Fitness functions map large combinatorial spaces of biological sequences to properties of interest. Inferring these multimodal functions from experimental data is a central task in modern protein engineering. Global epistasis models are an effective and physically-grounded class of models for estimating fitness functions from observed data. These models assume that a sparse latent function is transformed by a monotonic nonlinearity to emit measurable fitness. Here we demonstrate that minimizing contrastive loss functions, such as the Bradley-Terry loss, is a simple and flexible technique for extracting the sparse latent function implied by global epistasis. We argue by way of a fitness-epistasis uncertainty principle that the nonlinearities in global epistasis models can produce observed fitness functions that do not admit sparse representations, and thus may be inefficient to learn from observations when using a Mean Squared Error (MSE) loss (a common practice). We show that contrastive losses are able to accurately estimate a ranking function from limited data even in regimes where MSE is ineffective. We validate the practical utility of this insight by showing contrastive loss functions result in consistently improved performance on benchmark tasks.
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Weakly hard real-time systems can, to some degree, tolerate deadline misses, but their schedulability still needs to be analyzed to ensure their quality of service. Such analysis usually occurs at early design stages to provide implementation guidelines to engineers so that they can make better design decisions. Estimating worst-case execution times (WCET) is a key input to schedulability analysis. However, early on during system design, estimating WCET values is challenging and engineers usually determine them as plausible ranges based on their domain knowledge. Our approach aims at finding restricted, safe WCET sub-ranges given a set of ranges initially estimated by experts in the context of weakly hard real-time systems. To this end, we leverage (1) multi-objective search aiming at maximizing the violation of weakly hard constraints in order to find worst-case scheduling scenarios and (2) polynomial logistic regression to infer safe WCET ranges with a probabilistic interpretation. We evaluated our approach by applying it to an industrial system in the satellite domain and several realistic synthetic systems. The results indicate that our approach significantly outperforms a baseline relying on random search without learning, and estimates safe WCET ranges with a high degree of confidence in practical time (< 23h).
With the advent of large language models (LLMs), the trend in NLP has been to train LLMs on vast amounts of data to solve diverse language understanding and generation tasks. The list of LLM successes is long and varied. Nevertheless, several recent papers provide empirical evidence that LLMs fail to capture important aspects of linguistic meaning. Focusing on universal quantification, we provide a theoretical foundation for these empirical findings by proving that LLMs cannot learn certain fundamental semantic properties including semantic entailment and consistency as they are defined in formal semantics. More generally, we show that LLMs are unable to learn concepts beyond the first level of the Borel Hierarchy, which imposes severe limits on the ability of LMs, both large and small, to capture many aspects of linguistic meaning. This means that LLMs will continue to operate without formal guarantees on tasks that require entailments and deep linguistic understanding.
The Plackett--Luce model is a popular approach for ranking data analysis, where a utility vector is employed to determine the probability of each outcome based on Luce's choice axiom. In this paper, we investigate the asymptotic theory of utility vector estimation by maximizing different types of likelihood, such as the full-, marginal-, and quasi-likelihood. We provide a rank-matching interpretation for the estimating equations of these estimators and analyze their asymptotic behavior as the number of items being compared tends to infinity. In particular, we establish the uniform consistency of these estimators under conditions characterized by the topology of the underlying comparison graph sequence and demonstrate that the proposed conditions are sharp for common sampling scenarios such as the nonuniform random hypergraph model and the hypergraph stochastic block model; we also obtain the asymptotic normality of these estimators and discuss the trade-off between statistical efficiency and computational complexity for practical uncertainty quantification. Both results allow for nonuniform and inhomogeneous comparison graphs with varying edge sizes and different asymptotic orders of edge probabilities. We verify our theoretical findings by conducting detailed numerical experiments.
Image classification has improved with the development of training techniques. However, these techniques often require careful parameter tuning to balance the strength of regularization, limiting their potential benefits. In this paper, we propose a novel way to use regularization called Augmenting Sub-model (AugSub). AugSub consists of two models: the main model and the sub-model. While the main model employs conventional training recipes, the sub-model leverages the benefit of additional regularization. AugSub achieves this by mitigating adverse effects through a relaxed loss function similar to self-distillation loss. We demonstrate the effectiveness of AugSub with three drop techniques: dropout, drop-path, and random masking. Our analysis shows that all AugSub improves performance, with the training loss converging even faster than regular training. Among the three, AugMask is identified as the most practical method due to its performance and cost efficiency. We further validate AugMask across diverse training recipes, including DeiT-III, ResNet, MAE fine-tuning, and Swin Transformer. The results show that AugMask consistently provides significant performance gain. AugSub provides a practical and effective solution for introducing additional regularization under various training recipes. Code is available at \url{//github.com/naver-ai/augsub}.
Double generalized linear models provide a flexible framework for modeling data by allowing the mean and the dispersion to vary across observations. Common members of the exponential dispersion family including the Gaussian, Poisson, compound Poisson-gamma (CP-g), Gamma and inverse-Gaussian are known to admit such models. The lack of their use can be attributed to ambiguities that exist in model specification under a large number of covariates and complications that arise when data display complex spatial dependence. In this work we consider a hierarchical specification for the CP-g model with a spatial random effect. The spatial effect is targeted at performing uncertainty quantification by modeling dependence within the data arising from location based indexing of the response. We focus on a Gaussian process specification for the spatial effect. Simultaneously, we tackle the problem of model specification for such models using Bayesian variable selection. It is effected through a continuous spike and slab prior on the model parameters, specifically the fixed effects. The novelty of our contribution lies in the Bayesian frameworks developed for such models. We perform various synthetic experiments to showcase the accuracy of our frameworks. They are then applied to analyze automobile insurance premiums in Connecticut, for the year of 2008.
