ProtiGeno: a prokaryotic short gene finder using protein language models

Prokaryotic gene prediction plays an important role in understanding the biology of organisms and their function with applications in medicine and biotechnology. Although the current gene finders are highly sensitive in finding long genes, their sensitivity decreases noticeably in finding shorter genes (<180 nts). The culprit is insufficient annotated gene data to identify distinguishing features in short open reading frames (ORFs). We develop a deep learning-based method called ProtiGeno, specifically targeting short prokaryotic genes using a protein language model trained on millions of evolved proteins. In systematic large-scale experiments on 4,288 prokaryotic genomes, we demonstrate that ProtiGeno predicts short coding and noncoding genes with higher accuracy and recall than the current state-of-the-art gene finders. We discuss the predictive features of ProtiGeno and possible limitations by visualizing the three-dimensional structure of the predicted short genes. Data, codes, and models are available at https://github.com/tonytu16/protigeno.

Efficiently Computing Sparse Fourier Transforms of $q$-ary Functions

Fourier transformations of pseudo-Boolean functions are popular tools for analyzing functions of binary sequences. Real-world functions often have structures that manifest in a sparse Fourier transform, and previous works have shown that under the assumption of sparsity the transform can be computed efficiently. But what if we want to compute the Fourier transform of functions defined over a $q$-ary alphabet? These types of functions arise naturally in many areas including biology. A typical workaround is to encode the $q$-ary sequence in binary, however, this approach is computationally inefficient and fundamentally incompatible with the existing sparse Fourier transform techniques. Herein, we develop a sparse Fourier transform algorithm specifically for $q$-ary functions of length $n$ sequences, dubbed $q$-SFT, which provably computes an $S$-sparse transform with vanishing error as $q^n \rightarrow \infty$ in $O(Sn)$ function evaluations and $O(S n^2 \log q)$ computations, where $S = q^{n\delta}$ for some $\delta < 1$. Under certain assumptions, we show that for fixed $q$, a robust version of $q$-SFT has a sample complexity of $O(Sn^2)$ and a computational complexity of $O(Sn^3)$ with the same asymptotic guarantees. We present numerical simulations on synthetic and real-world RNA data, demonstrating the scalability of $q$-SFT to massively high dimensional $q$-ary functions.

Spectral Regularization Allows Data-frugal Learning over Combinatorial Spaces

Data-driven machine learning models are being increasingly employed in several important inference problems in biology, chemistry, and physics which require learning over combinatorial spaces. Recent empirical evidence (see, e.g., [1], [2], [3]) suggests that regularizing the spectral representation of such models improves their generalization power when labeled data is scarce. However, despite these empirical studies, the theoretical underpinning of when and how spectral regularization enables improved generalization is poorly understood. In this paper, we focus on learning pseudo-Boolean functions and demonstrate that regularizing the empirical mean squared error by the L_1 norm of the spectral transform of the learned function reshapes the loss landscape and allows for data-frugal learning, under a restricted secant condition on the learner's empirical error measured against the ground truth function. Under a weaker quadratic growth condition, we show that stationary points which also approximately interpolate the training data points achieve statistically optimal generalization performance. Complementing our theory, we empirically demonstrate that running gradient descent on the regularized loss results in a better generalization performance compared to baseline algorithms in several data-scarce real-world problems.

Group-Structured Adversarial Training

Robust training methods against perturbations to the input data have received great attention in the machine learning literature. A standard approach in this direction is adversarial training which learns a model using adversarially-perturbed training samples. However, adversarial training performs suboptimally against perturbations structured across samples such as universal and group-sparse shifts that are commonly present in biological data such as gene expression levels of different tissues. In this work, we seek to close this optimality gap and introduce Group-Structured Adversarial Training (GSAT) which learns a model robust to perturbations structured across samples. We formulate GSAT as a non-convex concave minimax optimization problem which minimizes a group-structured optimal transport cost. Specifically, we focus on the applications of GSAT for group-sparse and rank-constrained perturbations modeled using group and nuclear norm penalties. In order to solve GSAT's non-smooth optimization problem in those cases, we propose a new minimax optimization algorithm called GDADMM by combining Gradient Descent Ascent (GDA) and Alternating Direction Method of Multipliers (ADMM). We present several applications of the GSAT framework to gain robustness against structured perturbations for image recognition and computational biology datasets.

BEAR: Sketching BFGS Algorithm for Ultra-High Dimensional Feature Selection in Sublinear Memory

We consider feature selection for applications in machine learning where the dimensionality of the data is so large that it exceeds the working memory of the (local) computing machine. Unfortunately, current large-scale sketching algorithms show poor memory-accuracy trade-off due to the irreversible collision and accumulation of the stochastic gradient noise in the sketched domain. Here, we develop a second-order ultra-high dimensional feature selection algorithm, called BEAR, which avoids the extra collisions by storing the second-order gradients in the celebrated Broyden-Fletcher-Goldfarb-Shannon (BFGS) algorithm in Count Sketch, a sublinear memory data structure from the streaming literature. Experiments on real-world data sets demonstrate that BEAR requires up to three orders of magnitude less memory space to achieve the same classification accuracy compared to the first-order sketching algorithms. Theoretical analysis proves convergence of BEAR with rate O(1/t) in t iterations of the sketched algorithm. Our algorithm reveals an unexplored advantage of second-order optimization for memory-constrained sketching of models trained on ultra-high dimensional data sets.

MISSION: Ultra Large-Scale Feature Selection using Count-Sketches

Feature selection is an important challenge in machine learning. It plays a crucial role in the explainability of machine-driven decisions that are rapidly permeating throughout modern society. Unfortunately, the explosion in the size and dimensionality of real-world datasets poses a severe challenge to standard feature selection algorithms. Today, it is not uncommon for datasets to have billions of dimensions. At such scale, even storing the feature vector is impossible, causing most existing feature selection methods to fail. Workarounds like feature hashing, a standard approach to large-scale machine learning, helps with the computational feasibility, but at the cost of losing the interpretability of features. In this paper, we present MISSION, a novel framework for ultra large-scale feature selection that performs stochastic gradient descent while maintaining an efficient representation of the features in memory using a Count-Sketch data structure. MISSION retains the simplicity of feature hashing without sacrificing the interpretability of the features while using only O(log^2(p)) working memory. We demonstrate that MISSION accurately and efficiently performs feature selection on real-world, large-scale datasets with billions of dimensions.