arXiv subjects

Zhiqiang Hu

Publications and source records attributed to Zhiqiang Hu.

At least 37 records · Page 2Linked to original sources

arXiv2025

Rethinking the generalization of drug target affinity prediction algorithms via similarity aware evaluation

Drug-target binding affinity prediction is a fundamental task for drug discovery. It has been extensively explored in literature and promising results are reported. However, in this paper, we demonstrate that the results may be misleading and cannot be well generalized to real practice. The core observation is that the canonical randomized split of a test set in conventional evaluation leaves the test set dominated by samples with high similarity to the training set. The performance of models is severely degraded on samples with lower similarity to the training set but the drawback is highly overlooked in current evaluation. As a result, the performance can hardly be trusted when the model meets low-similarity samples in real practice. To address this problem, we propose a framework of similarity aware evaluation in which a novel split methodology is proposed to adapt to any desired distribution. This is achieved by a formulation of optimization problems which are approximately and efficiently solved by gradient descent. We perform extensive experiments across five representative methods in four datasets for two typical target evaluations and compare them with various counterpart methods. Results demonstrate that the proposed split methodology can significantly better fit desired distributions and guide the development of models. Code is released at https://github.com/Amshoreline/SAE/tree/main.

cs.LG↗

arXiv2024

Pro-PRIME: A general Temperature-Guided Language model to engineer enhanced Stability and Activity in Proteins

Designing protein mutants of both high stability and activity is a critical yet challenging task in protein engineering. Here, we introduce PRIME, a deep learning model, which can suggest protein mutants of improved stability and activity without any prior experimental mutagenesis data of the specified protein. Leveraging temperature-aware language modeling, PRIME demonstrated superior predictive power compared to current state-of-the-art models on the public mutagenesis dataset over 283 protein assays. Furthermore, we validated PRIME's predictions on five proteins, examining the top 30-45 single-site mutations' impact on various protein properties, including thermal stability, antigen-antibody binding affinity, and the ability to polymerize non-natural nucleic acid or resilience to extreme alkaline conditions. Remarkably, over 30% of the AI-recommended mutants exhibited superior performance compared to their pre-mutation counterparts across all proteins and desired properties. Moreover, we have developed an efficient, and successful method based on PRIME to rapidly obtain multi-site mutants with enhanced activity and stability. Hence, PRIME demonstrates the general applicability in protein engineering.

q-bio.BM↗

arXiv2024

Breaking the Memory Barrier: Near Infinite Batch Size Scaling for Contrastive Loss

Contrastive loss is a powerful approach for representation learning, where larger batch sizes enhance performance by providing more negative samples to better distinguish between similar and dissimilar data. However, scaling batch sizes is constrained by the quadratic growth in GPU memory consumption, primarily due to the full instantiation of the similarity matrix. To address this, we propose a tile-based computation strategy that partitions the contrastive loss calculation into arbitrary small blocks, avoiding full materialization of the similarity matrix. Furthermore, we introduce a multi-level tiling strategy to leverage the hierarchical structure of distributed systems, employing ring-based communication at the GPU level to optimize synchronization and fused kernels at the CUDA core level to reduce I/O overhead. Experimental results show that the proposed method scales batch sizes to unprecedented levels. For instance, it enables contrastive training of a CLIP-ViT-L/14 model with a batch size of 4M or 12M using 8 or 32 A800 80GB without sacrificing any accuracy. Compared to SOTA memory-efficient solutions, it achieves a two-order-of-magnitude reduction in memory while maintaining comparable speed. The code will be made publicly available.

cs.CV↗

arXiv2024

LLM-Based Agent Society Investigation: Collaboration and Confrontation in Avalon Gameplay

This paper explores the open research problem of understanding the social behaviors of LLM-based agents. Using Avalon as a testbed, we employ system prompts to guide LLM agents in gameplay. While previous studies have touched on gameplay with LLM agents, research on their social behaviors is lacking. We propose a novel framework, tailored for Avalon, features a multi-agent system facilitating efficient communication and interaction. We evaluate its performance based on game success and analyze LLM agents' social behaviors. Results affirm the framework's effectiveness in creating adaptive agents and suggest LLM-based agents' potential in navigating dynamic social interactions. By examining collaboration and confrontation behaviors, we offer insights into this field's research and applications. Our code is publicly available at https://github.com/3DAgentWorld/LLM-Game-Agent.

