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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., Comment: 10 PAGES, 4 FIGURES; bibm 2024

Complex news events, such as natural disasters and socio-political conflicts, require swift responses from the government and society. Relying on historical events to project the future is insufficient as such events are sparse and do not cover all possible conditions and nuanced situations. Simulation of these complex events can help better prepare and reduce the negative impact. We develop a controllable complex news event simulator guided by both the event schema representing domain knowledge about the scenario and user-provided assumptions representing case-specific conditions. As event dynamics depend on the fine-grained social and cultural context, we further introduce a geo-diverse commonsense and cultural norm-aware knowledge enhancement component. To enhance the coherence of the simulation, apart from the global timeline of events, we take an agent-based approach to simulate the individual character states, plans, and actions. By incorporating the schema and cultural norms, our generated simulations achieve much higher coherence and appropriateness and are received favorably by participants from a humanitarian assistance organization., Comment: Accepted as EMNLP 2024 Demo

Mental health disorders are one of the most serious diseases in the world. Most people with such a disease lack access to adequate care, which highlights the importance of training models for the diagnosis and treatment of mental health disorders. However, in the mental health domain, privacy concerns limit the accessibility of personalized treatment data, making it challenging to build powerful models. In this paper, we introduce MentalArena, a self-play framework to train language models by generating domain-specific personalized data, where we obtain a better model capable of making a personalized diagnosis and treatment (as a therapist) and providing information (as a patient). To accurately model human-like mental health patients, we devise Symptom Encoder, which simulates a real patient from both cognition and behavior perspectives. To address intent bias during patient-therapist interactions, we propose Symptom Decoder to compare diagnosed symptoms with encoded symptoms, and dynamically manage the dialogue between patient and therapist according to the identified deviations. We evaluated MentalArena against 6 benchmarks, including biomedicalQA and mental health tasks, compared to 6 advanced models. Our models, fine-tuned on both GPT-3.5 and Llama-3-8b, significantly outperform their counterparts, including GPT-4o. We hope that our work can inspire future research on personalized care. Code is available in https://github.com/Scarelette/MentalArena/tree/main, Comment: Technical Report; 27 pages

While Vision-Language Models (VLMs) have shown remarkable abilities in visual and language reasoning tasks, they invariably generate flawed responses. Self-correction that instructs models to refine their outputs presents a promising solution to this issue. Previous studies have mainly concentrated on Large Language Models (LLMs), while the self-correction abilities of VLMs, particularly concerning both visual and linguistic information, remain largely unexamined. This study investigates the self-correction capabilities of VLMs during both inference and fine-tuning stages. We introduce a Self-Correction Learning (SCL) approach that enables VLMs to learn from their self-generated self-correction data through Direct Preference Optimization (DPO) without relying on external feedback, facilitating self-improvement. Specifically, we collect preferred and disfavored samples based on the correctness of initial and refined responses, which are obtained by two-turn self-correction with VLMs during the inference stage. Experimental results demonstrate that although VLMs struggle to self-correct effectively during iterative inference without additional fine-tuning and external feedback, they can enhance their performance and avoid previous mistakes through preference fine-tuning when their self-generated self-correction data are categorized into preferred and disfavored samples. This study emphasizes that self-correction is not merely a refinement process; rather, it should enhance the reasoning abilities of models through additional training, enabling them to generate high-quality responses directly without further refinement.

This paper investigates data-driven cooperative output regulation for continuous-time multi-agent systems with unknown network topology. Unlike existing studies that typically assume a known network topology to directly compute controller parameters, a novel approach is proposed that allows for the computation of the parameter without prior knowledge of the topology. A lower bound on the minimum non-zero eigenvalue of the Laplacian matrix is estimated using only edge weight bounds, enabling the output regulation controller design to be independent of global network information. Additionally, the common need for state derivative measurements is eliminated, reducing the amount of data requirements. Furthermore, necessary and sufficient conditions are established to ensure that the data are informative for cooperative output regulation, leading to the design of a distributed output regulation controller. For the case with noisy data, the bound of the output error is provided, which is positively correlated with the noise bound, and a distributed controller is constructed for the approximate cooperative output regulation. Finally, the effectiveness of the proposed methods is verified through numerical simulations.

