Training large language models (LLMs) from scratch can yield models with unique functionalities and strengths, but it is costly and often leads to redundant capabilities. A more cost-effective alternative is to fuse existing pre-trained LLMs with different architectures into a more powerful model. However, a key challenge in existing model fusion is their dependence on manually predefined vocabulary alignment, which may not generalize well across diverse contexts, leading to performance degradation in several evaluation. To solve this, we draw inspiration from distribution learning and propose the probabilistic token alignment method as a general and soft mapping for alignment, named as PTA-LLM. Our approach innovatively reformulates token alignment into a classic mathematical problem: optimal transport, seamlessly leveraging distribution-aware learning to facilitate more coherent model fusion. Apart from its inherent generality, PTA-LLM exhibits interpretability from a distributional perspective, offering insights into the essence of the token alignment. Empirical results demonstrate that probabilistic token alignment enhances the target model's performance across multiple capabilities.

Training large language models (LLMs) from scratch can yield models with unique functionalities and strengths, but it is costly and often leads to redundant capabilities. A more cost-effective alternative is to fuse existing pre-trained LLMs with different architectures into a more powerful model. However, a key challenge in existing model fusion is their dependence on manually predefined vocabulary alignment, which may not generalize well across diverse contexts, leading to performance degradation in several evaluation. To solve this, we draw inspiration from distribution learning and propose the probabilistic token alignment method as a general and soft mapping for alignment, named as PTA-LLM. Our approach innovatively reformulates token alignment into a classic mathematical problem: optimal transport, seamlessly leveraging distribution-aware learning to facilitate more coherent model fusion. Apart from its inherent generality, PTA-LLM exhibits interpretability from a distributional perspective, offering insights into the essence of the token alignment. Empirical results demonstrate that probabilistic token alignment enhances the target model's performance across multiple capabilities. Our code is avaliable at https://runjia.tech/neurips_pta-llm/.

Phishing attacks remain one of the most prevalent and persistent cybersecurity threat with attackers continuously evolving and intensifying tactics to evade the general detection system. Despite significant advances in artificial intelligence and machine learning, faithfully reproducing the interpretable reasoning with classification and explainability that underpin phishing judgments remains challenging. Due to recent advancement in Natural Language Processing, Large Language Models (LLMs) show a promising direction and potential for improving domain specific phishing classification tasks. However, enhancing the reliability and robustness of classification models requires not only accurate predictions from LLMs but also consistent and trustworthy explanations aligning with those predictions. Therefore, a key question remains: can LLMs not only classify phishing emails accurately but also generate explanations that are reliably aligned with their predictions and internally self-consistent? To answer these questions, we have fine-tuned transformer based models, including BERT, Llama models, and Wizard, to improve domain relevance and make them more tailored to phishing specific distinctions, using Binary Sequence Classification, Contrastive Learning (CL) and Direct Preference Optimization (DPO). To that end, we examined their performance in phishing classification and explainability by applying the ConsistenCy measure based on SHAPley values (CC SHAP), which measures prediction explanation token alignment to test the model's internal faithfulness and consistency and uncover the rationale behind its predictions and reasoning. Overall, our findings show that Llama models exhibit stronger prediction explanation token alignment with higher CC SHAP scores despite lacking reliable decision making accuracy, whereas Wizard achieves better prediction accuracy but lower CC SHAP scores.

Gene expression is a cellular process that plays a fundamental role in human phenotypical variations and diseases. Despite advances of deep learning models for gene expression prediction, recent benchmarks have revealed their inability to learn distal regulatory grammar. Here, we address this challenge by leveraging a pretrained large language model to enhance gene expression prediction. We introduce Genetic sequence Token Alignment (GTA), which aligns genetic sequence features with natural language tokens, allowing for symbolic reasoning of genomic sequence features via the frozen language model. This cross-modal adaptation learns the regulatory grammar and allows us to further incorporate gene-specific human annotations as prompts, enabling in-context learning that is not possible with existing models. Trained on lymphoblastoid cells, GTA was evaluated on cells from the Geuvadis consortium and outperforms state-of-the-art models such as Enformer, achieving a Spearman correlation of 0.65, a 10\% improvement. Additionally, GTA offers improved interpretation of long-range interactions through the identification of the most meaningful sections of the input genetic context. GTA represents a powerful and novel cross-modal approach to gene expression prediction by utilizing a pretrained language model, in a paradigm shift from conventional gene expression models trained only on sequence data.

Generative models, widely utilized in various applications, can often struggle with prompts corresponding to partial tokens. This struggle stems from tokenization, where partial tokens fall out of distribution during inference, leading to incorrect or nonsensical outputs. This paper examines a technique to alleviate the tokenization artifact on text completion in generative models, maintaining performance even in regular non-subword cases. The method, termed token alignment, involves backtracking to the last complete tokens and ensuring the model's generation aligns with the prompt. This approach showcases marked improvement across many partial token scenarios, including nuanced cases like space-prefix and partial indentation, with only a minor time increase. The technique and analysis detailed in this paper contribute to the continuous advancement of generative models in handling partial inputs, bearing relevance for applications like code completion and text autocompletion. Generative models have shown remarkable efficacy in a range of applications. However, they have been observed to falter when dealing with partially provided inputs or subwords during text completion. For instance, a generative model might struggle to predict the remaining part of the word where a prompt ending in a subword often leads to incorrect or nonsensical outputs. This issue arises due to the artifact of tokenization where a partial token can be out-of-distribution during inference.