Generative machine learning models are increasingly being used to design novel proteins for therapeutic and biotechnological applications. However, the current methods mostly focus on the design of proteins with a fixed backbone structure, which leads to their limited ability to account for protein flexibility, one of the crucial properties for protein function. Learning to engineer protein flexibility is problematic because the available data are scarce, heterogeneous, and costly to obtain using computational as well as experimental methods. Our contributions to address this problem are three-fold. First, we comprehensively compare methods for quantifying protein flexibility and identify data relevant to learning. Second, we design and train flexibility predictors utilizing sequential or both sequential and structural information on the input. We overcome the data scarcity issue by leveraging a pre-trained protein language model. Third, we introduce a method for fine-tuning a protein inverse folding model to steer it toward desired flexibility in specified regions. We demonstrate that our method Flexpert-Design enables guidance of inverse folding models toward increased flexibility. This opens up new possibilities for protein flexibility engineering and the development of proteins with enhanced biological activities.
We consider the generative modeling of speech over multiple minutes, a requirement for long-form multimedia generation and audio-native voice assistants. However, current spoken language models struggle to generate plausible speech past tens of seconds, from high temporal resolution of speech tokens causing loss of coherence, to architectural issues with long-sequence training or extrapolation, to memory costs at inference time. With these considerations we propose SpeechSSM, the first speech language model to learn from and sample long-form spoken audio (e.g., 16 minutes of read or extemporaneous speech) in a single decoding session without text intermediates, based on recent advances in linear-time sequence modeling. Furthermore, to address growing challenges in spoken language evaluation, especially in this new long-form setting, we propose: new embedding-based and LLM-judged metrics; quality measurements over length and time; and a new benchmark for long-form speech processing and generation, LibriSpeech-Long. Speech samples and the dataset are released at https://google.github.io/tacotron/publications/speechssm/
With the goal of supporting scalable lexical semantic annotation, analysis, and theorizing, we conduct a comprehensive evaluation of different methods for generating event descriptions under both syntactic constraints -- e.g. desired clause structure -- and semantic constraints -- e.g. desired verb sense. We compare three different methods -- (i) manual generation by experts; (ii) sampling from a corpus annotated for syntactic and semantic information; and (iii) sampling from a language model (LM) conditioned on syntactic and semantic information -- along three dimensions of the generated event descriptions: (a) naturalness, (b) typicality, and (c) distinctiveness. We find that all methods reliably produce natural, typical, and distinctive event descriptions, but that manual generation continues to produce event descriptions that are more natural, typical, and distinctive than the automated generation methods. We conclude that the automated methods we consider produce event descriptions of sufficient quality for use in downstream annotation and analysis insofar as the methods used for this annotation and analysis are robust to a small amount of degradation in the resulting event descriptions.
The scaling capability has been widely validated in neural language models with respect to the number of parameters and the size of training data. One important question is that does the scaling capability also exists similarly with respect to the number of vision tokens in large vision language Model? This study fills the gap by investigating the relationship between the number of vision tokens and the performance on vision-language models. Our theoretical analysis and empirical evaluations demonstrate that the model exhibits scalable performance \(S(N_l)\) with respect to the number of vision tokens \(N_l\), characterized by the relationship \(S(N_l) \approx (c/N_l)^{\alpha}\). Furthermore, we also investigate the impact of a fusion mechanism that integrates the user's question with vision tokens. The results reveal two key findings. First, the scaling capability remains intact with the incorporation of the fusion mechanism. Second, the fusion mechanism enhances model performance, particularly when the user's question is task-specific and relevant. The analysis, conducted on fifteen diverse benchmarks spanning a broad range of tasks and domains, validates the effectiveness of the proposed approach.
