arXiv subjects

Tao Ji

Publications and source records attributed to Tao Ji.

At least 37 records · Page 2Linked to original sources

arXiv2025

Protein Design with Dynamic Protein Vocabulary

Protein design is a fundamental challenge in biotechnology, aiming to design novel sequences with specific functions within the vast space of possible proteins. Recent advances in deep generative models have enabled function-based protein design from textual descriptions, yet struggle with structural plausibility. Inspired by classical protein design methods that leverage natural protein structures, we explore whether incorporating fragments from natural proteins can enhance foldability in generative models. Our empirical results show that even random incorporation of fragments improves foldability. Building on this insight, we introduce ProDVa, a novel protein design approach that integrates a text encoder for functional descriptions, a protein language model for designing proteins, and a fragment encoder to dynamically retrieve protein fragments based on textual functional descriptions. Experimental results demonstrate that our approach effectively designs protein sequences that are both functionally aligned and structurally plausible. Compared to state-of-the-art models, ProDVa achieves comparable function alignment using less than 0.04% of the training data, while designing significantly more well-folded proteins, with the proportion of proteins having pLDDT above 70 increasing by 7.38% and those with PAE below 10 increasing by 9.6%.

cs.LG↗

arXiv2025

Towards Economical Inference: Enabling DeepSeek's Multi-Head Latent Attention in Any Transformer-based LLMs

Multi-head Latent Attention (MLA) is an innovative architecture proposed by DeepSeek, designed to ensure efficient and economical inference by significantly compressing the Key-Value (KV) cache into a latent vector. Compared to MLA, standard LLMs employing Multi-Head Attention (MHA) and its variants such as Grouped-Query Attention (GQA) exhibit significant cost disadvantages. Enabling well-trained LLMs (e.g., Llama) to rapidly adapt to MLA without pre-training from scratch is both meaningful and challenging. This paper proposes the first data-efficient fine-tuning method for transitioning from MHA to MLA (MHA2MLA), which includes two key components: for partial-RoPE, we remove RoPE from dimensions of queries and keys that contribute less to the attention scores, for low-rank approximation, we introduce joint SVD approximations based on the pre-trained parameters of keys and values. These carefully designed strategies enable MHA2MLA to recover performance using only a small fraction (0.3% to 0.6%) of the data, significantly reducing inference costs while seamlessly integrating with compression techniques such as KV cache quantization. For example, the KV cache size of Llama2-7B is reduced by 92.19%, with only a 0.5% drop in LongBench performance.

cs.CL↗

arXiv2025

From Scores to Preferences: Redefining MOS Benchmarking for Speech Quality Reward Modeling

Assessing the perceptual quality of synthetic speech is crucial for guiding the development and refinement of speech generation models. However, it has traditionally relied on human subjective ratings such as the Mean Opinion Score (MOS), which depend on manual annotations and often suffer from inconsistent rating standards and poor reproducibility. To address these limitations, we introduce MOS-RMBench, a unified benchmark that reformulates diverse MOS datasets into a preference-comparison setting, enabling rigorous evaluation across different datasets. Building on MOS-RMBench, we systematically construct and evaluate three paradigms for reward modeling: scalar reward models, semi-scalar reward models, and generative reward models (GRMs). Our experiments reveal three key findings: (1) scalar models achieve the strongest overall performance, consistently exceeding 74% accuracy; (2) most models perform considerably worse on synthetic speech than on human speech; and (3) all models struggle on pairs with very small MOS differences. To improve performance on these challenging pairs, we propose a MOS-aware GRM that incorporates an MOS-difference-based reward function, enabling the model to adaptively scale rewards according to the difficulty of each sample pair. Experimental results show that the MOS-aware GRM significantly improves fine-grained quality discrimination and narrows the gap with scalar models on the most challenging cases. We hope this work will establish both a benchmark and a methodological framework to foster more rigorous and scalable research in automatic speech quality assessment.

