The tasks of designing messenger RNAs and non-coding RNAs are discrete optimization problems, and several versions of these problems are NP-hard. As an alternative to commonly used local search methods, we formulate these problems as continuous optimization and develop a general framework for this optimization based on a new concept of "expected partition function". The basic idea is to start with a distribution over all possible candidate sequences, and extend the objective function from a sequence to a distribution. We then use gradient descent-based optimization methods to improve the extended objective function, and the distribution will gradually shrink towards a one-hot sequence (i.e., a single sequence). We consider two important case studies within this framework, the mRNA design problem optimizing for partition function (i.e., ensemble free energy) and the non-coding RNA design problem optimizing for conditional (i.e., Boltzmann) probability. In both cases, our approach demonstrate promising preliminary results.

Recent technological advances have led to contemporary applications that demand real-time processing and analysis of sequentially arriving tensor data. Traditional offline learning, involving the storage and utilization of all data in each computational iteration, becomes impractical for high-dimensional tensor data due to its voluminous size. Furthermore, existing low-rank tensor methods lack the capability for statistical inference in an online fashion, which is essential for real-time predictions and informed decision-making. This paper addresses these challenges by introducing a novel online inference framework for low-rank tensor learning. Our approach employs Stochastic Gradient Descent (SGD) to enable efficient real-time data processing without extensive memory requirements, thereby significantly reducing computational demands. We establish a non-asymptotic convergence result for the online low-rank SGD estimator, nearly matches the minimax optimal rate of estimation error in offline models that store all historical data. Building upon this foundation, we propose a simple yet powerful online debiasing approach for sequential statistical inference in low-rank tensor learning. The entire online procedure, covering both estimation and inference, eliminates the need for data splitting or storing historical data, making it suitable for on-the-fly hypothesis testing. Given the sequential nature of our data collection, traditional analyses relying on offline methods and sample splitting are inadequate. In our analysis, we control the sum of constructed super-martingales to ensure estimates along the entire solution path remain within the benign region. Additionally, a novel spectral representation tool is employed to address statistical dependencies among iterative estimates, establishing the desired asymptotic normality.

Neural networks (NNs), both living and artificial, work due to being complex systems of neurons, each having its own specialization. Revealing these specializations is important for understanding NNs inner working mechanisms. The only way to do this for a living system, the neural response of which to a stimulus is not a known (let alone differentiable) function is to build a feedback loop of exposing it to stimuli, the properties of which can be iteratively varied aiming in the direction of maximal response. To test such a loop on a living network, one should first learn how to run it quickly and efficiently, reaching most effective stimuli (ones that maximize certain neurons activation) in least possible number of iterations. We present a framework with an effective design of such a loop, successfully testing it on an artificial spiking neural network (SNN, a model that mimics the behaviour of NNs in living brains). Our optimization method used for activation maximization (AM) was based on low-rank tensor decomposition (Tensor Train, TT) of the activation function's discretization over its domain the latent parameter space of stimuli (CIFAR10-size color images, generated by either VQ-VAE or SN-GAN from their latent description vectors, fed to the SNN). To our knowledge, the present work is the first attempt to perform effective AM for SNNs. The source code of our framework, MANGO (for Maximization of neural Activation via Non-Gradient Optimization) is available on GitHub.

Large machine learning models are revolutionary technologies of artificial intelligence whose bottlenecks include huge computational expenses, power, and time used both in the pre-training and fine-tuning process. In this work, we show that fault-tolerant quantum computing could possibly provide provably efficient resolutions for generic (stochastic) gradient descent algorithms, scaling as O(T^2 polylog(n)), where n is the size of the models and T is the number of iterations in the training, as long as the models are both sufficiently dissipative and sparse, with small learning rates. Based on earlier efficient quantum algorithms for dissipative differential equations, we find and prove that similar algorithms work for (stochastic) gradient descent, the primary algorithm for machine learning. In practice, we benchmark instances of large machine learning models from 7 million to 103 million parameters. We find that, in the context of sparse training, a quantum enhancement is possible at the early stage of learning after model pruning, motivating a sparse parameter download and re-upload scheme. Our work shows solidly that fault-tolerant quantum algorithms could potentially contribute to most state-of-the-art, large-scale machine-learning problems.