Generative adversarial networks constitute a powerful approach to generative modeling. While generated samples often are indistinguishable from real data, there is no guarantee that they will follow the true data distribution. In this work, we propose a method to ensure that the distributions of certain generated data statistics coincide with the respective distributions of the real data. In order to achieve this, we add a Kullback-Leibler term to the generator loss function: the KL divergence is taken between the true distributions as represented by a conditional energy-based model, and the corresponding generated distributions obtained from minibatch values at each iteration. We evaluate the method on a synthetic dataset and two real-world datasets and demonstrate improved performance of our method.
Supervised machine learning (ML) and deep learning (DL) algorithms excel at predictive tasks, but it is commonly assumed that they often do so by exploiting non-causal correlations, which may limit both interpretability and generalizability. Here, we show that this trade-off between explanation and prediction is not as deep and fundamental as expected. Whereas ML and DL algorithms will indeed tend to use non-causal features for prediction when fed indiscriminately with all data, it is possible to constrain the learning process of any ML and DL algorithm by selecting features according to Pearl's backdoor adjustment criterion. In such a situation, some algorithms, in particular deep neural networks, can provide near unbiased effect estimates under feature collinearity. Remaining biases are explained by the specific algorithmic structures as well as hyperparameter choice. Consequently, optimal hyperparameter settings are different when tuned for prediction or inference, confirming the general expectation of a trade-off between prediction and explanation. However, the effect of this trade-off is small compared to the effect of a causally constrained feature selection. Thus, once the causal relationship between the features is accounted for, the difference between prediction and explanation may be much smaller than commonly assumed. We also show that such causally constrained models generalize better to new data with altered collinearity structures, suggesting generalization failure may often be due to a lack of causal learning. Our results not only provide a perspective for using ML for inference of (causal) effects but also help to improve the generalizability of fitted ML and DL models to new data.
This paper presents SimCLR: a simple framework for contrastive learning of visual representations. We simplify recently proposed contrastive self-supervised learning algorithms without requiring specialized architectures or a memory bank. In order to understand what enables the contrastive prediction tasks to learn useful representations, we systematically study the major components of our framework. We show that (1) composition of data augmentations plays a critical role in defining effective predictive tasks, (2) introducing a learnable nonlinear transformation between the representation and the contrastive loss substantially improves the quality of the learned representations, and (3) contrastive learning benefits from larger batch sizes and more training steps compared to supervised learning. By combining these findings, we are able to considerably outperform previous methods for self-supervised and semi-supervised learning on ImageNet. A linear classifier trained on self-supervised representations learned by SimCLR achieves 76.5% top-1 accuracy, which is a 7% relative improvement over previous state-of-the-art, matching the performance of a supervised ResNet-50. When fine-tuned on only 1% of the labels, we achieve 85.8% top-5 accuracy, outperforming AlexNet with 100X fewer labels.
With the rapid increase of large-scale, real-world datasets, it becomes critical to address the problem of long-tailed data distribution (i.e., a few classes account for most of the data, while most classes are under-represented). Existing solutions typically adopt class re-balancing strategies such as re-sampling and re-weighting based on the number of observations for each class. In this work, we argue that as the number of samples increases, the additional benefit of a newly added data point will diminish. We introduce a novel theoretical framework to measure data overlap by associating with each sample a small neighboring region rather than a single point. The effective number of samples is defined as the volume of samples and can be calculated by a simple formula $(1-\beta^{n})/(1-\beta)$, where $n$ is the number of samples and $\beta \in [0,1)$ is a hyperparameter. We design a re-weighting scheme that uses the effective number of samples for each class to re-balance the loss, thereby yielding a class-balanced loss. Comprehensive experiments are conducted on artificially induced long-tailed CIFAR datasets and large-scale datasets including ImageNet and iNaturalist. Our results show that when trained with the proposed class-balanced loss, the network is able to achieve significant performance gains on long-tailed datasets.
High spectral dimensionality and the shortage of annotations make hyperspectral image (HSI) classification a challenging problem. Recent studies suggest that convolutional neural networks can learn discriminative spatial features, which play a paramount role in HSI interpretation. However, most of these methods ignore the distinctive spectral-spatial characteristic of hyperspectral data. In addition, a large amount of unlabeled data remains an unexploited gold mine for efficient data use. Therefore, we proposed an integration of generative adversarial networks (GANs) and probabilistic graphical models for HSI classification. Specifically, we used a spectral-spatial generator and a discriminator to identify land cover categories of hyperspectral cubes. Moreover, to take advantage of a large amount of unlabeled data, we adopted a conditional random field to refine the preliminary classification results generated by GANs. Experimental results obtained using two commonly studied datasets demonstrate that the proposed framework achieved encouraging classification accuracy using a small number of data for training.
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