AVIDa-hIL6: A Large-Scale VHH Dataset Produced from an Immunized Alpaca for Predicting Antigen-Antibody Interactions

Antibodies have become an important class of therapeutic agents to treat human diseases. To accelerate therapeutic antibody discovery, computational methods, especially machine learning, have attracted considerable interest for predicting specific interactions between antibody candidates and target antigens such as viruses and bacteria. However, the publicly available datasets in existing works have notable limitations, such as small sizes and the lack of non-binding samples and exact amino acid sequences. To overcome these limitations, we have developed AVIDa-hIL6, a large-scale dataset for predicting antigen-antibody interactions in the variable domain of heavy chain of heavy chain antibodies (VHHs), produced from an alpaca immunized with the human interleukin-6 (IL-6) protein, as antigens. By leveraging the simple structure of VHHs, which facilitates identification of full-length amino acid sequences by DNA sequencing technology, AVIDa-hIL6 contains 573,891 antigen-VHH pairs with amino acid sequences. All the antigen-VHH pairs have reliable labels for binding or non-binding, as generated by a novel labeling method. Furthermore, via introduction of artificial mutations, AVIDa-hIL6 contains 30 different mutants in addition to wild-type IL-6 protein. This characteristic provides opportunities to develop machine learning models for predicting changes in antibody binding by antigen mutations. We report experimental benchmark results on AVIDa-hIL6 by using neural network-based baseline models. The results indicate that the existing models have potential, but further research is needed to generalize them to predict effective antibodies against unknown mutants. The dataset is available at https://avida-hil6.cognanous.com.

Plex: Towards Reliability using Pretrained Large Model Extensions

A recent trend in artificial intelligence is the use of pretrained models for language and vision tasks, which have achieved extraordinary performance but also puzzling failures. Probing these models' abilities in diverse ways is therefore critical to the field. In this paper, we explore the reliability of models, where we define a reliable model as one that not only achieves strong predictive performance but also performs well consistently over many decision-making tasks involving uncertainty (e.g., selective prediction, open set recognition), robust generalization (e.g., accuracy and proper scoring rules such as log-likelihood on in- and out-of-distribution datasets), and adaptation (e.g., active learning, few-shot uncertainty). We devise 10 types of tasks over 40 datasets in order to evaluate different aspects of reliability on both vision and language domains. To improve reliability, we developed ViT-Plex and T5-Plex, pretrained large model extensions for vision and language modalities, respectively. Plex greatly improves the state-of-the-art across reliability tasks, and simplifies the traditional protocol as it improves the out-of-the-box performance and does not require designing scores or tuning the model for each task. We demonstrate scaling effects over model sizes up to 1B parameters and pretraining dataset sizes up to 4B examples. We also demonstrate Plex's capabilities on challenging tasks including zero-shot open set recognition, active learning, and uncertainty in conversational language understanding.

Pre-training helps Bayesian optimization too

Bayesian optimization (BO) has become a popular strategy for global optimization of many expensive real-world functions. Contrary to a common belief that BO is suited to optimizing black-box functions, it actually requires domain knowledge on characteristics of those functions to deploy BO successfully. Such domain knowledge often manifests in Gaussian process priors that specify initial beliefs on functions. However, even with expert knowledge, it is not an easy task to select a prior. This is especially true for hyperparameter tuning problems on complex machine learning models, where landscapes of tuning objectives are often difficult to comprehend. We seek an alternative practice for setting these functional priors. In particular, we consider the scenario where we have data from similar functions that allow us to pre-train a tighter distribution a priori. To verify our approach in realistic model training setups, we collected a large multi-task hyperparameter tuning dataset by training tens of thousands of configurations of near-state-of-the-art models on popular image and text datasets, as well as a protein sequence dataset. Our results show that on average, our method is able to locate good hyperparameters at least 3 times more efficiently than the best competing methods.

Ensembling over Classifiers: a Bias-Variance Perspective

Ensembles are a straightforward, remarkably effective method for improving the accuracy,calibration, and robustness of models on classification tasks; yet, the reasons that underlie their success remain an active area of research. We build upon the extension to the bias-variance decomposition by Pfau (2013) in order to gain crucial insights into the behavior of ensembles of classifiers. Introducing a dual reparameterization of the bias-variance tradeoff, we first derive generalized laws of total expectation and variance for nonsymmetric losses typical of classification tasks. Comparing conditional and bootstrap bias/variance estimates, we then show that conditional estimates necessarily incur an irreducible error. Next, we show that ensembling in dual space reduces the variance and leaves the bias unchanged, whereas standard ensembling can arbitrarily affect the bias. Empirically, standard ensembling reducesthe bias, leading us to hypothesize that ensembles of classifiers may perform well in part because of this unexpected reduction.We conclude by an empirical analysis of recent deep learning methods that ensemble over hyperparameters, revealing that these techniques indeed favor bias reduction. This suggests that, contrary to classical wisdom, targeting bias reduction may be a promising direction for classifier ensembles.

Understanding the bias-variance tradeoff of Bregman divergences

This paper builds upon the work of Pfau (2013), which generalized the bias variance tradeoff to any Bregman divergence loss function. Pfau (2013) showed that for Bregman divergences, the bias and variances are defined with respect to a central label, defined as the mean of the label variable, and a central prediction, of a more complex form. We show that, similarly to the label, the central prediction can be interpreted as the mean of a random variable, where the mean operates in a dual space defined by the loss function itself. Viewing the bias-variance tradeoff through operations taken in dual space, we subsequently derive several results of interest. In particular, (a) the variance terms satisfy a generalized law of total variance; (b) if a source of randomness cannot be controlled, its contribution to the bias and variance has a closed form; (c) there exist natural ensembling operations in the label and prediction spaces which reduce the variance and do not affect the bias.

