Predicting the biophysical and functional properties of proteins is essential for in silico protein design. Machine learning has emerged as a promising technique for such prediction tasks. However, the relative scarcity of in vitro annotations means that these models often have little, or no, specific data on the desired fitness prediction task. As a result of limited data, protein language models (PLMs) are typically trained on general protein sequence modeling tasks, and then fine-tuned, or applied zero-shot, to protein fitness prediction. When no task data is available, the models make strong assumptions about the correlation between the protein sequence likelihood and fitness scores. In contrast, we propose meta-learning over a distribution of standard fitness prediction tasks, and demonstrate positive transfer to unseen fitness prediction tasks. Our method, called Metalic (Meta-Learning In-Context), uses in-context learning and fine-tuning, when data is available, to adapt to new tasks. Crucially, fine-tuning enables considerable generalization, even though it is not accounted for during meta-training. Our fine-tuned models achieve strong results with 18 times fewer parameters than state-of-the-art models. Moreover, our method sets a new state-of-the-art in low-data settings on ProteinGym, an established fitness-prediction benchmark. Due to data scarcity, we believe meta-learning will play a pivotal role in advancing protein engineering.

Prior work has shown that text-conditioned diffusion models can learn to identify and manipulate primitive concepts underlying a compositional data-generating process, enabling generalization to entirely novel, out-of-distribution compositions. Beyond performance evaluations, these studies develop a rich empirical phenomenology of learning dynamics, showing that models generalize sequentially, respecting the compositional hierarchy of the data-generating process. Moreover, concept-centric structures within the data significantly influence a model's speed of learning the ability to manipulate a concept. In this paper, we aim to better characterize these empirical results from a theoretical standpoint. Specifically, we propose an abstraction of prior work's compositional generalization problem by introducing a structured identity mapping (SIM) task, where a model is trained to learn the identity mapping on a Gaussian mixture with structurally organized centroids. We mathematically analyze the learning dynamics of neural networks trained on this SIM task and show that, despite its simplicity, SIM's learning dynamics capture and help explain key empirical observations on compositional generalization with diffusion models identified in prior work. Our theory also offers several new insights -- e.g., we find a novel mechanism for non-monotonic learning dynamics of test loss in early phases of training. We validate our new predictions by training a text-conditioned diffusion model, bridging our simplified framework and complex generative models. Overall, this work establishes the SIM task as a meaningful theoretical abstraction of concept learning dynamics in modern generative models.

Machine learning (ML) has become a ubiquitous tool across various domains of data mining and big data analysis. The efficacy of ML models depends heavily on high-quality datasets, which are often complicated by the presence of missing values. Consequently, the performance and generalization of ML models are at risk in the face of such datasets. This paper aims to examine the nuanced impact of missing values on ML workflows, including their types, causes, and consequences. Our analysis focuses on the challenges posed by missing values, including biased inferences, reduced predictive power, and increased computational burdens. The paper further explores strategies for handling missing values, including imputation techniques and removal strategies, and investigates how missing values affect model evaluation metrics and introduces complexities in cross-validation and model selection. The study employs case studies and real-world examples to illustrate the practical implications of addressing missing values. Finally, the discussion extends to future research directions, emphasizing the need for handling missing values ethically and transparently. The primary goal of this paper is to provide insights into the pervasive impact of missing values on ML models and guide practitioners toward effective strategies for achieving robust and reliable model outcomes.

While momentum-based optimization algorithms are commonly used in the notoriously non-convex optimization problems of deep learning, their analysis has historically been restricted to the convex and strongly convex setting. In this article, we partially close this gap between theory and practice and demonstrate that virtually identical guarantees can be obtained in optimization problems with a `benign' non-convexity. We show that these weaker geometric assumptions are well justified in overparametrized deep learning, at least locally. Variations of this result are obtained for a continuous time model of Nesterov's accelerated gradient descent algorithm (NAG), the classical discrete time version of NAG, and versions of NAG with stochastic gradient estimates with purely additive noise and with noise that exhibits both additive and multiplicative scaling.

We investigate the dynamics of labial constriction trajectories during the production of /b/ and /m/ in English and Mandarin. We find that, across languages and contexts, the ratio of instantaneous displacement to instantaneous velocity generally follows an exponential decay curve from movement onset to movement offset. We formalize this empirical discovery in a differential equation and, in combination with an assumption of point attractor dynamics, derive a nonlinear second-order dynamical system describing labial constriction trajectories. The equation has only two parameters, T and r. T corresponds to the target state and r corresponds to movement rapidity. Thus, each of the parameters corresponds to a phonetically relevant dimension of control. Nonlinear regression demonstrates that the model provides excellent fits to individual movement trajectories. Moreover, trajectories simulated from the model qualitatively match empirical trajectories, and capture key kinematic variables like duration, peak velocity, and time to achieve peak velocity. The model constitutes a proposal for the dynamics of individual articulatory movements, and thus offers a novel foundation from which to understand additional influences on articulatory kinematics like prosody, inter-movement coordination, and stochastic noise.

Mutual information provides a powerful, general-purpose metric for quantifying the amount of shared information between variables. Estimating normalized mutual information using a k-Nearest Neighbor (k-NN) based approach involves the calculation of the scaling-invariant k-NN radius. Calculation of the radius suffers from numerical overflow when the joint dimensionality of the data becomes high, typically in the range of several hundred dimensions. To address this issue, we propose a logarithmic transformation technique that improves the numerical stability of the radius calculation in high-dimensional spaces. By applying the proposed transformation during the calculation of the radius, numerical overflow is avoided, and precision is maintained. Proposed transformation is validated through both theoretical analysis and empirical evaluation, demonstrating its ability to stabilize the calculation without compromizing the precision of the results.