To address an important gap in creating children's stories for vocabulary enrichment, we investigate the automatic evaluation of how well stories convey the semantics of target vocabulary words, a task with substantial implications for generating educational content. We motivate this task, which we call measuring contextual informativeness in children's stories, and provide a formal task definition as well as a dataset for the task. We further propose a method for automating the task using a large language model (LLM). Our experiments show that our approach reaches a Spearman correlation of 0.4983 with human judgments of informativeness, while the strongest baseline only obtains a correlation of 0.3534. An additional analysis shows that the LLM-based approach is able to generalize to measuring contextual informativeness in adult-directed text, on which it also outperforms all baselines.
Given news articles about an entity, such as a public figure or organization, timeline summarization (TLS) involves generating a timeline that summarizes the key events about the entity. However, the TLS task is too underspecified, since what is of interest to each reader may vary, and hence there is not a single ideal or optimal timeline. In this paper, we introduce a novel task, called Constrained Timeline Summarization (CTLS), where a timeline is generated in which all events in the timeline meet some constraint. An example of a constrained timeline concerns the legal battles of Tiger Woods, where only events related to his legal problems are selected to appear in the timeline. We collected a new human-verified dataset of constrained timelines involving 47 entities and 5 constraints per entity. We propose an approach that employs a large language model (LLM) to summarize news articles according to a specified constraint and cluster them to identify key events to include in a constrained timeline. In addition, we propose a novel self-reflection method during summary generation, demonstrating that this approach successfully leads to improved performance.
Parameter-efficient fine-tuning (PEFT) methods optimize large language models (LLMs) by modifying or introducing a small number of parameters to enhance alignment with downstream tasks. However, they can result in catastrophic forgetting, where LLMs prioritize new knowledge at the expense of comprehensive world knowledge. A promising approach to mitigate this issue is to recall prior memories based on the original knowledge. To this end, we propose a model-agnostic PEFT framework, IMSM, which Interweaves Memories of a Siamese Large Language Model. Specifically, our siamese LLM is equipped with an existing PEFT method. Given an incoming query, it generates two distinct memories based on the pre-trained and fine-tuned parameters. IMSM then incorporates an interweaving mechanism that regulates the contributions of both original and enhanced memories when generating the next token. This framework is theoretically applicable to all open-source LLMs and existing PEFT methods. We conduct extensive experiments across various benchmark datasets, evaluating the performance of popular open-source LLMs using the proposed IMSM, in comparison to both classical and leading PEFT methods. Our findings indicate that IMSM maintains comparable time and space efficiency to backbone PEFT methods while significantly improving performance and effectively mitigating catastrophic forgetting.
Effective pre-training of large language models (LLMs) has been challenging due to the immense resource demands and the complexity of the technical processes involved. This paper presents a detailed technical report on YuLan-Mini, a highly capable base model with 2.42B parameters that achieves top-tier performance among models of similar parameter scale. Our pre-training approach focuses on enhancing training efficacy through three key technical contributions: an elaborate data pipeline combines data cleaning with data schedule strategies, a robust optimization method to mitigate training instability, and an effective annealing approach that incorporates targeted data selection and long context training. Remarkably, YuLan-Mini, trained on 1.08T tokens, achieves performance comparable to industry-leading models that require significantly more data. To facilitate reproduction, we release the full details of the data composition for each training phase. Project details can be accessed at the following link: https://github.com/RUC-GSAI/YuLan-Mini.
Speech brain-computer interfaces aim to decipher what a person is trying to say from neural activity alone, restoring communication to people with paralysis who have lost the ability to speak intelligibly. The Brain-to-Text Benchmark '24 and associated competition was created to foster the advancement of decoding algorithms that convert neural activity to text. Here, we summarize the lessons learned from the competition ending on June 1, 2024 (the top 4 entrants also presented their experiences in a recorded webinar). The largest improvements in accuracy were achieved using an ensembling approach, where the output of multiple independent decoders was merged using a fine-tuned large language model (an approach used by all 3 top entrants). Performance gains were also found by improving how the baseline recurrent neural network (RNN) model was trained, including by optimizing learning rate scheduling and by using a diphone training objective. Improving upon the model architecture itself proved more difficult, however, with attempts to use deep state space models or transformers not yet appearing to offer a benefit over the RNN baseline. The benchmark will remain open indefinitely to support further work towards increasing the accuracy of brain-to-text algorithms.