Automatic prior selection for meta Bayesian optimization with a case study on tuning deep neural network optimizers

The performance of deep neural networks can be highly sensitive to the choice of a variety of meta-parameters, such as optimizer parameters and model hyperparameters. Tuning these well, however, often requires extensive and costly experimentation. Bayesian optimization (BO) is a principled approach to solve such expensive hyperparameter tuning problems efficiently. Key to the performance of BO is specifying and refining a distribution over functions, which is used to reason about the optima of the underlying function being optimized. In this work, we consider the scenario where we have data from similar functions that allows us to specify a tighter distribution a priori. Specifically, we focus on the common but potentially costly task of tuning optimizer parameters for training neural networks. Building on the meta BO method from Wang et al. (2018), we develop practical improvements that (a) boost its performance by leveraging tuning results on multiple tasks without requiring observations for the same meta-parameter points across all tasks, and (b) retain its regret bound for a special case of our method. As a result, we provide a coherent BO solution for iterative optimization of continuous optimizer parameters. To verify our approach in realistic model training setups, we collected a large multi-task hyperparameter tuning dataset by training tens of thousands of configurations of near-state-of-the-art models on popular image and text datasets, as well as a protein sequence dataset. Our results show that on average, our method is able to locate good hyperparameters at least 3 times more efficiently than the best competing methods.

Uncertainty Baselines: Benchmarks for Uncertainty & Robustness in Deep Learning

High-quality estimates of uncertainty and robustness are crucial for numerous real-world applications, especially for deep learning which underlies many deployed ML systems. The ability to compare techniques for improving these estimates is therefore very important for research and practice alike. Yet, competitive comparisons of methods are often lacking due to a range of reasons, including: compute availability for extensive tuning, incorporation of sufficiently many baselines, and concrete documentation for reproducibility. In this paper we introduce Uncertainty Baselines: high-quality implementations of standard and state-of-the-art deep learning methods on a variety of tasks. As of this writing, the collection spans 19 methods across 9 tasks, each with at least 5 metrics. Each baseline is a self-contained experiment pipeline with easily reusable and extendable components. Our goal is to provide immediate starting points for experimentation with new methods or applications. Additionally we provide model checkpoints, experiment outputs as Python notebooks, and leaderboards for comparing results. Code available at https://github.com/google/uncertainty-baselines.

Population-Based Black-Box Optimization for Biological Sequence Design

The use of black-box optimization for the design of new biological sequences is an emerging research area with potentially revolutionary impact. The cost and latency of wet-lab experiments requires methods that find good sequences in few experimental rounds of large batches of sequences--a setting that off-the-shelf black-box optimization methods are ill-equipped to handle. We find that the performance of existing methods varies drastically across optimization tasks, posing a significant obstacle to real-world applications. To improve robustness, we propose Population-Based Black-Box Optimization (P3BO), which generates batches of sequences by sampling from an ensemble of methods. The number of sequences sampled from any method is proportional to the quality of sequences it previously proposed, allowing P3BO to combine the strengths of individual methods while hedging against their innate brittleness. Adapting the hyper-parameters of each of the methods online using evolutionary optimization further improves performance. Through extensive experiments on in-silico optimization tasks, we show that P3BO outperforms any single method in its population, proposing higher quality sequences as well as more diverse batches. As such, P3BO and Adaptive-P3BO are a crucial step towards deploying ML to real-world sequence design.

Weighting Is Worth the Wait: Bayesian Optimization with Importance Sampling

Many contemporary machine learning models require extensive tuning of hyperparameters to perform well. A variety of methods, such as Bayesian optimization, have been developed to automate and expedite this process. However, tuning remains extremely costly as it typically requires repeatedly fully training models. We propose to accelerate the Bayesian optimization approach to hyperparameter tuning for neural networks by taking into account the relative amount of information contributed by each training example. To do so, we leverage importance sampling (IS); this significantly increases the quality of the black-box function evaluations, but also their runtime, and so must be done carefully. Casting hyperparameter search as a multi-task Bayesian optimization problem over both hyperparameters and importance sampling design achieves the best of both worlds: by learning a parameterization of IS that trades-off evaluation complexity and quality, we improve upon Bayesian optimization state-of-the-art runtime and final validation error across a variety of datasets and complex neural architectures.

DPPNet: Approximating Determinantal Point Processes with Deep Networks

Determinantal Point Processes (DPPs) provide an elegant and versatile way to sample sets of items that balance the point-wise quality with the set-wise diversity of selected items. For this reason, they have gained prominence in many machine learning applications that rely on subset selection. However, sampling from a DPP over a ground set of size $N$ is a costly operation, requiring in general an $O(N^3)$ preprocessing cost and an $O(Nk^3)$ sampling cost for subsets of size $k$. We approach this problem by introducing DPPNets: generative deep models that produce DPP-like samples for arbitrary ground sets. We develop an inhibitive attention mechanism based on transformer networks that captures a notion of dissimilarity between feature vectors. We show theoretically that such an approximation is sensible as it maintains the guarantees of inhibition or dissimilarity that makes DPPs so powerful and unique. Empirically, we demonstrate that samples from our model receive high likelihood under the more expensive DPP alternative.