Gene-Metabolite Association Prediction with Interactive Knowledge Transfer Enhanced Graph for Metabolite Production

In the rapidly evolving field of metabolic engineering, the quest for efficient and precise gene target identification for metabolite production enhancement presents significant challenges. Traditional approaches, whether knowledge-based or model-based, are notably time-consuming and labor-intensive, due to the vast scale of research literature and the approximation nature of genome-scale metabolic model (GEM) simulations. Therefore, we propose a new task, Gene-Metabolite Association Prediction based on metabolic graphs, to automate the process of candidate gene discovery for a given pair of metabolite and candidate-associated genes, as well as presenting the first benchmark containing 2474 metabolites and 1947 genes of two commonly used microorganisms Saccharomyces cerevisiae (SC) and Issatchenkia orientalis (IO). This task is challenging due to the incompleteness of the metabolic graphs and the heterogeneity among distinct metabolisms. To overcome these limitations, we propose an Interactive Knowledge Transfer mechanism based on Metabolism Graph (IKT4Meta), which improves the association prediction accuracy by integrating the knowledge from different metabolism graphs. First, to build a bridge between two graphs for knowledge transfer, we utilize Pretrained Language Models (PLMs) with external knowledge of genes and metabolites to help generate inter-graph links, significantly alleviating the impact of heterogeneity. Second, we propagate intra-graph links from different metabolic graphs using inter-graph links as anchors. Finally, we conduct the gene-metabolite association prediction based on the enriched metabolism graphs, which integrate the knowledge from multiple microorganisms. Experiments on both types of organisms demonstrate that our proposed methodology outperforms baselines by up to 12.3% across various link prediction frameworks.

Knowledge Overshadowing Causes Amalgamated Hallucination in Large Language Models

Hallucination is often regarded as a major impediment for using large language models (LLMs), especially for knowledge-intensive tasks. Even when the training corpus consists solely of true statements, language models still generate hallucinations in the form of amalgamations of multiple facts. We coin this phenomenon as ``knowledge overshadowing'': when we query knowledge from a language model with multiple conditions, some conditions overshadow others, leading to hallucinated outputs. This phenomenon partially stems from training data imbalance, which we verify on both pretrained models and fine-tuned models, over a wide range of LM model families and sizes.From a theoretical point of view, knowledge overshadowing can be interpreted as over-generalization of the dominant conditions (patterns). We show that the hallucination rate grows with both the imbalance ratio (between the popular and unpopular condition) and the length of dominant condition description, consistent with our derived generalization bound. Finally, we propose to utilize overshadowing conditions as a signal to catch hallucination before it is produced, along with a training-free self-contrastive decoding method to alleviate hallucination during inference. Our proposed approach showcases up to 82% F1 for hallucination anticipation and 11.2% to 39.4% hallucination control, with different models and datasets.

EVEDIT: Event-based Knowledge Editing with Deductive Editing Boundaries

The dynamic nature of real-world information necessitates efficient knowledge editing (KE) in large language models (LLMs) for knowledge updating. However, current KE approaches, which typically operate on (subject, relation, object) triples, ignore the contextual information and the relation among different knowledge. Such editing methods could thus encounter an uncertain editing boundary, leaving a lot of relevant knowledge in ambiguity: Queries that could be answered pre-edit cannot be reliably answered afterward. In this work, we analyze this issue by introducing a theoretical framework for KE that highlights an overlooked set of knowledge that remains unchanged and aids in knowledge deduction during editing, which we name as the deduction anchor. We further address this issue by proposing a novel task of event-based knowledge editing that pairs facts with event descriptions. This task manifests not only a closer simulation of real-world editing scenarios but also a more logically sound setting, implicitly defining the deduction anchor to address the issue of indeterminate editing boundaries. We empirically demonstrate the superiority of event-based editing over the existing setting on resolving uncertainty in edited models, and curate a new benchmark dataset EvEdit derived from the CounterFact dataset. Moreover, while we observe that the event-based setting is significantly challenging for existing approaches, we propose a novel approach Self-Edit that showcases stronger performance, achieving 55.6% consistency improvement while maintaining the naturalness of generation.

