Neural architecture search (NAS) in expressive search spaces is a computationally hard problem, but it also holds the potential to automatically discover completely novel and performant architectures. To achieve this we need effective search algorithms that can identify powerful components and reuse them in new candidate architectures. In this paper, we introduce two adapted variants of the Smith-Waterman algorithm for local sequence alignment and use them to compute the edit distance in a grammar-based evolutionary architecture search. These algorithms enable us to efficiently calculate a distance metric for neural architectures and to generate a set of hybrid offspring from two parent models. This facilitates the deployment of crossover-based search heuristics, allows us to perform a thorough analysis on the architectural loss landscape, and track population diversity during search. We highlight how our method vastly improves computational complexity over previous work and enables us to efficiently compute shortest paths between architectures. When instantiating the crossover in evolutionary searches, we achieve competitive results, outperforming competing methods. Future work can build upon this new tool, discovering novel components that can be used more broadly across neural architecture design, and broadening its applications beyond NAS.

Embedding models trained separately on similar data often produce representations that encode stable information but are not directly interchangeable. This lack of interoperability raises challenges in several practical applications, such as model retraining, partial model upgrades, and multimodal search. Driven by these challenges, we study when two sets of embeddings can be aligned by an orthogonal transformation. We show that if pairwise dot products are approximately preserved, then there exists an isometry that closely aligns the two sets, and we provide a tight bound on the alignment error. This insight yields a simple alignment recipe, Procrustes post-processing, that makes two embedding models interoperable while preserving the geometry of each embedding space. Empirically, we demonstrate its effectiveness in three applications: maintaining compatibility across retrainings, combining different models for text retrieval, and improving mixed-modality search, where it achieves state-of-the-art performance.

Proteins are essential biological macromolecules that execute life functions. Local motifs within protein structures, such as active sites, are the most critical components for linking structure to function and are key to understanding protein evolution and enabling protein engineering. Existing computational methods struggle to identify and compare these local structures, which leaves a significant gap in understanding protein structures and harnessing their functions. This study presents PLASMA, the first deep learning framework for efficient and interpretable residue-level protein substructure alignment. We reformulate the problem as a regularized optimal transport task and leverage differentiable Sinkhorn iterations. Through extensive quantitative evaluations and three biological case studies, we demonstrate that PLASMA achieves accurate, lightweight, and interpretable residue-level alignment. Additionally, we introduce PLASMA-PF, a training-free variant that provides a practical alternative when training data are unavailable. Our method addresses a critical gap in protein structure analysis tools and offers new opportunities for functional annotation, evolutionary studies, and structure-based drug design. Proteins are essential macromolecules responsible for life functions, from catalysis and signal transduction to structural support and transport. Functional motifs (e.g., catalytic residues, binding pockets, metal-binding sites) are critical for understanding mechanisms, designing therapeutics, and guiding protein engineering (Mills et al., 2018).

However, fine-tuning all parameters of LLMs requires significant hardware resources, which can be impractical for typical users.

The advent of Large Language Models (LLMs) has provided unprecedented capabilities for analyzing unstructured text data. However, deploying these models as reliable, robust, and scalable classifiers in production environments presents significant methodological challenges. Standard fine-tuning approaches can be resource-intensive and often struggle with the dynamic nature of real-world data distributions, which is common in the industry. In this paper, we propose a comprehensive, semi-supervised framework that leverages the zero- and few-shot capabilities of LLMs for building hierarchical text classifiers as a framework for a solution to these industry-wide challenges. Our methodology emphasizes an iterative, human-in-the-loop process that begins with domain knowledge elicitation and progresses through prompt refinement, hierarchical expansion, and multi-faceted validation. We introduce techniques for assessing and mitigating sequence-based biases and outline a protocol for continuous monitoring and adaptation. This framework is designed to bridge the gap between the raw power of LLMs and the practical need for accurate, interpretable, and maintainable classification systems in industry applications.

We use a convolutional encoder and decoder similar to the standard DCGAN discriminator and generator architecture respectively.