cs.CL↗

arXiv2024

Math-LLaVA: Bootstrapping Mathematical Reasoning for Multimodal Large Language Models

Large language models (LLMs) have demonstrated impressive reasoning capabilities, particularly in textual mathematical problem-solving. However, existing open-source image instruction fine-tuning datasets, containing limited question-answer pairs per image, do not fully exploit visual information to enhance the multimodal mathematical reasoning capabilities of Multimodal LLMs (MLLMs). To bridge this gap, we address the lack of high-quality, diverse multimodal mathematical datasets by collecting 40K high-quality images with question-answer pairs from 24 existing datasets and synthesizing 320K new pairs, creating the MathV360K dataset, which enhances both the breadth and depth of multimodal mathematical questions. We introduce Math-LLaVA, a LLaVA-1.5-based model fine-tuned with MathV360K. This novel approach significantly improves the multimodal mathematical reasoning capabilities of LLaVA-1.5, achieving a 19-point increase and comparable performance to GPT-4V on MathVista's minitest split, and yielding leading performance on Math-V and MathVerse. Furthermore, Math-LLaVA demonstrates enhanced generalizability, showing substantial improvements on the MMMU benchmark. Our research highlights the importance of dataset diversity and synthesis in advancing MLLMs' mathematical reasoning abilities. The code and data are available at: \url{https://github.com/HZQ950419/Math-LLaVA}.

cs.CL↗

arXiv2024

GalleryGPT: Analyzing Paintings with Large Multimodal Models

Artwork analysis is important and fundamental skill for art appreciation, which could enrich personal aesthetic sensibility and facilitate the critical thinking ability. Understanding artworks is challenging due to its subjective nature, diverse interpretations, and complex visual elements, requiring expertise in art history, cultural background, and aesthetic theory. However, limited by the data collection and model ability, previous works for automatically analyzing artworks mainly focus on classification, retrieval, and other simple tasks, which is far from the goal of AI. To facilitate the research progress, in this paper, we step further to compose comprehensive analysis inspired by the remarkable perception and generation ability of large multimodal models. Specifically, we first propose a task of composing paragraph analysis for artworks, i.e., painting in this paper, only focusing on visual characteristics to formulate more comprehensive understanding of artworks. To support the research on formal analysis, we collect a large dataset PaintingForm, with about 19k painting images and 50k analysis paragraphs. We further introduce a superior large multimodal model for painting analysis composing, dubbed GalleryGPT, which is slightly modified and fine-tuned based on LLaVA architecture leveraging our collected data. We conduct formal analysis generation and zero-shot experiments across several datasets to assess the capacity of our model. The results show remarkable performance improvements comparing with powerful baseline LMMs, demonstrating its superb ability of art analysis and generalization. \textcolor{blue}{The codes and model are available at: https://github.com/steven640pixel/GalleryGPT.

cs.CL↗

arXiv2024

SeaLLMs 3: Open Foundation and Chat Multilingual Large Language Models for Southeast Asian Languages

Large Language Models (LLMs) have shown remarkable abilities across various tasks, yet their development has predominantly centered on high-resource languages like English and Chinese, leaving low-resource languages underserved. To address this disparity, we present SeaLLMs 3, the latest iteration of the SeaLLMs model family, tailored for Southeast Asian languages. This region, characterized by its rich linguistic diversity, has lacked adequate language technology support. SeaLLMs 3 aims to bridge this gap by covering a comprehensive range of languages spoken in this region, including English, Chinese, Indonesian, Vietnamese, Thai, Tagalog, Malay, Burmese, Khmer, Lao, Tamil, and Javanese. Leveraging efficient language enhancement techniques and a specially constructed instruction tuning dataset, SeaLLMs 3 significantly reduces training costs while maintaining high performance and versatility. Our model excels in tasks such as world knowledge, mathematical reasoning, translation, and instruction following, achieving state-of-the-art performance among similarly sized models. Additionally, we prioritized safety and reliability by addressing both general and culture-specific considerations and incorporated mechanisms to reduce hallucinations. This work underscores the importance of inclusive AI, showing that advanced LLM capabilities can benefit underserved linguistic and cultural communities.