Pose skeleton images are an important reference in pose-controllable image generation. In order to enrich the source of skeleton images, recent works have investigated the generation of pose skeletons based on natural language. These methods are based on GANs. However, it remains challenging to perform diverse, structurally correct and aesthetically pleasing human pose skeleton generation with various textual inputs. To address this problem, we propose a framework with GUNet as the main model, PoseDiffusion. It is the first generative framework based on a diffusion model and also contains a series of variants fine-tuned based on a stable diffusion model. PoseDiffusion demonstrates several desired properties that outperform existing methods. 1) Correct Skeletons. GUNet, a denoising model of PoseDiffusion, is designed to incorporate graphical convolutional neural networks. It is able to learn the spatial relationships of the human skeleton by introducing skeletal information during the training process. 2) Diversity. We decouple the key points of the skeleton and characterise them separately, and use cross-attention to introduce textual conditions. Experimental results show that PoseDiffusion outperforms existing SoTA algorithms in terms of stability and diversity of text-driven pose skeleton generation. Qualitative analyses further demonstrate its superiority for controllable generation in Stable Diffusion.

Machine learning research, crucial for technological advancements and innovation, often faces significant challenges due to its inherent complexity, slow pace of experimentation, and the necessity for specialized expertise. Motivated by this, we present a new systematic framework, autonomous Machine Learning Research with large language models (MLR-Copilot), designed to enhance machine learning research productivity through the automatic generation and implementation of research ideas using Large Language Model (LLM) agents. The framework consists of three phases: research idea generation, experiment implementation, and implementation execution. First, existing research papers are used to generate hypotheses and experimental plans vis IdeaAgent powered by LLMs. Next, the implementation generation phase translates these plans into executables with ExperimentAgent. This phase leverages retrieved prototype code and optionally retrieves candidate models and data. Finally, the execution phase, also managed by ExperimentAgent, involves running experiments with mechanisms for human feedback and iterative debugging to enhance the likelihood of achieving executable research outcomes. We evaluate our framework on five machine learning research tasks and the experimental results show the framework's potential to facilitate the research progress and innovations.

To address the challenge of automating knowledge discovery from a vast volume of literature, in this paper, we introduce a novel framework based on large language models (LLMs) that combines a progressive ontology prompting (POP) algorithm with a dual-agent system, named LLM-Duo, designed to enhance the automation of knowledge extraction from scientific articles. The POP algorithm utilizes a prioritized breadth-first search (BFS) across a predefined ontology to generate structured prompt templates and action orders, thereby guiding LLMs to discover knowledge in an automatic manner. Additionally, our LLM-Duo employs two specialized LLM agents: an explorer and an evaluator. These two agents work collaboratively and adversarially to enhance the reliability of the discovery and annotation processes. Experiments demonstrate that our method outperforms advanced baselines, enabling more accurate and complete annotations. To validate the effectiveness of our method in real-world scenarios, we employ our method in a case study of speech-language intervention discovery. Our method identifies 2,421 interventions from 64,177 research articles in the speech-language therapy domain. We curate these findings into a publicly accessible intervention knowledge base that holds significant potential to benefit the speech-language therapy community., Comment: in submission

Language-molecule models have emerged as an exciting direction for molecular discovery and understanding. However, training these models is challenging due to the scarcity of molecule-language pair datasets. At this point, datasets have been released which are 1) small and scraped from existing databases, 2) large but noisy and constructed by performing entity linking on the scientific literature, and 3) built by converting property prediction datasets to natural language using templates. In this document, we detail the $\textit{L+M-24}$ dataset, which has been created for the Language + Molecules Workshop shared task at ACL 2024. In particular, $\textit{L+M-24}$ is designed to focus on three key benefits of natural language in molecule design: compositionality, functionality, and abstraction., Comment: The dataset, finetuned baselines, and evaluation code are released publicly at https://github.com/language-plus-molecules/LPM-24-Dataset through https://huggingface.co/language-plus-molecules

Fine-grained few-shot entity extraction in the chemical domain faces two unique challenges. First, compared with entity extraction tasks in the general domain, sentences from chemical papers usually contain more entities. Moreover, entity extraction models usually have difficulty extracting entities of long-tailed types. In this paper, we propose Chem-FINESE, a novel sequence-to-sequence (seq2seq) based few-shot entity extraction approach, to address these two challenges. Our Chem-FINESE has two components: a seq2seq entity extractor to extract named entities from the input sentence and a seq2seq self-validation module to reconstruct the original input sentence from extracted entities. Inspired by the fact that a good entity extraction system needs to extract entities faithfully, our new self-validation module leverages entity extraction results to reconstruct the original input sentence. Besides, we design a new contrastive loss to reduce excessive copying during the extraction process. Finally, we release ChemNER+, a new fine-grained chemical entity extraction dataset that is annotated by domain experts with the ChemNER schema. Experiments in few-shot settings with both ChemNER+ and CHEMET datasets show that our newly proposed framework has contributed up to 8.26% and 6.84% absolute F1-score gains respectively., Comment: 16 pages. Accepted by Findings of the Association for Computational Linguistics: EACL 2024. Code and resources are available at https://github.com/EagleW/Chem-FINESE