Transformers evaluated in a single, fixed-depth pass are provably limited in expressive power to the constant-depth circuit class TC0. Running a Transformer autoregressively removes that ceiling -- first in next-token prediction and, more recently, in chain-of-thought reasoning. Both regimes rely on feedback loops that decode internal states into tokens only to re-encode them in subsequent steps. While this "thinking aloud" mirrors human reasoning, biological brains iterate without externalising intermediate states as language. To boost the expressive power of encoder Transformers without resorting to token-level autoregression, we introduce the SELF-Transformer: an encoder layer that iteratively refines its own attention weights to a fixed point. Instead of producing -- in one pass -- the alignment matrix that remixes the input sequence, the SELF-Transformer iteratively updates that matrix internally, scaling test-time computation with input difficulty. This adaptivity yields up to 20\% accuracy gains on encoder-style benchmarks without increasing parameter count, demonstrating that input-adaptive alignment at test time offers substantial benefits for only a modest extra compute budget. Self-Transformers thus recover much of the expressive power of iterative reasoning while preserving the simplicity of pure encoder architectures.

Tokenization serves as a foundational step for Large Language Models (LLMs) to process text. In new domains or languages, the inefficiency of the tokenizer will slow down the training and generation of LLM. The mismatch in vocabulary also hinders deep knowledge transfer between LLMs like token-level distillation. To mitigate this gap, we propose an efficient method named TokAlign to replace the vocabulary of LLM from the token co-occurrences view, and further transfer the token-level knowledge between models. It first aligns the source vocabulary to the target one by learning a one-to-one mapping matrix for token IDs. Model parameters, including embeddings, are rearranged and progressively fine-tuned for the new vocabulary. Our method significantly improves multilingual text compression rates and vocabulary initialization for LLMs, decreasing the perplexity from 3.4$\text{e}^2$ of strong baseline methods to 1.2$\text{e}^2$ after initialization. Experimental results on models across multiple parameter scales demonstrate the effectiveness and generalization of TokAlign, which costs as few as 5k steps to restore the performance of the vanilla model. After unifying vocabularies between LLMs, token-level distillation can remarkably boost (+4.4% than sentence-level distillation) the base model, costing only 235M tokens.

Large Language Models (LLMs) have shown remarkable capabilities in natural language processing but exhibit significant performance gaps among different languages. Most existing approaches to address these disparities rely on pretraining or fine-tuning, which are resource-intensive. To overcome these limitations without incurring significant costs, we propose Inference-Time Cross-Lingual Intervention (INCLINE), a novel framework that enhances LLM performance on low-performing (source) languages by aligning their internal representations with those of high-performing (target) languages during inference. INCLINE initially learns alignment matrices using parallel sentences from source and target languages through a Least-Squares optimization, and then applies these matrices during inference to transform the low-performing language representations toward the high-performing language space. Extensive experiments on nine benchmarks with five LLMs demonstrate that INCLINE significantly improves performance across diverse tasks and languages, compared to recent strong baselines. Our analysis demonstrates that INCLINE is highly cost-effective and applicable to a wide range of applications. In addition, we release the code to foster research along this line: https://github.com/weixuan-wang123/INCLINE.

While large language models (LLMs) such as Llama-2 or GPT-4 have shown impressive zero-shot performance, fine-tuning is still necessary to enhance their performance for customized datasets, domain-specific tasks, or other private needs. However, fine-tuning all parameters of LLMs requires significant hardware resources, which can be impractical for typical users. Therefore, parameter-efficient fine-tuning such as LoRA have emerged, allowing users to fine-tune LLMs without the need for considerable computing resources, with little performance degradation compared to fine-tuning all parameters. Unfortunately, recent studies indicate that fine-tuning can increase the risk to the safety of LLMs, even when data does not contain malicious content. To address this challenge, we propose Safe LoRA, a simple one-liner patch to the original LoRA implementation by introducing the projection of LoRA weights from selected layers to the safety-aligned subspace, effectively reducing the safety risks in LLM fine-tuning while maintaining utility. It is worth noting that Safe LoRA is a training-free and data-free approach, as it only requires the knowledge of the weights from the base and aligned LLMs. Our extensive experiments demonstrate that when fine-tuning on purely malicious data, Safe LoRA retains similar safety performance as the original aligned model. Moreover, when the fine-tuning dataset contains a mixture of both benign and malicious data, Safe LoRA mitigates the negative effect made by malicious data while preserving performance on downstream tasks.