cs.CL↗

arXiv2024

InstructAV: Instruction Fine-tuning Large Language Models for Authorship Verification

Large Language Models (LLMs) have demonstrated remarkable proficiency in a wide range of NLP tasks. However, when it comes to authorship verification (AV) tasks, which involve determining whether two given texts share the same authorship, even advanced models like ChatGPT exhibit notable limitations. This paper introduces a novel approach, termed InstructAV, for authorship verification. This approach utilizes LLMs in conjunction with a parameter-efficient fine-tuning (PEFT) method to simultaneously improve accuracy and explainability. The distinctiveness of InstructAV lies in its ability to align classification decisions with transparent and understandable explanations, representing a significant progression in the field of authorship verification. Through comprehensive experiments conducted across various datasets, InstructAV demonstrates its state-of-the-art performance on the AV task, offering high classification accuracy coupled with enhanced explanation reliability.

cs.CL↗

arXiv2024

SeaLLMs -- Large Language Models for Southeast Asia

Despite the remarkable achievements of large language models (LLMs) in various tasks, there remains a linguistic bias that favors high-resource languages, such as English, often at the expense of low-resource and regional languages. To address this imbalance, we introduce SeaLLMs, an innovative series of language models that specifically focuses on Southeast Asian (SEA) languages. SeaLLMs are built upon the Llama-2 model and further advanced through continued pre-training with an extended vocabulary, specialized instruction and alignment tuning to better capture the intricacies of regional languages. This allows them to respect and reflect local cultural norms, customs, stylistic preferences, and legal considerations. Our comprehensive evaluation demonstrates that SeaLLM-13b models exhibit superior performance across a wide spectrum of linguistic tasks and assistant-style instruction-following capabilities relative to comparable open-source models. Moreover, they outperform ChatGPT-3.5 in non-Latin languages, such as Thai, Khmer, Lao, and Burmese, by large margins while remaining lightweight and cost-effective to operate.

cs.CL↗

arXiv2024

TemPL: A Novel Deep Learning Model for Zero-Shot Prediction of Protein Stability and Activity Based on Temperature-Guided Language Modeling

We introduce TemPL, a novel deep learning approach for zero-shot prediction of protein stability and activity, harnessing temperature-guided language modeling. By assembling an extensive dataset of 96 million sequence-host bacterial strain optimal growth temperatures (OGTs) and ΔTm data for point mutations under consistent experimental conditions, we effectively compared TemPL with state-of-the-art models. Notably, TemPL demonstrated superior performance in predicting protein stability. An ablation study was conducted to elucidate the influence of OGT prediction and language modeling modules on TemPL's performance, revealing the importance of integrating both components. Consequently, TemPL offers considerable promise for protein engineering applications, facilitating the design of mutation sequences with enhanced stability and activity.

q-bio.QM↗

arXiv2024

All in an Aggregated Image for In-Image Learning

This paper introduces a new in-context learning (ICL) mechanism called In-Image Learning (I$^2$L) that combines demonstration examples, visual cues, and chain-of-thought reasoning into an aggregated image to enhance the capabilities of Large Multimodal Models (e.g., GPT-4V) in multimodal reasoning tasks. Unlike previous approaches that rely on converting images to text or incorporating visual input into language models, I$^2$L consolidates all information into an aggregated image and leverages image processing, understanding, and reasoning abilities. This has several advantages: it reduces inaccurate textual descriptions of complex images, provides flexibility in positioning demonstration examples, and avoids multiple input images and lengthy prompts. We also introduce I$^2$L-Hybrid, a method that combines the strengths of I$^2$L with other ICL methods. Specifically, it uses an automatic strategy to select the most suitable method (I$^2$L or another certain ICL method) for a specific task instance. We conduct extensive experiments to assess the effectiveness of I$^2$L and I$^2$L-Hybrid on MathVista, which covers a variety of complex multimodal reasoning tasks. Additionally, we investigate the influence of image resolution, the number of demonstration examples in a single image, and the positions of these demonstrations in the aggregated image on the effectiveness of I$^2$L. Our code is publicly available at https://github.com/AGI-Edgerunners/IIL.

cs.CV↗

arXiv2024

New constraints on Triton's atmosphere from the 6 October 2022 stellar occultation