Named entity recognition is a key component of Information Extraction (IE), particularly in scientific domains such as biomedicine and chemistry, where large language models (LLMs), e.g., ChatGPT, fall short. We investigate the applicability of transfer learning for enhancing a named entity recognition model trained in the biomedical domain (the source domain) to be used in the chemical domain (the target domain). A common practice for training such a model in a few-shot learning setting is to pretrain the model on the labeled source data, and then, to finetune it on a hand-full of labeled target examples. In our experiments, we observed that such a model is prone to mislabeling the source entities, which can often appear in the text, as the target entities. To alleviate this problem, we propose a model to transfer the knowledge from the source domain to the target domain, but, at the same time, to project the source entities and target entities into separate regions of the feature space. This diminishes the risk of mislabeling the source entities as the target entities. Our model consists of two stages: 1) entity grouping in the source domain, which incorporates knowledge from annotated events to establish relations between entities, and 2) entity discrimination in the target domain, which relies on pseudo labeling and contrastive learning to enhance discrimination between the entities in the two domains. We conduct our extensive experiments across three source and three target datasets, demonstrating that our method outperforms the baselines by up to 5% absolute value., Comment: 21 pages; Accepted by the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies; Code, data, and resources are publicly available for research purposes: https://github.com/Lhtie/Bio-Domain-Transfer

We explore and enhance the ability of neural language models to generate novel scientific directions grounded in literature. Work on literature-based hypothesis generation has traditionally focused on binary link prediction--severely limiting the expressivity of hypotheses. This line of work also does not focus on optimizing novelty. We take a dramatic departure with a novel setting in which models use as input background contexts (e.g., problems, experimental settings, goals), and output natural language ideas grounded in literature. We present SciMON, a modeling framework that uses retrieval of "inspirations" from past scientific papers, and explicitly optimizes for novelty by iteratively comparing to prior papers and updating idea suggestions until sufficient novelty is achieved. Comprehensive evaluations reveal that GPT-4 tends to generate ideas with overall low technical depth and novelty, while our methods partially mitigate this issue. Our work represents a first step toward evaluating and developing language models that generate new ideas derived from the scientific literature, Comment: 21 pages. Code and resource are available at https://github.com/EagleW/CLBD Accepted by the 62nd Annual Meeting of the Association for Computational Linguistics (ACL 2024)

Electroweak baryogenesis (EWBG) offers a compelling narrative for the generation of the baryon asymmetry, however it cannot be realised in the Standard Model, and leads to severe experimental tensions in the Minimal Supersymmetric Standard Model (MSSM). One of the reasons for these experimental tensions is that in traditional approaches to EWBG new physics is required to enter at the electroweak phase transition, which conventionally is fixed near $\sim$100 GeV. Here we demonstrate that the addition of sub-TeV fields in supersymmetric extensions of the Standard Model permits TeV-scale strongly first-order electroweak phase transition. While earlier literature suggested no-go arguments with regards to high-temperature symmetry breaking in supersymmetric models, we show these can be evaded by employing a systematic suppression of certain thermal corrections in theories with a large number of states. The models presented push the new physics needed for EWBG to higher scales, hence presenting new parameter regions in which to realize EWBG and evade experimental tensions, however they are not expected to render EWBG completely outside of the foreseeable future experimental reach., Comment: version accepted for publication in JHEP

