DPLM-2: A Multimodal Diffusion Protein Language Model

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates a multimodal approach to simultaneously model, understand, and generate both sequences and structures. However, existing methods typically use separate models for each modality, limiting their ability to capture the intricate relationships between sequence and structure. This results in suboptimal performance in tasks that requires joint understanding and generation of both modalities. In this paper, we introduce DPLM-2, a multimodal protein foundation model that extends discrete diffusion protein language model (DPLM) to accommodate both sequences and structures. To enable structural learning with the language model, 3D coordinates are converted to discrete tokens using a lookup-free quantization-based tokenizer. By training on both experimental and high-quality synthetic structures, DPLM-2 learns the joint distribution of sequence and structure, as well as their marginals and conditionals. We also implement an efficient warm-up strategy to exploit the connection between large-scale evolutionary data and structural inductive biases from pre-trained sequence-based protein language models. Empirical evaluation shows that DPLM-2 can simultaneously generate highly compatible amino acid sequences and their corresponding 3D structures eliminating the need for a two-stage generation approach. Moreover, DPLM-2 demonstrates competitive performance in various conditional generation tasks, including folding, inverse folding, and scaffolding with multimodal motif inputs, as well as providing structure-aware representations for predictive tasks.

Formality is Favored: Unraveling the Learning Preferences of Large Language Models on Data with Conflicting Knowledge

Having been trained on massive pretraining data, large language models have shown excellent performance on many knowledge-intensive tasks. However, pretraining data tends to contain misleading and even conflicting information, and it is intriguing to understand how LLMs handle these noisy data during training. In this study, we systematically analyze LLMs' learning preferences for data with conflicting knowledge. We find that pretrained LLMs establish learning preferences similar to humans, i.e., preferences towards formal texts and texts with fewer spelling errors, resulting in faster learning and more favorable treatment of knowledge in data with such features when facing conflicts. This finding is generalizable across models and languages and is more evident in larger models. An in-depth analysis reveals that LLMs tend to trust data with features that signify consistency with the majority of data, and it is possible to instill new preferences and erase old ones by manipulating the degree of consistency with the majority data.

MoE-LPR: Multilingual Extension of Large Language Models through Mixture-of-Experts with Language Priors Routing

Large Language Models (LLMs) are often English-centric due to the disproportionate distribution of languages in their pre-training data. Enhancing non-English language capabilities through post-pretraining often results in catastrophic forgetting of the ability of original languages. Previous methods either achieve good expansion with severe forgetting or slight forgetting with poor expansion, indicating the challenge of balancing language expansion while preventing forgetting. In this paper, we propose a method called MoE-LPR (Mixture-of-Experts with Language Priors Routing) to alleviate this problem. MoE-LPR employs a two-stage training approach to enhance the multilingual capability. First, the model is post-pretrained into a Mixture-of-Experts (MoE) architecture by upcycling, where all the original parameters are frozen and new experts are added. In this stage, we focus improving the ability on expanded languages, without using any original language data. Then, the model reviews the knowledge of the original languages with replay data amounting to less than 1% of post-pretraining, where we incorporate language priors routing to better recover the abilities of the original languages. Evaluations on multiple benchmarks show that MoE-LPR outperforms other post-pretraining methods. Freezing original parameters preserves original language knowledge while adding new experts preserves the learning ability. Reviewing with LPR enables effective utilization of multilingual knowledge within the parameters. Additionally, the MoE architecture maintains the same inference overhead while increasing total model parameters. Extensive experiments demonstrate MoE-LPR's effectiveness in improving expanded languages and preserving original language proficiency with superior scalability. Code and scripts are freely available at https://github.com/zjwang21/MoE-LPR.git.

