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Training Compute-Optimal Protein Language Models

Neural Information Processing Systems

We explore optimally training protein language models, an area of significant interest in biological research where guidance on best practices is limited.Most models are trained with extensive compute resources until performance gains plateau, focusing primarily on increasing model sizes rather than optimizing the efficient compute frontier that balances performance and compute budgets.Our investigation is grounded in a massive dataset consisting of 939 million protein sequences. We trained over 300 models ranging from 3.5 million to 10.7 billion parameters on 5 to 200 billion unique tokens, to investigate the relations between model sizes, training token numbers, and objectives.First, we observed the effect of diminishing returns for the Causal Language Model (CLM) and that of overfitting for Masked Language Model (MLM) when repeating the commonly used Uniref database. To address this, we included metagenomic protein sequences in the training set to increase the diversity and avoid the plateau or overfitting effects. Second, we obtained the scaling laws of CLM and MLM on Transformer, tailored to the specific characteristics of protein sequence data. Third, we observe a transfer scaling phenomenon from CLM to MLM, further demonstrating the effectiveness of transfer through scaling behaviors based on estimated Effectively Transferred Tokens.Finally, to validate our scaling laws, we compare the large-scale versions of ESM-2 and PROGEN2 on downstream tasks, encompassing evaluations of protein generation as well as structure-and function-related tasks, all within less or equivalent pre-training compute budgets.


Transcormer: Transformer for Sentence Scoring with Sliding Language Modeling

Neural Information Processing Systems

Sentence scoring aims at measuring the likelihood score of a sentence and is widely used in many natural language processing scenarios, like reranking, which is to select the best sentence from multiple candidates. Previous works on sentence scoring mainly adopted either causal language modeling (CLM) like GPT or masked language modeling (MLM) like BERT, which have some limitations: 1) CLM only utilizes unidirectional information for the probability estimation of a sentence without considering bidirectional context, which affects the scoring quality; 2) MLM can only estimate the probability of partial tokens at a time and thus requires multiple forward passes to estimate the probability of the whole sentence, which incurs large computation and time cost. In this paper, we propose \textit{Transcormer} -- a Transformer model with a novel \textit{sliding language modeling} (SLM) for sentence scoring. Specifically, our SLM adopts a triple-stream self-attention mechanism to estimate the probability of all tokens in a sentence with bidirectional context and only requires a single forward pass. SLM can avoid the limitations of CLM (only unidirectional context) and MLM (multiple forward passes) and inherit their advantages, and thus achieve high effectiveness and efficiency in scoring. Experimental results on multiple tasks demonstrate that our method achieves better performance than other language modelings.


A Content-Preserving Secure Linguistic Steganography

Xiang, Lingyun, Ou, Chengfu, He, Xu, Yang, Zhongliang, Liu, Yuling

arXiv.org Artificial Intelligence

Existing linguistic steganography methods primarily rely on content transformations to conceal secret messages. However, they often cause subtle yet looking-innocent deviations between normal and stego texts, posing potential security risks in real-world applications. To address this challenge, we propose a content-preserving linguistic steganography paradigm for perfectly secure covert communication without modifying the cover text. Based on this paradigm, we introduce CLstega (\textit{C}ontent-preserving \textit{L}inguistic \textit{stega}nography), a novel method that embeds secret messages through controllable distribution transformation. CLstega first applies an augmented masking strategy to locate and mask embedding positions, where MLM(masked language model)-predicted probability distributions are easily adjustable for transformation. Subsequently, a dynamic distribution steganographic coding strategy is designed to encode secret messages by deriving target distributions from the original probability distributions. To achieve this transformation, CLstega elaborately selects target words for embedding positions as labels to construct a masked sentence dataset, which is used to fine-tune the original MLM, producing a target MLM capable of directly extracting secret messages from the cover text. This approach ensures perfect security of secret messages while fully preserving the integrity of the original cover text. Experimental results show that CLstega can achieve a 100\% extraction success rate, and outperforms existing methods in security, effectively balancing embedding capacity and security.