The atmosphere of Triton was probed directly by observing a ground-based stellar occultation on 6 October 2022. This rare event yielded 23 positive light curves collected from 13 separate observation stations contributing to our campaign. The significance of this event lies in its potential to directly validate the modest pressure fluctuation on Triton, a phenomenon not definitively verified by previous observations, including only five stellar occultations, and the Voyager 2 radio occultation in 1989. Using an approach consistent with a comparable study, we precisely determined a surface pressure of $14.07_{-0.13}^{+0.21}~\mathrm{μbar}$ in 2022. This new pressure rules out any significant monotonic variation in pressure between 2017 and 2022 through direct observations, as it is in alignment with the 2017 value. Additionally, both the pressures in 2017 and 2022 align with the 1989 value. This provides further support for the conclusion drawn from the previous volatile transport model simulation, which is consistent with the observed alignment between the pressures in 1989 and 2017; that is to say, the pressure fluctuation is modest. Moreover, this conclusion suggests the existence of a northern polar cap extended down to at least $45^\circ$N$-60^\circ$N and the presence of nitrogen between $30^\circ$S and $0^\circ$.

astro-ph.EP↗

arXiv2023

Who Wrote it and Why? Prompting Large-Language Models for Authorship Verification

Authorship verification (AV) is a fundamental task in natural language processing (NLP) and computational linguistics, with applications in forensic analysis, plagiarism detection, and identification of deceptive content. Existing AV techniques, including traditional stylometric and deep learning approaches, face limitations in terms of data requirements and lack of explainability. To address these limitations, this paper proposes PromptAV, a novel technique that leverages Large-Language Models (LLMs) for AV by providing step-by-step stylometric explanation prompts. PromptAV outperforms state-of-the-art baselines, operates effectively with limited training data, and enhances interpretability through intuitive explanations, showcasing its potential as an effective and interpretable solution for the AV task.

cs.CL↗

arXiv2023

LLM-Adapters: An Adapter Family for Parameter-Efficient Fine-Tuning of Large Language Models

The success of large language models (LLMs), like GPT-4 and ChatGPT, has led to the development of numerous cost-effective and accessible alternatives that are created by finetuning open-access LLMs with task-specific data (e.g., ChatDoctor) or instruction data (e.g., Alpaca). Among the various fine-tuning methods, adapter-based parameter-efficient fine-tuning (PEFT) is undoubtedly one of the most attractive topics, as it only requires fine-tuning a few external parameters instead of the entire LLMs while achieving comparable or even better performance. To enable further research on PEFT methods of LLMs, this paper presents LLM-Adapters, an easy-to-use framework that integrates various adapters into LLMs and can execute these adapter-based PEFT methods of LLMs for different tasks. The framework includes state-of-the-art open-access LLMs such as LLaMA, BLOOM, and GPT-J, as well as widely used adapters such as Series adapters, Parallel adapter, Prompt-based learning and Reparametrization-based methods. Moreover, we conduct extensive empirical studies on the impact of adapter types, placement locations, and hyper-parameters to the best design for each adapter-based methods. We evaluate the effectiveness of the adapters on fourteen datasets from two different reasoning tasks, Arithmetic Reasoning and Commonsense Reasoning. The results demonstrate that using adapter-based PEFT in smaller-scale LLMs (7B) with few extra trainable parameters yields comparable, and in some cases superior, performance to powerful LLMs (175B) in zero-shot inference on both reasoning tasks.

cs.CL↗

arXiv2023

Dynamic Spectrum Mixer for Visual Recognition

Recently, MLP-based vision backbones have achieved promising performance in several visual recognition tasks. However, the existing MLP-based methods directly aggregate tokens with static weights, leaving the adaptability to different images untouched. Moreover, Recent research demonstrates that MLP-Transformer is great at creating long-range dependencies but ineffective at catching high frequencies that primarily transmit local information, which prevents it from applying to the downstream dense prediction tasks, such as semantic segmentation. To address these challenges, we propose a content-adaptive yet computationally efficient structure, dubbed Dynamic Spectrum Mixer (DSM). The DSM represents token interactions in the frequency domain by employing the Discrete Cosine Transform, which can learn long-term spatial dependencies with log-linear complexity. Furthermore, a dynamic spectrum weight generation layer is proposed as the spectrum bands selector, which could emphasize the informative frequency bands while diminishing others. To this end, the technique can efficiently learn detailed features from visual input that contains both high- and low-frequency information. Extensive experiments show that DSM is a powerful and adaptable backbone for a range of visual recognition tasks. Particularly, DSM outperforms previous transformer-based and MLP-based models, on image classification, object detection, and semantic segmentation tasks, such as 83.8 \% top-1 accuracy on ImageNet, and 49.9 \% mIoU on ADE20K.