Despite the recent advancement in Retrieval-Augmented Generation (RAG) systems, most retrieval methodologies are often developed for factual retrieval, which assumes query and positive documents are semantically similar. In this paper, we instead propose and study a more challenging type of retrieval task, called hidden rationale retrieval, in which query and document are not similar but can be inferred by reasoning chains, logic relationships, or empirical experiences. To address such problems, an instruction-tuned Large language model (LLM) with a cross-encoder architecture could be a reasonable choice. To further strengthen pioneering LLM-based retrievers, we design a special instruction that transforms the retrieval task into a generative task by prompting LLM to answer a binary-choice question. The model can be fine-tuned with direct preference optimization (DPO). The framework is also optimized for computational efficiency with no performance degradation. We name this retrieval framework by RaHoRe and verify its zero-shot and fine-tuned performance superiority on Emotional Support Conversation (ESC), compared with previous retrieval works. Our study suggests the potential to employ LLM as a foundation for a wider scope of retrieval tasks. Our codes, models, and datasets are available on https://github.com/flyfree5/LaHoRe.
Video question answering (VideoQA) aims to answer natural language questions according to the given videos. Although existing models perform well in the factoid VideoQA task, they still face challenges in deep video understanding (DVU) task, which focuses on story videos. Compared to factoid videos, the most significant feature of story videos is storylines, which are composed of complex interactions and long-range evolvement of core story topics including characters, actions and locations. Understanding these topics requires models to possess DVU capability. However, existing DVU datasets rarely organize questions according to these story topics, making them difficult to comprehensively assess VideoQA models' DVU capability of complex storylines. Additionally, the question quantity and video length of these dataset are limited by high labor costs of handcrafted dataset building method. In this paper, we devise a large language model based multi-agent collaboration framework, StoryMind, to automatically generate a new large-scale DVU dataset. The dataset, FriendsQA, derived from the renowned sitcom Friends with an average episode length of 1,358 seconds, contains 44.6K questions evenly distributed across 14 fine-grained topics. Finally, We conduct comprehensive experiments on 10 state-of-the-art VideoQA models using the FriendsQA dataset.
The impressive performance of Large Language Model (LLM) has prompted researchers to develop Multi-modal LLM (MLLM), which has shown great potential for various multi-modal tasks. However, current MLLM often struggles to effectively address fine-grained multi-modal challenges. We argue that this limitation is closely linked to the models' visual grounding capabilities. The restricted spatial awareness and perceptual acuity of visual encoders frequently lead to interference from irrelevant background information in images, causing the models to overlook subtle but crucial details. As a result, achieving fine-grained regional visual comprehension becomes difficult. In this paper, we break down multi-modal understanding into two stages, from Coarse to Fine (CoF). In the first stage, we prompt the MLLM to locate the approximate area of the answer. In the second stage, we further enhance the model's focus on relevant areas within the image through visual prompt engineering, adjusting attention weights of pertinent regions. This, in turn, improves both visual grounding and overall performance in downstream tasks. Our experiments show that this approach significantly boosts the performance of baseline models, demonstrating notable generalization and effectiveness. Our CoF approach is available online at https://github.com/Gavin001201/CoF.