MuChin: A Chinese Colloquial Description Benchmark for Evaluating Language Models in the Field of Music

The rapidly evolving multimodal Large Language Models (LLMs) urgently require new benchmarks to uniformly evaluate their performance on understanding and textually describing music. However, due to semantic gaps between Music Information Retrieval (MIR) algorithms and human understanding, discrepancies between professionals and the public, and low precision of annotations, existing music description datasets cannot serve as benchmarks. To this end, we present MuChin, the first open-source music description benchmark in Chinese colloquial language, designed to evaluate the performance of multimodal LLMs in understanding and describing music. We established the Caichong Music Annotation Platform (CaiMAP) that employs an innovative multi-person, multi-stage assurance method, and recruited both amateurs and professionals to ensure the precision of annotations and alignment with popular semantics. Utilizing this method, we built a dataset with multi-dimensional, high-precision music annotations, the Caichong Music Dataset (CaiMD), and carefully selected 1,000 high-quality entries to serve as the test set for MuChin. Based on MuChin, we analyzed the discrepancies between professionals and amateurs in terms of music description, and empirically demonstrated the effectiveness of annotated data for fine-tuning LLMs. Ultimately, we employed MuChin to evaluate existing music understanding models on their ability to provide colloquial descriptions of music. All data related to the benchmark and the code for scoring have been open-sourced.

PET Tracer Conversion among Brain PET via Variable Augmented Invertible Network

Positron emission tomography (PET) serves as an essential tool for diagnosis of encephalopathy and brain science research. However, it suffers from the limited choice of tracers. Nowadays, with the wide application of PET imaging in neuropsychiatric treatment, 6-18F-fluoro-3, 4-dihydroxy-L-phenylalanine (DOPA) has been found to be more effective than 18F-labeled fluorine-2-deoxyglucose (FDG) in the field. Nevertheless, due to the complexity of its preparation and other limitations, DOPA is far less widely used than FDG. To address this issue, a tracer conversion invertible neural network (TC-INN) for image projection is developed to map FDG images to DOPA images through deep learning. More diagnostic information is obtained by generating PET images from FDG to DOPA. Specifically, the proposed TC-INN consists of two separate phases, one for training traceable data, the other for rebuilding new data. The reference DOPA PET image is used as a learning target for the corresponding network during the training process of tracer conversion. Meanwhile, the invertible network iteratively estimates the resultant DOPA PET data and compares it to the reference DOPA PET data. Notably, the reversible model employs variable enhancement technique to achieve better power generation. Moreover, image registration needs to be performed before training due to the angular deviation of the acquired FDG and DOPA data information. Experimental results exhibited excellent generation capability in mapping between FDG and DOPA, suggesting that PET tracer conversion has great potential in the case of limited tracer applications.

Defining a New NLP Playground

The recent explosion of performance of large language models (LLMs) has changed the field of Natural Language Processing (NLP) more abruptly and seismically than any other shift in the field's 80-year history. This has resulted in concerns that the field will become homogenized and resource-intensive. The new status quo has put many academic researchers, especially PhD students, at a disadvantage. This paper aims to define a new NLP playground by proposing 20+ PhD-dissertation-worthy research directions, covering theoretical analysis, new and challenging problems, learning paradigms, and interdisciplinary applications.

Self Information Update for Large Language Models through Mitigating Exposure Bias

Current LLMs have demonstrated remarkable capabilities in addressing users' requests for various types of information. However, these models are limited by the most recent data available in their pretraining corpora, rendering them incapable of providing up-to-date information. Retraining LLMs from scratch is cost-prohibitive, and the effectiveness of continual fine-tuning on new corpora has not been thoroughly examined. Additionally, current update procedures typically demand significant human input to prepare the information into more structured format, such as knowledge triples, conversational data or responses with human feedback. In this study, we conduct a comprehensive examination of a novel self information update task in LLMs, which only requires the provision of informative text corpora. For instance, we can use the latest news articles to update the LLMs' existing knowledge. We define the self information update task and assess the continual fine-tuning approach for this purpose. We observe that the naive method of continual fine-tuning can be problematic due to LLMs' exposure bias, which prioritizes existing information over new information we aim to integrate and leads to incorrect reasoning chains that ultimately diminish the efficacy of information updates. Based on our analysis, we propose an effective method to mitigate exposure bias by incorporating the selection of relevant facts into training losses. Furthermore, we develop a dataset to evaluate information updates, derived from news articles published after March 2023. Experimental results demonstrate that our proposed approach significantly increases the factual consistency score (0 to 1) by 0.16 while having minimal impact on performance for instructions not directly related to the new information.