Goal-oriented generative script learning aims to generate subsequent steps to reach a particular goal, which is an essential task to assist robots or humans in performing stereotypical activities. An important aspect of this process is the ability to capture historical states visually, which provides detailed information that is not covered by text and will guide subsequent steps. Therefore, we propose a new task, Multimedia Generative Script Learning, to generate subsequent steps by tracking historical states in both text and vision modalities, as well as presenting the first benchmark containing 5,652 tasks and 79,089 multimedia steps. This task is challenging in three aspects: the multimedia challenge of capturing the visual states in images, the induction challenge of performing unseen tasks, and the diversity challenge of covering different information in individual steps. We propose to encode visual state changes through a selective multimedia encoder to address the multimedia challenge, transfer knowledge from previously observed tasks using a retrieval-augmented decoder to overcome the induction challenge, and further present distinct information at each step by optimizing a diversity-oriented contrastive learning objective. We define metrics to evaluate both generation and inductive quality. Experiment results demonstrate that our approach significantly outperforms strong baselines., Comment: 21 pages, Accepted by Findings of the Association for Computational Linguistics: ACL 2023, Code and Resources at https://github.com/EagleW/Multimedia-Generative-Script-Learning

In this paper, the possibility of detecting topological variations by observing output trajectories from networked linear time-invariant systems is investigated, where the network topology can be general, but the nodes have identical higher-dimensional dynamics. A necessary and sufficient condition on the discernibility of topological variations is derived, in terms of the eigenspaces of the original and the modified network configuarations. By taking the specific network structures into consideration, some lower-dimensional conditions are derived, which reveal how the network topologies, sensor locations, node-system dynamics and output, as well as inner interactions altogether affect the discernibility. Furthermore, the output discernibility of topological changes for networked multi-agent systems is revisited, showing that some criterion reported in the literature does not hold. Consequently, a modified necessary and sufficient condition is established. The effectiveness of the results is demonstrated through several examples.

This paper studies the long-term migration of disturbed regolith materials on the surface of Solar System small bodies from the viewpoint of nonlinear dynamics. We propose an approximation model for secular mass movement, which combines the complex topography and irregular gravitational field. Choosing asteroid 101955 Bennu as a representative, the global change of the dynamical environment is examined, which presents a division of the creeping-sliding-shedding regions for a spun-up asteroid. In the creeping region, the dynamical equation of disturbed regolith grains is established based on the assumption of "trigger-slide" motion mode. The equilibrium points, local manifolds and large-scale trajectories of the system are calculated to clarify the dynamical characteristics of long-term regolith movement. Generally, we find for a low spin rate, the surface regolith grains flow toward the middle latitudes from the polar/equatorial regions, which is dominated by the gradient of the geopotential. While spun up to a high rate, regolith grains tend to migrate toward the equator, which happens in parallel with a topological shift of the local equilibria at low latitudes. From a long-term perspective, we find the equilibrium points dominate the global trends of regolith movements. Using the methodology developed in this paper, we give a prospect or retrospect to the secular motion of regolith materials during the spin-up process, and the results reveal a significant regulatory role of the equilibria. Through a detailed look at the dynamical scheme under different spin rates, we achieve a macro forecast of the global trends of regolith motion during the spin-up process, which explains the global geologic evolution driven by the long-term movements of regolith materials.

Restoration of the electroweak symmetry at temperatures around the Higgs mass is linked to tight phenomenological constraints on many baryogenesis scenarios. A potential remedy can be found in mechanisms of electroweak symmetry non-restoration (SNR), in which symmetry breaking is extended to higher temperatures due to new states with couplings to the Standard Model. Here we show that, in the presence of a second Higgs doublet, SNR can be realized with only a handful of new fermions which can be identified as viable dark matter candidates consistent with all current observational constraints. The competing requirements on this class of models allow for SNR at temperatures up to $\sim$TeV, and imply the presence of sub-TeV new physics with sizable interactions with the Standard Model. As a result this scenario is highly testable with signals in reach of next-generation collider and dark matter direct detection experiments., Comment: 26 pages, 10 Figures, v2: matches version published in JHEP

Graph-to-text generation has benefited from pre-trained language models (PLMs) in achieving better performance than structured graph encoders. However, they fail to fully utilize the structure information of the input graph. In this paper, we aim to further improve the performance of the pre-trained language model by proposing a structured graph-to-text model with a two-step fine-tuning mechanism which first fine-tunes the model on Wikipedia before adapting to the graph-to-text generation. In addition to using the traditional token and position embeddings to encode the knowledge graph (KG), we propose a novel tree-level embedding method to capture the inter-dependency structures of the input graph. This new approach has significantly improved the performance of all text generation metrics for the English WebNLG 2017 dataset., Comment: 10 pages, Accepted by Proceedings of ACL-IJCNLP 2021 Student Research Workshop, Code and Resources at https://github.com/EagleW/Stage-wise-Fine-tuning