During a virus's evolution,various regions of the genome are subjected to distinct levels of functional constraints.Combined with factors like codon bias and DNA repair efficiency,these constraints contribute to unique mutation patterns within the genome or a specific gene. In this project, we harnessed the power of Large Language Models(LLMs) to predict the evolution of SARS-CoV-2. By treating the mutation process from one generation to the next as a translation task, we trained a transformer model, called VirusT5, to capture the mutation patterns underlying SARS-CoV-2 evolution. We evaluated the VirusT5's ability to detect these mutation patterns including its ability to identify mutation hotspots and explored the potential of using VirusT5 to predict future virus variants. Our findings demonstrate the feasibility of using a large language model to model viral evolution as a translation process. This study establishes the groundbreaking concept of "mutation-as-translation," paving the way for new methodologies and tools for combating virus threats
We introduce LLM4AD, a unified Python platform for algorithm design (AD) with large language models (LLMs). LLM4AD is a generic framework with modularized blocks for search methods, algorithm design tasks, and LLM interface. The platform integrates numerous key methods and supports a wide range of algorithm design tasks across various domains including optimization, machine learning, and scientific discovery. We have also designed a unified evaluation sandbox to ensure a secure and robust assessment of algorithms. Additionally, we have compiled a comprehensive suite of support resources, including tutorials, examples, a user manual, online resources, and a dedicated graphical user interface (GUI) to enhance the usage of LLM4AD. We believe this platform will serve as a valuable tool for fostering future development in the merging research direction of LLM-assisted algorithm design.
Retrieval-augmented generation (RAG) helps address the limitations of the parametric knowledge embedded within a language model (LM). However, investigations of how LMs utilise retrieved information of varying complexity in real-world scenarios have been limited to synthetic contexts. We introduce DRUID (Dataset of Retrieved Unreliable, Insufficient and Difficult-to-understand contexts) with real-world queries and contexts manually annotated for stance. The dataset is based on the prototypical task of automated claim verification, for which automated retrieval of real-world evidence is crucial. We compare DRUID to synthetic datasets (CounterFact, ConflictQA) and find that artificial datasets often fail to represent the complex and diverse real-world context settings. We show that synthetic datasets exaggerate context characteristics rare in real retrieved data, which leads to inflated context utilisation results, as measured by our novel ACU score. Moreover, while previous work has mainly focused on singleton context characteristics to explain context utilisation, correlations between singleton context properties and ACU on DRUID are surprisingly small compared to other properties related to context source. Overall, our work underscores the need for real-world aligned context utilisation studies to represent and improve performance in real-world RAG settings.
Preference-based reinforcement learning (PbRL) provides a powerful paradigm to avoid meticulous reward engineering by learning rewards based on human preferences. However, real-time human feedback is hard to obtain in online tasks. Most work suppose there is a "scripted teacher" that utilizes privileged predefined reward to provide preference feedback. In this paper, we propose a RL Self-augmented Large Language Model Feedback (RL-SaLLM-F) technique that does not rely on privileged information for online PbRL. RL-SaLLM-F leverages the reflective and discriminative capabilities of LLM to generate self-augmented trajectories and provide preference labels for reward learning. First, we identify an failure issue in LLM-based preference discrimination, specifically "query ambiguity", in online PbRL. Then LLM is employed to provide preference labels and generate self-augmented imagined trajectories that better achieve the task goal, thereby enhancing the quality and efficiency of feedback. Additionally, a double-check mechanism is introduced to mitigate randomness in the preference labels, improving the reliability of LLM feedback. The experiment across multiple tasks in the MetaWorld benchmark demonstrates the specific contributions of each proposed module in RL-SaLLM-F, and shows that self-augmented LLM feedback can effectively replace the impractical "scripted teacher" feedback. In summary, RL-SaLLM-F introduces a new direction of feedback acquisition in online PbRL that does not rely on any online privileged information, offering an efficient and lightweight solution with LLM-driven feedback.
This paper presents a novel approach to fine-tuning the Qwen2-1.5B model for Arabic language processing using Quantized Low-Rank Adaptation (QLoRA) on a system with only 4GB VRAM. We detail the process of adapting this large language model to the Arabic domain, using diverse datasets including Bactrian, OpenAssistant, and Wikipedia Arabic corpora. Our methodology involves custom data preprocessing, model configuration, and training optimization techniques such as gradient accumulation and mixed-precision training. We address specific challenges in Arabic NLP, including morphological complexity, dialectal variations, and diacritical mark handling. Experimental results over 10,000 training steps show significant performance improvements, with the final loss converging to 0.1083. We provide comprehensive analysis of GPU memory usage, training dynamics, and model evaluation across various Arabic language tasks, including text classification, question answering, and dialect identification. The fine-tuned model demonstrates robustness to input perturbations and improved handling of Arabic-specific linguistic phenomena. This research contributes to multilingual AI by demonstrating a resource-efficient approach for creating specialized language models, potentially democratizing access to advanced NLP technologies for diverse linguistic communities. Our work paves the way for future research in low-resource language adaptation and efficient fine-tuning of large language models.