RCOT: Detecting and Rectifying Factual Inconsistency in Reasoning by Reversing Chain-of-Thought

Large language Models (LLMs) have achieved promising performance on arithmetic reasoning tasks by incorporating step-by-step chain-of-thought (CoT) prompting. However, LLMs face challenges in maintaining factual consistency during reasoning, exhibiting tendencies to condition overlooking, question misinterpretation, and condition hallucination over given problems. Existing methods use coarse-grained feedback (e.g., whether the answer is correct) to improve factual consistency. In this work, we propose RCoT (Reversing Chain-of-Thought), a novel method to improve LLMs' reasoning abilities by automatically detecting and rectifying factual inconsistency in LLMs' generated solutions. To detect factual inconsistency, RCoT first asks LLMs to reconstruct the problem based on generated solutions. Then fine-grained comparisons between the original problem and the reconstructed problem expose the factual inconsistency in the original solutions. To rectify the solution, RCoT formulates detected factual inconsistency into fine-grained feedback to guide LLMs in revising solutions. Experimental results demonstrate consistent improvements of RCoT over standard CoT across seven arithmetic datasets. Moreover, we find that manually written fine-grained feedback can dramatically improve LLMs' reasoning abilities (e.g., ChatGPT reaches 94.6% accuracy on GSM8K), encouraging the community to further explore the fine-grained feedback generation methods.

SongDriver: Real-time Music Accompaniment Generation without Logical Latency nor Exposure Bias

Real-time music accompaniment generation has a wide range of applications in the music industry, such as music education and live performances. However, automatic real-time music accompaniment generation is still understudied and often faces a trade-off between logical latency and exposure bias. In this paper, we propose SongDriver, a real-time music accompaniment generation system without logical latency nor exposure bias. Specifically, SongDriver divides one accompaniment generation task into two phases: 1) The arrangement phase, where a Transformer model first arranges chords for input melodies in real-time, and caches the chords for the next phase instead of playing them out. 2) The prediction phase, where a CRF model generates playable multi-track accompaniments for the coming melodies based on previously cached chords. With this two-phase strategy, SongDriver directly generates the accompaniment for the upcoming melody, achieving zero logical latency. Furthermore, when predicting chords for a timestep, SongDriver refers to the cached chords from the first phase rather than its previous predictions, which avoids the exposure bias problem. Since the input length is often constrained under real-time conditions, another potential problem is the loss of long-term sequential information. To make up for this disadvantage, we extract four musical features from a long-term music piece before the current time step as global information. In the experiment, we train SongDriver on some open-source datasets and an original \`aiSong Dataset built from Chinese-style modern pop music scores. The results show that SongDriver outperforms existing SOTA (state-of-the-art) models on both objective and subjective metrics, meanwhile significantly reducing the physical latency.

MUSE: Illustrating Textual Attributes by Portrait Generation

We propose a novel approach, MUSE, to illustrate textual attributes visually via portrait generation. MUSE takes a set of attributes written in text, in addition to facial features extracted from a photo of the subject as input. We propose 11 attribute types to represent inspirations from a subject's profile, emotion, story, and environment. We propose a novel stacked neural network architecture by extending an image-to-image generative model to accept textual attributes. Experiments show that our approach significantly outperforms several state-of-the-art methods without using textual attributes, with Inception Score score increased by 6% and Fr\'echet Inception Distance (FID) score decreased by 11%, respectively. We also propose a new attribute reconstruction metric to evaluate whether the generated portraits preserve the subject's attributes. Experiments show that our approach can accurately illustrate 78% textual attributes, which also help MUSE capture the subject in a more creative and expressive way.