Large language models have made remarkable progress in the field of molecular science, particularly in understanding and generating functional small molecules. This success is largely attributed to the effectiveness of molecular tokenization strategies. In protein science, the amino acid sequence serves as the sole tokenizer for LLMs. However, many fundamental challenges in protein science are inherently structure-dependent. The absence of structure-aware tokens significantly limits the capabilities of LLMs for comprehensive biomolecular comprehension and multimodal generation. To address these challenges, we introduce a novel framework, ProtTeX, which tokenizes the protein sequences, structures, and textual information into a unified discrete space. This innovative approach enables joint training of the LLM exclusively through the Next-Token Prediction paradigm, facilitating multimodal protein reasoning and generation. ProtTeX enables general LLMs to perceive and process protein structures through sequential text input, leverage structural information as intermediate reasoning components, and generate or manipulate structures via sequential text output. Experiments demonstrate that our model achieves significant improvements in protein function prediction, outperforming the state-of-the-art domain expert model with a twofold increase in accuracy. Our framework enables high-quality conformational generation and customizable protein design. For the first time, we demonstrate that by adopting the standard training and inference pipelines from the LLM domain, ProtTeX empowers decoder-only LLMs to effectively address diverse spectrum of protein-related tasks.

Goal-oriented de novo molecule design, namely generating molecules with specific property or substructure constraints, is a crucial yet challenging task in drug discovery. Existing methods, such as Bayesian optimization and reinforcement learning, often require training multiple property predictors and struggle to incorporate substructure constraints. Inspired by the success of Large Language Models (LLMs) in text generation, we propose ChatMol, a novel approach that leverages LLMs for molecule design across diverse constraint settings. Initially, we crafted a molecule representation compatible with LLMs and validated its efficacy across multiple online LLMs. Afterwards, we developed specific prompts geared towards diverse constrained molecule generation tasks to further fine-tune current LLMs while integrating feedback learning derived from property prediction. Finally, to address the limitations of LLMs in numerical recognition, we referred to the position encoding method and incorporated additional encoding for numerical values within the prompt. Experimental results across single-property, substructure-property, and multi-property constrained tasks demonstrate that ChatMol consistently outperforms state-of-the-art baselines, including VAE and RL-based methods. Notably, in multi-objective binding affinity maximization task, ChatMol achieves a significantly lower KD value of 0.25 for the protein target ESR1, while maintaining the highest overall performance, surpassing previous methods by 4.76%. Meanwhile, with numerical enhancement, the Pearson correlation coefficient between the instructed property values and those of the generated molecules increased by up to 0.49. These findings highlight the potential of LLMs as a versatile framework for molecule generation, offering a promising alternative to traditional latent space and RL-based approaches.

Proteins play a pivotal role in living organisms, yet understanding their functions presents significant challenges, including the limited flexibility of classification-based methods, the inability to effectively leverage spatial structural information, and the lack of systematic evaluation metrics for protein Q&A systems. To address these limitations, we propose Prot2Chat, a novel framework that integrates multimodal protein representations with natural language through a unified module, enabling large language model (LLM)-driven answer generation. Our model incorporates a modified ProteinMPNN encoder, which encodes protein sequence and structural information in a unified manner, a protein-text adapter with cross-attention mechanisms, and a LLaMA3 decoder. To optimize training efficiency, we freeze the encoder and employ LoRA techniques for the decoder. We conducted experiments on two datasets, both automated metrics and expert evaluations demonstrate the superior performance of our model. Furthermore, zero-shot prediction results highlight its strong generalization capabilities. This framework offers a promising solution for bridging protein domain knowledge with natural language understanding, paving the way for transformative advancements in protein-related research.

