Cell identity encompasses various semantic aspects of a cell, including cell type, pathway information, disease information, and more, which are essential for biologists to gain insights into its biological characteristics. Understanding cell identity from the transcriptomic data, such as annotating cell types, has become an important task in bioinformatics. As these semantic aspects are determined by human experts, it is impossible for AI models to effectively carry out cell identity understanding tasks without the supervision signals provided by single-cell and label pairs. The single-cell pre-trained language models (PLMs) currently used for this task are trained only on a single modality, transcriptomics data, lack an understanding of cell identity knowledge. As a result, they have to be fine-tuned for downstream tasks and struggle when lacking labeled data with the desired semantic labels. To address this issue, we propose an innovative solution by constructing a unified representation of single-cell data and natural language during the pre-training phase, allowing the model to directly incorporate insights related to cell identity. More specifically, we introduce $\textbf{LangCell}$, the first $\textbf{Lang}$uage-$\textbf{Cell}$ pre-training framework. LangCell utilizes texts enriched with cell identity information to gain a profound comprehension of cross-modal knowledge. Results from experiments conducted on different benchmarks show that LangCell is the only single-cell PLM that can work effectively in zero-shot cell identity understanding scenarios, and also significantly outperforms existing models in few-shot and fine-tuning cell identity understanding scenarios.

In recent years, there has been a growing emphasis on compressing large pre-trained transformer models for resource-constrained devices. However, traditional pruning methods often leave the embedding layer untouched, leading to model over-parameterization. Additionally, they require extensive compression time with large datasets to maintain performance in pruned models. To address these challenges, we propose VTrans, an iterative pruning framework guided by the Variational Information Bottleneck (VIB) principle. Our method compresses all structural components, including embeddings, attention heads, and layers using VIB-trained masks. This approach retains only essential weights in each layer, ensuring compliance with specified model size or computational constraints. Notably, our method achieves upto 70% more compression than prior state-of-the-art approaches, both task-agnostic and task-specific. We further propose faster variants of our method: Fast-VTrans utilizing only 3% of the data and Faster-VTrans, a time efficient alternative that involves exclusive finetuning of VIB masks, accelerating compression by upto 25 times with minimal performance loss compared to previous methods. Extensive experiments on BERT, ROBERTa, and GPT-2 models substantiate the efficacy of our method. Moreover, our method demonstrates scalability in compressing large models such as LLaMA-2-7B, achieving superior performance compared to previous pruning methods. Additionally, we use attention-based probing to qualitatively assess model redundancy and interpret the efficiency of our approach. Notably, our method considers heads with high attention to special and current tokens in un-pruned model as foremost candidates for pruning while retained heads are observed to attend more to task-critical keywords.

Multiple-choice questions (MCQ) are frequently used to assess large language models (LLMs). Typically, an LLM is given a question and selects the answer deemed most probable after adjustments for factors like length. Unfortunately, LLMs may inherently favor certain answer choice IDs, such as A/B/C/D, due to inherent biases of priori unbalanced probabilities, influencing the prediction of answers based on these IDs. Previous research has introduced methods to reduce this ''selection bias'' by simply permutating options on a few test samples and applying to new ones. Another problem of MCQ is the lottery ticket choice by ''random guessing''. The LLM does not learn particular knowledge, but the option is guessed correctly. This situation is especially serious for those small-scale LLMs. To address them, a more thorough approach involves shifting from MCQ to open-style questions, which can fundamentally eliminate selection bias and random guessing issues. However, transitioning causes its own set of challenges in (1) identifying suitable open-style questions and (2) validating the correctness of LLM open-style responses against human-annotated ground-truths. This work aims to tackle these significant difficulties, and establish a new LLM evaluation benchmark through entirely open-style questions. Consequently, we introduce the Open-LLM-Leaderboard to track various LLMs' performance and reflect true capability of them, such as GPT-4o/4/3.5, Claude 3, Gemini, etc. Our code and dataset are available at https://github.com/VILA-Lab/Open-LLM-Leaderboard.

Large language models (LLMs) exhibit outstanding performance in machine translation via in-context learning. In contrast to sentence-level translation, document-level translation (DOCMT) by LLMs based on in-context learning faces two major challenges: firstly, document translations generated by LLMs are often incoherent; secondly, the length of demonstration for in-context learning is usually limited. To address these issues, we propose a Context-Aware Prompting method (CAP), which enables LLMs to generate more accurate, cohesive, and coherent translations via in-context learning. CAP takes into account multi-level attention, selects the most relevant sentences to the current one as context, and then generates a summary from these collected sentences. Subsequently, sentences most similar to the summary are retrieved from the datastore as demonstrations, which effectively guide LLMs in generating cohesive and coherent translations. We conduct extensive experiments across various DOCMT tasks, and the results demonstrate the effectiveness of our approach, particularly in zero pronoun translation (ZPT) and literary translation tasks.