cs.SD↗

arXiv2025

BMMR: A Large-Scale Bilingual Multimodal Multi-Discipline Reasoning Dataset

In this paper, we introduce BMMR, a large-scale bilingual, multimodal, multi-disciplinary reasoning dataset for the community to develop and evaluate large multimodal models (LMMs). BMMR comprises 110k college-level questions spanning 300 UNESCO-defined subjects, spanning diverse formats-multiple-choice, fill-in-the-blank, and open-ended QA-and sourced from both print and digital media such as books, exams, and quizzes. All data are curated and filtered via a human-in-the-loop and scalable framework, and each instance is paired with a high-quality reasoning path. The dataset is organized into two parts: BMMR-Eval that comprises 20,458 high-quality instances to comprehensively assess LMMs' knowledge and reasoning across multiple disciplines in both Chinese and English; and BMMR-Train that contains 88,991 instances to support further research and development, extending the current focus on mathematical reasoning to diverse disciplines and domains. In addition, we propose the process-based multi-discipline verifier (i.e., BMMR-Verifier) for accurate and fine-grained evaluation of reasoning paths. Extensive experiments on 24 models reveal that (i) even SOTA models (e.g., o3 and Gemini-2.5-Pro) leave substantial headroom on BMMR-Eval; (ii) reasoning models exhibit discipline bias and outperform LMMs only on specific subjects; (iii) open-source models still trail their proprietary counterparts; and (iv) fine-tuning on BMMR-Train narrows this gap. Additionally, we conduct reasoning-chain analyses using BMMR-Verifier and other in-depth studies, uncovering the challenges LMMs currently face in multidisciplinary reasoning. We will release the data, and we hope our work can offer insights and contributions to the community.

cs.CL↗

arXiv2025

The Role of Visual Modality in Multimodal Mathematical Reasoning: Challenges and Insights

Recent research has increasingly focused on multimodal mathematical reasoning, particularly emphasizing the creation of relevant datasets and benchmarks. Despite this, the role of visual information in reasoning has been underexplored. Our findings show that existing multimodal mathematical models minimally leverage visual information, and model performance remains largely unaffected by changes to or removal of images in the dataset. We attribute this to the dominance of textual information and answer options that inadvertently guide the model to correct answers. To improve evaluation methods, we introduce the HC-M3D dataset, specifically designed to require image reliance for problem-solving and to challenge models with similar, yet distinct, images that change the correct answer. In testing leading models, their failure to detect these subtle visual differences suggests limitations in current visual perception capabilities. Additionally, we observe that the common approach of improving general VQA capabilities by combining various types of image encoders does not contribute to math reasoning performance. This finding also presents a challenge to enhancing visual reliance during math reasoning. Our benchmark and code would be available at \href{https://github.com/Yufang-Liu/visual_modality_role}{https://github.com/Yufang-Liu/visual\_modality\_role}.

cs.CV↗

arXiv2025

Quasar identifications from the slitless spectra: a test from 3D-HST

Slitless spectroscopy is a traditional method for selecting quasars. In this paper, we develop a procedure for selecting quasars (QSOs) using the 3D-HST G141 slitless spectra. We initially identify over 6,000 sources with emission lines broader than those typically found in emission line galaxies (ELGs) by analyzing the 1D spectra. These ``broad'' emission lines may originate from actual QSO broad lines ($\rm FWHM\geq1200~\rm km/s$) or the convolved narrow lines ($\rm FWHM = 200\sim 300\rm km/s$) in ELGs with effective radii $\geq$0.3" (2.5Kpc at z=1). We then propose a criterion based on the reliability of the QSO component in the forward modeling results. Using the known QSOs, ELGs, and simulation spectra, we find that our criterion successfully selects about 90\% of known QSOs with H$α$ or H$β$ line detection and point-like structures, with an ELG contamination rate of about 5\%. We apply this method to emission line sources without significant contamination and select 19 QSO candidates at redshift $z=0.12-1.56$. 12 of these candidates have Chandra X-ray detections. This sample covers a broader range of the rest-frame UV colors and has redder optical slopes compared to the SDSS QSOs, yet it is more likely to be composed of normal QSOs rather than little red dots. Through spectral analysis, the estimated black hole masses of the sample are $10^{6.9}-10^{8.3} M_{\odot}$. Our new candidates improve the completeness of the QSO sample at $z=0.8-1.6$ in the 3D-HST field. The proposed method will also be helpful for QSO selections via slitless spectroscopy in Euclid and the Chinese Space Station Telescope.

astro-ph.GA↗

arXiv2025

Effective Length Extrapolation via Dimension-Wise Positional Embeddings Manipulation