Chain-of-Thought (CoT) prompting elicits large language models (LLMs) to produce a series of intermediate reasoning steps before arriving at the final answer. However, when transitioning to vision-language models (VLMs), their text-only rationales struggle to express the fine-grained associations with the original image. In this paper, we propose an image-incorporated multimodal Chain-of-Thought, named \textbf{Interleaved-modal Chain-of-Thought (ICoT)}, which generates sequential reasoning steps consisting of paired visual and textual rationales to infer the final answer. Intuitively, the novel ICoT requires VLMs to enable the generation of fine-grained interleaved-modal content, which is hard for current VLMs to fulfill. Considering that the required visual information is usually part of the input image, we propose \textbf{Attention-driven Selection (ADS)} to realize ICoT over existing VLMs. ADS intelligently inserts regions of the input image to generate the interleaved-modal reasoning steps with ignorable additional latency. ADS relies solely on the attention map of VLMs without the need for parameterization, and therefore it is a plug-and-play strategy that can be generalized to a spectrum of VLMs. We apply ADS to realize ICoT on two popular VLMs of different architectures. Extensive evaluations of three benchmarks have shown that ICoT prompting achieves substantial performance (up to 14\%) and interpretability improvements compared to existing multimodal CoT prompting methods.

In-context learning (ICL) facilitates Large Language Models (LLMs) exhibiting emergent ability on downstream tasks without updating billions of parameters. However, in the area of multi-modal Large Language Models (MLLMs), two problems hinder the application of multi-modal ICL: (1) Most primary MLLMs are only trained on single-image datasets, making them unable to read multi-modal demonstrations. (2) With the demonstrations increasing, thousands of visual tokens highly challenge hardware and degrade ICL performance. During preliminary explorations, we discovered that the inner LLM tends to focus more on the linguistic modality within multi-modal demonstrations to generate responses. Therefore, we propose a general and light-weighted framework \textbf{AIM} to tackle the mentioned problems through \textbf{A}ggregating \textbf{I}mage information of \textbf{M}ultimodal demonstrations to the dense latent space of the corresponding linguistic part. Specifically, AIM first uses the frozen backbone MLLM to read each image-text demonstration and extracts the vector representations on top of the text. These vectors naturally fuse the information of the image-text pair, and AIM transforms them into fused virtual tokens acceptable for the inner LLM via a trainable projection layer. Ultimately, these fused tokens function as variants of multi-modal demonstrations, fed into the MLLM to direct its response to the current query as usual. Because these fused tokens stem from the textual component of the image-text pair, a multi-modal demonstration is nearly reduced to a pure textual demonstration, thus seamlessly applying to any MLLMs. With its de facto MLLM frozen, AIM is parameter-efficient and we train it on public multi-modal web corpora which have nothing to do with downstream test tasks.

Long prompt leads to huge hardware costs when using transformer-based Large Language Models (LLMs). Unfortunately, many tasks, such as summarization, inevitably introduce long documents, and the wide application of in-context learning easily makes the prompt length explode. This paper proposes a Self-Compressor (SelfCP), which employs the target LLM itself to compress over-limit prompts into dense vectors while keeping the allowed prompts unmodified. Dense vectors are then projected into dense tokens via a learnable connector to make the same LLM unburden to understand. The connector is supervised-tuned under the language modeling objective of the LLM on relatively long texts selected from publicly accessed datasets, involving an instruction dataset to make SelfCP respond to various prompts, while the target LLM keeps frozen during training. We build the lightweight SelfCP upon 2 different backbones with merely 17M learnable parameters originating from the connector and a learnable embedding. Evaluation on both English and Chinese benchmarks demonstrate that SelfCP effectively substitutes 12$\times$ over-limit prompts with dense tokens to reduce memory costs and booster inference throughputs, yet improving response quality. The outstanding performance brings an efficient solution for LLMs to tackle long prompts without training LLMs from scratch.

In-context learning (ICL) facilitates large language models (LLMs) exhibiting spectacular emergent capabilities in various scenarios. Unfortunately, introducing demonstrations easily makes the prompt length explode, bringing a significant burden to hardware. In addition, random demonstrations usually achieve limited improvements in ICL, necessitating demonstration selection among accessible candidates. Previous studies introduce extra modules to perform demonstration compression or selection independently. In this paper, we propose an ICL framework UniICL, which Unifies demonstration selection and compression, and final response generation via a single frozen LLM. Specifically, UniICL first projects actual demonstrations and inference text inputs into short virtual tokens, respectively. Then, virtual tokens are applied to select suitable demonstrations by measuring semantic similarity within latent space among candidate demonstrations and inference input. Finally, inference text inputs together with selected virtual demonstrations are fed into the same frozen LLM for response generation. Notably, UniICL is a parameter-efficient framework that only contains 17M trainable parameters originating from the projection layer. We conduct experiments and analysis over in- and out-domain datasets of both generative and understanding tasks, encompassing ICL scenarios with plentiful and limited demonstration candidates. Results show that UniICL effectively unifies $12 \times$ compression, demonstration selection, and response generation, efficiently scaling up the baseline from 4-shot to 64-shot ICL in IMDb with 24 GB CUDA allocation