In this note, we consider the highly nonconvex optimization problem associated with computing the rank decomposition of symmetric tensors. We formulate the invariance properties of the loss function and show that critical points detected by standard gradient based methods are \emph{symmetry breaking} with respect to the target tensor. The phenomena, seen for different choices of target tensors and norms, make possible the use of recently developed analytic and algebraic tools for studying nonconvex optimization landscapes exhibiting symmetry breaking phenomena of similar nature.

signSGD is popular in nonconvex optimization due to its communication efficiency. Yet, existing analyses of signSGD rely on assuming that data are sampled with replacement in each iteration, contradicting the practical implementation where data are randomly reshuffled and sequentially fed into the algorithm. We bridge this gap by proving the first convergence result of signSGD with random reshuffling (SignRR) for nonconvex optimization. Given the dataset size $n$, the number of epochs of data passes $T$, and the variance bound of a stochastic gradient $\sigma^2$, we show that SignRR has the same convergence rate $O(\log(nT)/\sqrt{nT} + \|\sigma\|_1)$ as signSGD \citep{bernstein2018signsgd}. We then present SignRVR and SignRVM, which leverage variance-reduced gradients and momentum updates respectively, both converging at $O(\log (nT)/\sqrt{nT} + \log (nT)\sqrt{n}/\sqrt{T})$. In contrast with the analysis of signSGD, our results do not require an extremely large batch size in each iteration to be of the same order as the total number of iterations \citep{bernstein2018signsgd} or the signs of stochastic and true gradients match element-wise with a minimum probability of 1/2 \citep{safaryan2021stochastic}. We also extend our algorithms to cases where data are distributed across different machines, yielding dist-SignRVR and dist-SignRVM, both converging at $O(\log (n_0T)/\sqrt{n_0T} + \log (n_0T)\sqrt{n_0}/\sqrt{T})$, where $n_0$ is the dataset size of a single machine. We back up our theoretical findings through experiments on simulated and real-world problems, verifying that randomly reshuffled sign methods match or surpass existing baselines.

A wide array of modern machine learning applications - from adversarial models to multi-agent reinforcement learning - can be formulated as non-cooperative games whose Nash equilibria represent the system's desired operational states. Despite having a highly non-convex loss landscape, many cases of interest possess a latent convex structure that could potentially be leveraged to yield convergence to an equilibrium. Driven by this observation, our paper proposes a flexible first-order method that successfully exploits such "hidden structures" and achieves convergence under minimal assumptions for the transformation connecting the players' control variables to the game's latent, convex-structured layer. The proposed method - which we call preconditioned hidden gradient descent (PHGD) - hinges on a judiciously chosen gradient preconditioning scheme related to natural gradient methods. Importantly, we make no separability assumptions for the game's hidden structure, and we provide explicit convergence rate guarantees for both deterministic and stochastic environments.

The 0/1 matrix factorization defines matrix products using logical AND and OR as product-sum operators, revealing the factors influencing various decision processes. Instances and their characteristics are arranged in rows and columns. Formulating matrix factorization as an energy minimization problem and exploring it with Simulated Annealing (SA) theoretically enables finding a minimum solution in sufficient time. However, searching for the optimal solution in practical time becomes problematic when the energy landscape has many plateaus with flat slopes. In this work, we propose a method to facilitate the solution process by applying a gradient to the energy landscape, using a rectified linear type cost function readily available in modern annealing machines. We also propose a method to quickly obtain a solution by updating the cost function's gradient during the search process. Numerical experiments were conducted, confirming the method's effectiveness with both noise-free artificial and real data.

This paper introduces novel alternate training procedures for hard-parameter sharing Multi-Task Neural Networks (MTNNs). Traditional MTNN training faces challenges in managing conflicting loss gradients, often yielding sub-optimal performance. The proposed alternate training method updates shared and task-specific weights alternately, exploiting the multi-head architecture of the model. This approach reduces computational costs, enhances training regularization, and improves generalization. Convergence properties similar to those of the classical stochastic gradient method are established. Empirical experiments demonstrate delayed overfitting, improved prediction, and reduced computational demands. In summary, our alternate training procedures offer a promising advancement for the training of hard-parameter sharing MTNNs.

Many neural network architectures have been shown to be Turing Complete, and can thus implement arbitrary algorithms. However, Transformers are unique in that they can implement gradient-based learning algorithms \emph{under simple parameter configurations}. A line of recent work shows that linear Transformers naturally learn to implement gradient descent (GD) when trained on a linear regression in-context learning task. But the linearity assumption (either in the Transformer architecture or in the learning task) is far from realistic settings where non-linear activations crucially enable Transformers to learn complicated non-linear functions. In this paper, we provide theoretical and empirical evidence that non-linear Transformers can, and \emph{in fact do}, learn to implement learning algorithms to learn non-linear functions in context. Our results apply to a broad class of combinations of non-linear architectures, and non-linear in-context learning tasks. Interestingly, we show that the optimal choice of non-linear activation depends in a natural way on the non-linearity of the learning task.