Time series data are inherently functions of time, yet current transformers often learn time series by modeling them as mere concatenations of time periods, overlooking their functional properties. In this work, we propose a novel objective for transformers that learn time series by re-interpreting them as temporal functions. We build an alternative sequence of time series by constructing degradation operators of different intensity in the functional space, creating augmented variants of the original sample that are abstracted or simplified to different degrees. Based on the new set of generated sequence, we train an autoregressive transformer that progressively recovers the original sample from the most simplified variant. Analogous to the next word prediction task in languages that learns narratives by connecting different words, our autoregressive transformer aims to learn the Narratives of Time Series (NoTS) by connecting different functions in time. Theoretically, we justify the construction of the alternative sequence through its advantages in approximating functions. When learning time series data with transformers, constructing sequences of temporal functions allows for a broader class of approximable functions (e.g., differentiation) compared to sequences of time periods, leading to a 26\% performance improvement in synthetic feature regression experiments. Experimentally, we validate NoTS in 3 different tasks across 22 real-world datasets, where we show that NoTS significantly outperforms other pre-training methods by up to 6\%. Additionally, combining NoTS on top of existing transformer architectures can consistently boost the performance. Our results demonstrate the potential of NoTS as a general-purpose dynamic learner, offering a viable alternative for developing foundation models for time series analysis.

Fine-tuning has become a popular approach to adapting large foundational models to specific tasks. As the size of models and datasets grows, parameter-efficient fine-tuning techniques are increasingly important. One of the most widely used methods is Low-Rank Adaptation (LoRA), with adaptation update expressed as the product of two low-rank matrices. While LoRA was shown to possess strong performance in fine-tuning, it often under-performs when compared to full-parameter fine-tuning (FPFT). Although many variants of LoRA have been extensively studied empirically, their theoretical optimization analysis is heavily under-explored. The starting point of our work is a demonstration that LoRA and its two extensions, Asymmetric LoRA and Chain of LoRA, indeed encounter convergence issues. To address these issues, we propose Randomized Asymmetric Chain of LoRA (RAC-LoRA) -- a general optimization framework that rigorously analyzes the convergence rates of LoRA-based methods. Our approach inherits the empirical benefits of LoRA-style heuristics, but introduces several small but important algorithmic modifications which turn it into a provably convergent method. Our framework serves as a bridge between FPFT and low-rank adaptation. We provide provable guarantees of convergence to the same solution as FPFT, along with the rate of convergence. Additionally, we present a convergence analysis for smooth, non-convex loss functions, covering gradient descent, stochastic gradient descent, and federated learning settings. Our theoretical findings are supported by experimental results.

Neural networks are trained by choosing an architecture and training the parameters. The choice of architecture is often by trial and error or with Neural Architecture Search (NAS) methods. While NAS provides some automation, it often relies on discrete steps that optimize the architecture and then train the parameters. We introduce a novel neural network training framework that fundamentally transforms the process by learning architecture and parameters simultaneously with gradient descent. With the appropriate setting of the loss function, it can discover sparse and compact neural networks for given datasets. Central to our approach is a multi-scale encoder-decoder, in which the encoder embeds pairs of neural networks with similar functionalities close to each other (irrespective of their architectures and weights). To train a neural network with a given dataset, we randomly sample a neural network embedding in the embedding space and then perform gradient descent using our custom loss function, which incorporates a sparsity penalty to encourage compactness. The decoder generates a neural network corresponding to the embedding. Experiments demonstrate that our framework can discover sparse and compact neural networks maintaining a high performance.

The Bradley-Terry-Luce (BTL) model is one of the most widely used models for ranking a collection of items or agents based on pairwise comparisons among them. In this work, our objective is to formulate a hypothesis test that determines whether a given pairwise comparison dataset, with k comparisons per pair of agents, originates from an underlying BTL model. We formalize this testing problem in the minimax sense and define the critical threshold of the problem. We then establish upper bounds on the critical threshold for general induced observation graphs (satisfying mild assumptions) and develop lower bounds for complete induced graphs. In particular, our test statistic for the upper bounds is based on a new approximation we derive for the separation distance between general pairwise comparison models and the class of BTL models. To further assess the performance of our statistical test, we prove upper bounds on the type I and type II probabilities of error. Much of our analysis is conducted within the context of a fixed observation graph structure, where the graph possesses certain "nice" properties, such as expansion and bounded principal ratio. Finally, we conduct several experiments on synthetic and real-world datasets to validate some of our theoretical results. Moreover, we also propose an approach based on permutation testing to determine the threshold of our test in a data-driven manner in these experiments. In recent years, the availability of pairwise comparison data and its subsequent analysis has significantly increased across diverse domains. Pairwise comparison data consists of information gathered in the form of comparisons made among a given set of items or agents. Many real-world applications, including sports tournaments, consumer preference surveys, and political voting, generate data in the form of pairwise comparisons. Such datasets serve a range of purposes, such as ranking items [2]-[12], analyzing team performance over time [13], studying market or sports competitiveness [14], [15], and even fine-tuning large language models using reinforcement learning from human feedback [16], [17]. A popular modeling assumption while performing such learning and inference tasks with pairwise comparison data is to assume that the data conforms to an underlying Bradley-Terry-Luce (BTL) model [2]-[6] as a generative model for the data. P(i is preferred over j) = . The BTL model is known to be a natural consequence of the assumption of independence of irrelevant alternatives (IIA), which is widely used in economics and social choice theory [3].