cs.CV↗

arXiv2023

A Laplacian Pyramid Based Generative H&E Stain Augmentation Network

Hematoxylin and Eosin (H&E) staining is a widely used sample preparation procedure for enhancing the saturation of tissue sections and the contrast between nuclei and cytoplasm in histology images for medical diagnostics. However, various factors, such as the differences in the reagents used, result in high variability in the colors of the stains actually recorded. This variability poses a challenge in achieving generalization for machine-learning based computer-aided diagnostic tools. To desensitize the learned models to stain variations, we propose the Generative Stain Augmentation Network (G-SAN) -- a GAN-based framework that augments a collection of cell images with simulated yet realistic stain variations. At its core, G-SAN uses a novel and highly computationally efficient Laplacian Pyramid (LP) based generator architecture, that is capable of disentangling stain from cell morphology. Through the task of patch classification and nucleus segmentation, we show that using G-SAN-augmented training data provides on average 15.7% improvement in F1 score and 7.3% improvement in panoptic quality, respectively. Our code is available at https://github.com/lifangda01/GSAN-Demo.

eess.IV↗

arXiv2023

Plan-and-Solve Prompting: Improving Zero-Shot Chain-of-Thought Reasoning by Large Language Models

Large language models (LLMs) have recently been shown to deliver impressive performance in various NLP tasks. To tackle multi-step reasoning tasks, few-shot chain-of-thought (CoT) prompting includes a few manually crafted step-by-step reasoning demonstrations which enable LLMs to explicitly generate reasoning steps and improve their reasoning task accuracy. To eliminate the manual effort, Zero-shot-CoT concatenates the target problem statement with "Let's think step by step" as an input prompt to LLMs. Despite the success of Zero-shot-CoT, it still suffers from three pitfalls: calculation errors, missing-step errors, and semantic misunderstanding errors. To address the missing-step errors, we propose Plan-and-Solve (PS) Prompting. It consists of two components: first, devising a plan to divide the entire task into smaller subtasks, and then carrying out the subtasks according to the plan. To address the calculation errors and improve the quality of generated reasoning steps, we extend PS prompting with more detailed instructions and derive PS+ prompting. We evaluate our proposed prompting strategy on ten datasets across three reasoning problems. The experimental results over GPT-3 show that our proposed zero-shot prompting consistently outperforms Zero-shot-CoT across all datasets by a large margin, is comparable to or exceeds Zero-shot-Program-of-Thought Prompting, and has comparable performance with 8-shot CoT prompting on the math reasoning problem. The code can be found at https://github.com/AGI-Edgerunners/Plan-and-Solve-Prompting.

cs.CL↗

arXiv2023

Adapter-TST: A Parameter Efficient Method for Multiple-Attribute Text Style Transfer

Adapting a large language model for multiple-attribute text style transfer via fine-tuning can be challenging due to the significant amount of computational resources and labeled data required for the specific task. In this paper, we address this challenge by introducing AdapterTST, a framework that freezes the pre-trained model's original parameters and enables the development of a multiple-attribute text style transfer model. Using BART as the backbone model, Adapter-TST utilizes different neural adapters to capture different attribute information, like a plug-in connected to BART. Our method allows control over multiple attributes, like sentiment, tense, voice, etc., and configures the adapters' architecture to generate multiple outputs respected to attributes or compositional editing on the same sentence. We evaluate the proposed model on both traditional sentiment transfer and multiple-attribute transfer tasks. The experiment results demonstrate that Adapter-TST outperforms all the state-of-the-art baselines with significantly lesser computational resources. We have also empirically shown that each adapter is able to capture specific stylistic attributes effectively and can be configured to perform compositional editing.

cs.CL↗