ChatGPT is instruct-tuned to generate general and human-expected content to align with human preference through Reinforcement Learning from Human Feedback (RLHF), meanwhile resulting in generated responses not salient enough. Therefore, in this case, ChatGPT may fail to satisfy domain requirements in zero-shot settings, leading to poor ROUGE scores. Inspired by the In-Context Learning (ICL) and retelling ability of ChatGPT, this paper proposes PADS, a \textbf{P}ipeline for \textbf{A}ssisting ChatGPT in \textbf{D}omain \textbf{S}ummarization. PADS consists of a retriever to retrieve similar examples from corpora and a rank model to rerank the multiple candidate summaries generated by ChatGPT. Specifically, given an inference document, we first retrieve an in-context demonstration via the retriever. Then, we require ChatGPT to generate $k$ candidate summaries for the inference document at a time under the guidance of the retrieved demonstration. Finally, the rank model independently scores the $k$ candidate summaries according to their quality and selects the optimal one. We extensively explore dense and sparse retrieval methods to select effective demonstrations for reference and efficiently train the rank model to reflect the quality of candidate summaries for each given summarized document. Additionally, PADS contains merely 400M trainable parameters originating from the rank model and we merely collect 2.5k data to train it. We evaluate PADS on five datasets from different domains, and the result indicates that each module in PADS is committed to effectively guiding ChatGPT to generate salient summaries fitting different domain requirements. Specifically, in the popular summarization dataset Gigaword, PADS achieves over +8 gain on ROUGE-L, compared with the naive ChatGPT in the zero-shot setting. \footnote{Our code are available at \url{https://github.com/jungao1106/PADS}}

Large language models (LLMs) have demonstrated the capacity to improve summary quality by mirroring a human-like iterative process of critique and refinement starting from the initial draft. Two strategies are designed to perform this iterative process: Prompt Chaining and Stepwise Prompt. Prompt chaining orchestrates the drafting, critiquing, and refining phases through a series of three discrete prompts, while Stepwise prompt integrates these phases within a single prompt. However, the relative effectiveness of the two methods has not been extensively studied. This paper is dedicated to examining and comparing these two methods in the context of text summarization to ascertain which method stands out as the most effective. Experimental results show that the prompt chaining method can produce a more favorable outcome. This might be because stepwise prompt might produce a simulated refinement process according to our various experiments. Since refinement is adaptable to diverse tasks, our conclusions have the potential to be extrapolated to other applications, thereby offering insights that may contribute to the broader development of LLMs.

Coherence evaluation aims to assess the organization and structure of a discourse, which remains challenging even in the era of large language models. Due to the scarcity of annotated data, data augmentation is commonly used for training coherence evaluation models. However, previous augmentations for this task primarily rely on heuristic rules, lacking designing criteria as guidance. In this paper, we take inspiration from linguistic theory of discourse structure, and propose a data augmentation framework named CoUDA. CoUDA breaks down discourse coherence into global and local aspects, and designs augmentation strategies for both aspects, respectively. Especially for local coherence, we propose a novel generative strategy for constructing augmentation samples, which involves post-pretraining a generative model and applying two controlling mechanisms to control the difficulty of generated samples. During inference, CoUDA also jointly evaluates both global and local aspects to comprehensively assess the overall coherence of a discourse. Extensive experiments in coherence evaluation show that, with only 233M parameters, CoUDA achieves state-of-the-art performance in both pointwise scoring and pairwise ranking tasks, even surpassing recent GPT-3.5 and GPT-4 based metrics.