EfficientRAG: Efficient Retriever for Multi-Hop Question Answering

Retrieval-augmented generation (RAG) methods encounter difficulties when addressing complex questions like multi-hop queries. While iterative retrieval methods improve performance by gathering additional information, current approaches often rely on multiple calls of large language models (LLMs). In this paper, we introduce EfficientRAG, an efficient retriever for multi-hop question answering. EfficientRAG iteratively generates new queries without the need for LLM calls at each iteration and filters out irrelevant information. Experimental results demonstrate that EfficientRAG surpasses existing RAG methods on three open-domain multi-hop question-answering datasets.

Hallu-PI: Evaluating Hallucination in Multi-modal Large Language Models within Perturbed Inputs

Multi-modal Large Language Models (MLLMs) have demonstrated remarkable performance on various visual-language understanding and generation tasks. However, MLLMs occasionally generate content inconsistent with the given images, which is known as "hallucination". Prior works primarily center on evaluating hallucination using standard, unperturbed benchmarks, which overlook the prevalent occurrence of perturbed inputs in real-world scenarios-such as image cropping or blurring-that are critical for a comprehensive assessment of MLLMs' hallucination. In this paper, to bridge this gap, we propose Hallu-PI, the first benchmark designed to evaluate Hallucination in MLLMs within Perturbed Inputs. Specifically, Hallu-PI consists of seven perturbed scenarios, containing 1,260 perturbed images from 11 object types. Each image is accompanied by detailed annotations, which include fine-grained hallucination types, such as existence, attribute, and relation. We equip these annotations with a rich set of questions, making Hallu-PI suitable for both discriminative and generative tasks. Extensive experiments on 12 mainstream MLLMs, such as GPT-4V and Gemini-Pro Vision, demonstrate that these models exhibit significant hallucinations on Hallu-PI, which is not observed in unperturbed scenarios. Furthermore, our research reveals a severe bias in MLLMs' ability to handle different types of hallucinations. We also design two baselines specifically for perturbed scenarios, namely Perturbed-Reminder and Perturbed-ICL. We hope that our study will bring researchers' attention to the limitations of MLLMs when dealing with perturbed inputs, and spur further investigations to address this issue. Our code and datasets are publicly available at https://github.com/NJUNLP/Hallu-PI.

PreAlign: Boosting Cross-Lingual Transfer by Early Establishment of Multilingual Alignment

Large language models demonstrate reasonable multilingual abilities, despite predominantly English-centric pretraining. However, the spontaneous multilingual alignment in these models is shown to be weak, leading to unsatisfactory cross-lingual transfer and knowledge sharing. Previous works attempt to address this issue by explicitly injecting multilingual alignment information during or after pretraining. Thus for the early stage in pretraining, the alignment is weak for sharing information or knowledge across languages. In this paper, we propose PreAlign, a framework that establishes multilingual alignment prior to language model pretraining. PreAlign injects multilingual alignment by initializing the model to generate similar representations of aligned words and preserves this alignment using a code-switching strategy during pretraining. Extensive experiments in a synthetic English to English-Clone setting demonstrate that PreAlign significantly outperforms standard multilingual joint training in language modeling, zero-shot cross-lingual transfer, and cross-lingual knowledge application. Further experiments in real-world scenarios further validate PreAlign's effectiveness across various model sizes.

Multilingual Contrastive Decoding via Language-Agnostic Layers Skipping

Decoding by contrasting layers (DoLa), is designed to improve the generation quality of large language models (LLMs) by contrasting the prediction probabilities between an early exit output (amateur logits) and the final output (expert logits). However, we find that this approach does not work well on non-English tasks. Inspired by previous interpretability work on language transition during the model's forward pass, we discover that this issue arises from a language mismatch between early exit output and final output. In this work, we propose an improved contrastive decoding algorithm that is effective for diverse languages beyond English. To obtain more helpful amateur logits, we devise two strategies to skip a set of bottom, language-agnostic layers based on our preliminary analysis. Experimental results on multilingual reasoning benchmarks demonstrate that our proposed method outperforms previous contrastive decoding baselines and substantially improves LLM's chain-of-thought reasoning accuracy across 11 languages. The project will be available at: https://github.com/NJUNLP/SkipLayerCD.