The rapid development and deployment of large language models (LLMs) have introduced a new frontier in artificial intelligence, marked by unprecedented capabilities in natural language understanding and generation. However, the increasing integration of these models into critical applications raises substantial safety concerns, necessitating a thorough examination of their potential risks and associated mitigation strategies. This survey provides a comprehensive overview of the current landscape of LLM safety, covering four major categories: value misalignment, robustness to adversarial attacks, misuse, and autonomous AI risks. In addition to the comprehensive review of the mitigation methodologies and evaluation resources on these four aspects, we further explore four topics related to LLM safety: the safety implications of LLM agents, the role of interpretability in enhancing LLM safety, the technology roadmaps proposed and abided by a list of AI companies and institutes for LLM safety, and AI governance aimed at LLM safety with discussions on international cooperation, policy proposals, and prospective regulatory directions. Our findings underscore the necessity for a proactive, multifaceted approach to LLM safety, emphasizing the integration of technical solutions, ethical considerations, and robust governance frameworks. This survey is intended to serve as a foundational resource for academy researchers, industry practitioners, and policymakers, offering insights into the challenges and opportunities associated with the safe integration of LLMs into society. Ultimately, it seeks to contribute to the safe and beneficial development of LLMs, aligning with the overarching goal of harnessing AI for societal advancement and well-being. A curated list of related papers has been publicly available at https://github.com/tjunlp-lab/Awesome-LLM-Safety-Papers.
Vision Language Models (VLMs) can be trained more efficiently if training sets can be reduced in size. Recent work has shown the benefits of masking text during VLM training using a variety of approaches: truncation, random masking, block masking and syntax masking. In this paper, we show that the best masking strategy changes over training epochs and that, given sufficient training epochs, word frequency information is what you need to achieve the best performance. Experiments on a large range of data sets demonstrate the advantages of our approach, called Contrastive Language-Image Pre-training with word Frequency Masking (CLIPF). The benefits are particularly evident as the number of input tokens decreases. We analyze the impact of CLIPF vs. other masking approaches on word frequency balance and discuss the apparently critical contribution of CLIPF in maintaining word frequency balance across POS categories.
Problem: Pancreas radiological imaging is challenging due to the small size, blurred boundaries, and variability of shape and position of the organ among patients. Goal: In this work we present MiniGPT-Pancreas, a Multimodal Large Language Model (MLLM), as an interactive chatbot to support clinicians in pancreas cancer diagnosis by integrating visual and textual information. Methods: MiniGPT-v2, a general-purpose MLLM, was fine-tuned in a cascaded way for pancreas detection, tumor classification, and tumor detection with multimodal prompts combining questions and computed tomography scans from the National Institute of Health (NIH), and Medical Segmentation Decathlon (MSD) datasets. The AbdomenCT-1k dataset was used to detect the liver, spleen, kidney, and pancreas. Results: MiniGPT-Pancreas achieved an Intersection over Union (IoU) of 0.595 and 0.550 for the detection of pancreas on NIH and MSD datasets, respectively. For the pancreas cancer classification task on the MSD dataset, accuracy, precision, and recall were 0.876, 0.874, and 0.878, respectively. When evaluating MiniGPT-Pancreas on the AbdomenCT-1k dataset for multi-organ detection, the IoU was 0.8399 for the liver, 0.722 for the kidney, 0.705 for the spleen, and 0.497 for the pancreas. For the pancreas tumor detection task, the IoU score was 0.168 on the MSD dataset. Conclusions: MiniGPT-Pancreas represents a promising solution to support clinicians in the classification of pancreas images with pancreas tumors. Future research is needed to improve the score on the detection task, especially for pancreas tumors.