in machine learning. Our method optimizes a set of centroid points to compactly approximate the argmax distribution…
Randomized classifiers have been shown to provide a promising approach for achieving certified robustness against adversarial attacks in deep learning. However, most existing methods only leverage Gaussian smoothing noise and only work for $\ell_2$ perturbation. We propose a general framework of adv…
Recent empirical works show that large deep neural networks are often highly redundant and one can find much smaller subnetworks without a significant drop of accuracy. However, most existing methods of network pruning are empirical and heuristic, leaving it open whether good subnetworks provably ex…
Recently, substantial progress has been made in language modeling by using deep neural networks. However, in practice, large scale neural language models have been shown to be prone to overfitting. In this paper, we present a simple yet highly effective adversarial training mechanism for regularizin…
Batch Bayesian optimization has been shown to be an efficient and successful approach for black-box function optimization, especially when the evaluation of cost function is highly expensive but can be efficiently parallelized. In this paper, we introduce a novel variational framework for batch quer…
Continuous word representation (aka word embedding) is a basic building block in many neural network-based models used in natural language processing tasks. Although it is widely accepted that words with similar semantics should be close to each other in the embedding space, we find that word embedd…
A new model, named as deep dynamic poisson factorization model, is proposed in this paper for analyzing sequential count vectors. The model based on the Poisson Factor Analysis method captures dependence among time steps by neural networks, representing the implicit distributions. Local complicated…