Large Language Models (LLMs) often struggle to process and generate coherent context when the number of input tokens exceeds the pre-trained length. Recent advancements in long-context extension have significantly expanded the context window of LLMs but require expensive overhead to train the large-scale models with longer context. In this work, we propose Dimension-Wise Positional Embeddings Manipulation (DPE), a training-free framework to extrapolate the context window of LLMs by diving into RoPE's different hidden dimensions. Instead of manipulating all dimensions equally, DPE detects the effective length for every dimension and finds the key dimensions for context extension. We reuse the original position indices with their embeddings from the pre-trained model and manipulate the key dimensions' position indices to their most effective lengths. In this way, DPE adjusts the pre-trained models with minimal modifications while ensuring that each dimension reaches its optimal state for extrapolation. DPE significantly surpasses well-known baselines such as YaRN and Self-Extend. DPE enables Llama3-8k 8B to support context windows of 128k tokens without continual training and integrates seamlessly with Flash Attention 2. In addition to its impressive extrapolation capability, DPE also dramatically improves the models' performance within training length, such as Llama3.1 70B, by over 18 points on popular long-context benchmarks RULER. When compared with commercial models, Llama 3.1 70B with DPE even achieves better performance than GPT-4-128K.

cs.CL↗

arXiv2025

Mitigating Object Hallucinations in MLLMs via Multi-Frequency Perturbations

Recently, multimodal large language models (MLLMs) have demonstrated remarkable performance in visual-language tasks. However, the authenticity of the responses generated by MLLMs is often compromised by object hallucinations. We identify that a key cause of these hallucinations is the model's over-susceptibility to specific image frequency features in detecting objects. In this paper, we introduce Multi-Frequency Perturbations (MFP), a simple, cost-effective, and pluggable method that leverages both low-frequency and high-frequency features of images to perturb visual feature representations and explicitly suppress redundant frequency-domain features during inference, thereby mitigating hallucinations. Experimental results demonstrate that our method significantly mitigates object hallucinations across various model architectures. Furthermore, as a training-time method, MFP can be combined with inference-time methods to achieve state-of-the-art performance on the CHAIR benchmark.

cs.CV↗

arXiv2024

EvoLlama: Enhancing LLMs' Understanding of Proteins via Multimodal Structure and Sequence Representations

Current Large Language Models (LLMs) for understanding proteins primarily treats amino acid sequences as a text modality. Meanwhile, Protein Language Models (PLMs), such as ESM-2, have learned massive sequential evolutionary knowledge from the universe of natural protein sequences. Furthermore, structure-based encoders like ProteinMPNN learn the structural information of proteins through Graph Neural Networks. However, whether the incorporation of protein encoders can enhance the protein understanding of LLMs has not been explored. To bridge this gap, we propose EvoLlama, a multimodal framework that connects a structure-based encoder, a sequence-based protein encoder and an LLM for protein understanding. EvoLlama consists of a ProteinMPNN structure encoder, an ESM-2 protein sequence encoder, a multimodal projector to align protein and text representations and a Llama-3 text decoder. To train EvoLlama, we fine-tune it on protein-oriented instructions and protein property prediction datasets verbalized via natural language instruction templates. Our experiments show that EvoLlama's protein understanding capabilities have been significantly enhanced, outperforming other fine-tuned protein-oriented LLMs in zero-shot settings by an average of 1%-8% and surpassing the state-of-the-art baseline with supervised fine-tuning by an average of 6%. On protein property prediction datasets, our approach achieves promising results that are competitive with state-of-the-art task-specific baselines. We will release our code in a future version.

cs.LG↗

arXiv2024

ToolEyes: Fine-Grained Evaluation for Tool Learning Capabilities of Large Language Models in Real-world Scenarios

Existing evaluations of tool learning primarily focus on validating the alignment of selected tools for large language models (LLMs) with expected outcomes. However, these approaches rely on a limited set of scenarios where answers can be pre-determined, diverging from genuine needs. Furthermore, a sole emphasis on outcomes disregards the complex capabilities required for LLMs to effectively use tools. To tackle this issue, we propose ToolEyes, a fine-grained system tailored for the evaluation of the LLMs' tool learning capabilities in authentic scenarios. The system meticulously examines seven real-world scenarios, analyzing five dimensions crucial to LLMs in tool learning: format alignment, intent comprehension, behavior planning, tool selection, and answer organization. Additionally, ToolEyes incorporates a tool library boasting approximately 600 tools, serving as an intermediary between LLMs and the physical world. Evaluations involving ten LLMs across three categories reveal a preference for specific scenarios and limited cognitive abilities in tool learning. Intriguingly, expanding the model size even exacerbates the hindrance to tool learning. The code and data are available at https://github.com/Junjie-Ye/ToolEyes.