Large Language Models Are Cross-Lingual Knowledge-Free Reasoners

Large Language Models have demonstrated impressive reasoning capabilities across multiple languages. However, the relationship between capabilities in different languages is less explored. In this work, we decompose the process of reasoning tasks into two separated parts: knowledge retrieval and knowledge-free reasoning, and analyze the cross-lingual transferability of them. With adapted and constructed knowledge-free reasoning datasets, we show that the knowledge-free reasoning capability can be nearly perfectly transferred across various source-target language directions despite the secondary impact of resource in some specific target languages, while cross-lingual knowledge retrieval significantly hinders the transfer. Moreover, by analyzing the hidden states and feed-forward network neuron activation during the reasoning tasks, we show that higher similarity of hidden representations and larger overlap of activated neurons could explain the better cross-lingual transferability of knowledge-free reasoning than knowledge retrieval. Thus, we hypothesize that knowledge-free reasoning embeds in some language-shared mechanism, while knowledge is stored separately in different languages.

Limited Out-of-Context Knowledge Reasoning in Large Language Models

Large Language Models (LLMs) have demonstrated strong capabilities as knowledge bases and significant in-context reasoning capabilities. However, previous work challenges their out-of-context reasoning ability, i.e., the ability to infer information from their training data, instead of from the context or prompt. This paper focuses on a significant facet of out-of-context reasoning: Out-of-Context Knowledge Reasoning (OCKR), which is to combine multiple knowledge to infer new knowledge. We designed a synthetic dataset with seven representative OCKR tasks to systematically assess the OCKR capabilities of LLMs. Using this dataset, we evaluated the LLaMA2-13B-chat model and discovered that its proficiency in this aspect is limited, regardless of whether the knowledge is trained in a separate or adjacent training settings. Moreover, training the model to reason with complete reasoning data did not result in significant improvement. Training the model to perform explicit knowledge retrieval helps in only one of the tasks, indicating that the model's limited OCKR capabilities are due to difficulties in retrieving relevant knowledge. Furthermore, we treat cross-lingual knowledge transfer as a distinct form of OCKR, and evaluate this ability. Our results show that the evaluated model also exhibits limited ability in transferring knowledge across languages. The dataset used in this study is available at https://github.com/NJUNLP/ID-OCKR.

Extroversion or Introversion? Controlling The Personality of Your Large Language Models

Large language models (LLMs) exhibit robust capabilities in text generation and comprehension, mimicking human behavior and exhibiting synthetic personalities. However, some LLMs have displayed offensive personality, propagating toxic discourse. Existing literature neglects the origin and evolution of LLM personalities, as well as the effective personality control. To fill these gaps, our study embarked on a comprehensive investigation into LLM personality control. We investigated several typical methods to influence LLMs, including three training methods: Continual Pre-training, Supervised Fine-Tuning (SFT), and Reinforcement Learning from Human Feedback (RLHF), along with inference phase considerations (prompts). Our investigation revealed a hierarchy of effectiveness in control: Prompt > SFT > RLHF > Continual Pre-train. Notably, SFT exhibits a higher control success rate compared to prompt induction. While prompts prove highly effective, we found that prompt-induced personalities are less robust than those trained, making them more prone to showing conflicting personalities under reverse personality prompt induction. Besides, harnessing the strengths of both SFT and prompt, we proposed $\underline{\text{P}}$rompt $\underline{\text{I}}$nduction post $\underline{\text{S}}$upervised $\underline{\text{F}}$ine-tuning (PISF), which emerges as the most effective and robust strategy for controlling LLMs' personality, displaying high efficacy, high success rates, and high robustness. Even under reverse personality prompt induction, LLMs controlled by PISF still exhibit stable and robust personalities.