Large language models (LLMs) have showcased impressive multilingual machine translation ability. However, unlike encoder-decoder style models, decoder-only LLMs lack an explicit alignment between source and target contexts. Analyzing contribution scores during generation processes revealed that LLMs can be biased towards previously generated tokens over corresponding source tokens, leading to unfaithful translations. To address this issue, we propose to encourage LLMs to pay more attention to the source context from both source and target perspectives in zeroshot prompting: 1) adjust source context attention weights; 2) suppress irrelevant target prefix influence; Additionally, we propose 3) avoiding over-reliance on the target prefix in instruction tuning. Experimental results from both human-collected unfaithfulness test sets focusing on LLM-generated unfaithful translations and general test sets, verify our methods' effectiveness across multiple language pairs. Further human evaluation shows our method's efficacy in reducing hallucinatory translations and facilitating faithful translation generation.

Automatic methods for generating and gathering linguistic data have proven effective for fine-tuning Language Models (LMs) in languages less resourced than English. Still, while there has been emphasis on data quantity, less attention has been given to its quality. In this work, we investigate the impact of human intervention on machine-generated data when fine-tuning dialogical models. In particular, we study (1) whether post-edited dialogues exhibit higher perceived quality compared to the originals that were automatically generated; (2) whether fine-tuning with post-edited dialogues results in noticeable differences in the generated outputs; and (3) whether post-edited dialogues influence the outcomes when considering the parameter size of the LMs. To this end we created HED-IT, a large-scale dataset where machine-generated dialogues are paired with the version post-edited by humans. Using both the edited and unedited portions of HED-IT, we fine-tuned three different sizes of an LM. Results from both human and automatic evaluation show that the different quality of training data is clearly perceived and it has an impact also on the models trained on such data. Additionally, our findings indicate that larger models are less sensitive to data quality, whereas this has a crucial impact on smaller models. These results enhance our comprehension of the impact of human intervention on training data in the development of high-quality LMs.

This paper introduces a scholarly Question Answering (QA) system on top of the NFDI4DataScience Gateway, employing a Retrieval Augmented Generation-based (RAG) approach. The NFDI4DS Gateway, as a foundational framework, offers a unified and intuitive interface for querying various scientific databases using federated search. The RAG-based scholarly QA, powered by a Large Language Model (LLM), facilitates dynamic interaction with search results, enhancing filtering capabilities and fostering a conversational engagement with the Gateway search. The effectiveness of both the Gateway and the scholarly QA system is demonstrated through experimental analysis.

Autoregressive Large Language Models (LLMs) have achieved impressive performance in language tasks but face two significant bottlenecks: (1) quadratic complexity in the attention module as the number of tokens increases, and (2) limited efficiency due to the sequential processing nature of autoregressive LLMs during generation. While linear attention and speculative decoding offer potential solutions, their applicability and synergistic potential for enhancing autoregressive LLMs remain uncertain. We conduct the first comprehensive study on the efficacy of existing linear attention methods for autoregressive LLMs, integrating them with speculative decoding. We introduce an augmentation technique for linear attention that ensures compatibility with speculative decoding, enabling more efficient training and serving of LLMs. Extensive experiments and ablation studies involving seven existing linear attention models and five encoder/decoder-based LLMs consistently validate the effectiveness of our augmented linearized LLMs. Notably, our approach achieves up to a 6.67 reduction in perplexity on the LLaMA model and up to a 2$\times$ speedup during generation compared to prior linear attention methods. Codes and models are available at https://github.com/GATECH-EIC/Linearized-LLM.

This paper focuses on the task of hallucination detection, which aims to determine the truthfulness of LLM-generated statements. To address this problem, a popular class of methods utilize the LLM's self-consistencies in its beliefs in a set of logically related augmented statements generated by the LLM, which does not require external knowledge databases and can work with both white-box and black-box LLMs. However, in many existing approaches, the augmented statements tend to be very monotone and unstructured, which makes it difficult to integrate meaningful information from the LLM beliefs in these statements. Also, many methods work with the binarized version of the LLM's belief, instead of the continuous version, which significantly loses information. To overcome these limitations, in this paper, we propose Belief Tree Propagation (BTProp), a probabilistic framework for LLM hallucination detection. BTProp introduces a belief tree of logically related statements by recursively decomposing a parent statement into child statements with three decomposition strategies, and builds a hidden Markov tree model to integrate the LLM's belief scores in these statements in a principled way. Experiment results show that our method improves baselines by 3%-9% (evaluated by AUROC and AUC-PR) on multiple hallucination detection benchmarks. Code is available at https://github.com/UCSB-NLP-Chang/BTProp.

Large language models (LLMs) can significantly be improved by aligning to human preferences -- the so-called reinforcement learning from human feedback (RLHF). However, the cost of fine-tuning an LLM is prohibitive for many users. Due to their ability to bypass LLM finetuning, tokenwise reward-guided text generation (RGTG) methods have recently been proposed. They use a reward model trained on full sequences to score partial sequences during a tokenwise decoding, in a bid to steer the generation towards sequences with high rewards. However, these methods have so far been only heuristically motivated and poorly analyzed. In this work, we show that reward models trained on full sequences are not compatible with scoring partial sequences. To alleviate this issue, we propose to explicitly train a Bradley-Terry reward model on partial sequences, and autoregressively sample from the implied tokenwise policy during decoding time. We study the property of this reward model and the implied policy. In particular, we show that this policy is proportional to the ratio of two distinct RLHF policies. We show that our simple approach outperforms previous RGTG methods and achieves similar performance as strong offline baselines but without large-scale LLM finetuning.