Protein design, a grand challenge of the day, involves optimization on a fitness landscape, and leading methods adopt a model-based approach where a model is trained on a training set (protein sequences and fitness) and proposes candidates to explore next. These methods are challenged by sparsity of high-fitness samples in the training set, a problem that has been in the literature. A less recognized but equally important problem stems from the distribution of training samples in the design space: leading methods are not designed for scenarios where the desired optimum is in a region that is not only poorly represented in training data, but also relatively far from the highly represented low-fitness regions. We show that this problem of "separation" in the design space is a significant bottleneck in existing model-based optimization tools and propose a new approach that uses a novel VAE as its search model to overcome the problem. We demonstrate its advantage over prior methods in robustly finding improved samples, regardless of the imbalance and separation between low- and high-fitness training samples. Our comprehensive benchmark on real and semi-synthetic protein datasets as well as solution design for physics-informed neural networks, showcases the generality of our approach in discrete and continuous design spaces. Our implementation is available at https://github.com/sabagh1994/PGVAE.

This work proposes a solution for the problem of training physics informed networks under partial integro-differential equations. These equations require infinite or a large number of neural evaluations to construct a single residual for training. As a result, accurate evaluation may be impractical, and we show that naive approximations at replacing these integrals with unbiased estimates lead to biased loss functions and solutions. To overcome this bias, we investigate three types of solutions: the deterministic sampling approach, the double-sampling trick, and the delayed target method. We consider three classes of PDEs for benchmarking; one defining a Poisson problem with singular charges and weak solutions, another involving weak solutions on electro-magnetic fields and a Maxwell equation, and a third one defining a Smoluchowski coagulation problem. Our numerical results confirm the existence of the aforementioned bias in practice, and also show that our proposed delayed target approach can lead to accurate solutions with comparable quality to ones estimated with a large number of samples.

Learning accurate classifiers for novel categories from very few examples, known as few-shot image classification, is a challenging task in statistical machine learning and computer vision. The performance in few-shot classification suffers from the bias in the estimation of classifier parameters; however, an effective underlying bias reduction technique that could alleviate this issue in training few-shot classifiers has been overlooked. In this work, we demonstrate the effectiveness of Firth bias reduction in few-shot classification. Theoretically, Firth bias reduction removes the first order term $O(N^{-1})$ from the small-sample bias of the Maximum Likelihood Estimator. Here we show that the general Firth bias reduction technique simplifies to encouraging uniform class assignment probabilities for multinomial logistic classification, and almost has the same effect in cosine classifiers. We derive the optimization objective for Firth penalized multinomial logistic and cosine classifiers, and empirically evaluate that it is consistently effective across the board for few-shot image classification, regardless of (1) the feature representations from different backbones, (2) the number of samples per class, and (3) the number of classes. Finally, we show the robustness of Firth bias reduction, in the case of imbalanced data distribution. Our implementation is available at https://github.com/ehsansaleh/firth_bias_reduction