cs.CL↗

arXiv2024

AntLM: Bridging Causal and Masked Language Models

Causal Language Modeling (CLM) and Masked Language Modeling (MLM) are two mainstream learning paradigms based on Transformer networks, specifically the Decoder-only and Encoder-only architectures. The strengths of each paradigm in downstream tasks have shown a mix of advantages and disadvantages. In the past BabyLM Challenge 2023, although the MLM paradigm achieved the best average performance, the CLM paradigm demonstrated significantly faster convergence rates. For the BabyLM Challenge 2024, we propose a novel language modeling paradigm named $\textbf{AntLM}$, which integrates both CLM and MLM to leverage the advantages of these two classic paradigms. We chose the strict-small track and conducted experiments on two foundation models: BabyLlama, representing CLM, and LTG-BERT, representing MLM. During the training process for specific foundation models, we alternate between applying CLM or MLM training objectives and causal or bidirectional attention masks. Experimental results show that combining the two pretraining objectives leverages their strengths, enhancing overall training performance. Under the same epochs, $AntLM_{BabyLlama}$ improves Macro-average by 1%, and $AntLM_{LTG-BERT}$ achieves a 2.2% increase over the baselines.

cs.CL↗

arXiv2024

Enhancing LLM Reasoning via Critique Models with Test-Time and Training-Time Supervision

Training large language models (LLMs) to spend more time thinking and reflection before responding is crucial for effectively solving complex reasoning tasks in fields such as science, coding, and mathematics. However, the effectiveness of mechanisms like self-reflection and self-correction depends on the model's capacity to accurately assess its own performance, which can be limited by factors such as initial accuracy, question difficulty, and the lack of external feedback. In this paper, we delve into a two-player paradigm that separates the roles of reasoning and critique models, where the critique model provides step-level feedback to supervise the reasoning (actor) model during both test-time and train-time. We first propose AutoMathCritique, an automated and scalable framework for collecting critique data, resulting in a dataset of $76,321$ responses paired with step-level feedback. Fine-tuning language models with this dataset enables them to generate natural language feedback for mathematical reasoning. We demonstrate that the critique models consistently improve the actor's performance on difficult queries at test-time, especially when scaling up inference-time computation. Motivated by these findings, we introduce the critique-based supervision to the actor's self-training process, and propose a critique-in-the-loop self-improvement method. Experiments show that the method improves the actor's exploration efficiency and solution diversity, especially on challenging queries, leading to a stronger reasoning model. Lastly, we take the preliminary step to explore training self-talk reasoning models via critique supervision and showcase its potential. Our code and datasets are at \href{https://mathcritique.github.io/}{https://mathcritique.github.io/}.

cs.CL↗

arXiv2024

Multi-Programming Language Sandbox for LLMs

We introduce MPLSandbox, an out-of-the-box multi-programming language sandbox designed to provide unified and comprehensive feedback from compiler and analysis tools for Large Language Models (LLMs). It can automatically identify the programming language of the code, compiling and executing it within an isolated sub-sandbox to ensure safety and stability. In addition, MPLSandbox also integrates both traditional and LLM-based code analysis tools, providing a comprehensive analysis of generated code. MPLSandbox can be effortlessly integrated into the training and deployment of LLMs to improve the quality and correctness of their generated code. It also helps researchers streamline their workflows for various LLM-based code-related tasks, reducing the development cost. To validate the effectiveness of MPLSandbox, we integrate it into training and deployment approaches, and also employ it to optimize workflows for a wide range of real-world code-related tasks. Our goal is to enhance researcher productivity on LLM-based code-related tasks by simplifying and automating workflows through delegation to MPLSandbox.

cs.SE↗

arXiv2024

Have the VLMs Lost Confidence? A Study of Sycophancy in VLMs

In the study of LLMs, sycophancy represents a prevalent hallucination that poses significant challenges to these models. Specifically, LLMs often fail to adhere to original correct responses, instead blindly agreeing with users' opinions, even when those opinions are incorrect or malicious. However, research on sycophancy in visual language models (VLMs) has been scarce. In this work, we extend the exploration of sycophancy from LLMs to VLMs, introducing the MM-SY benchmark to evaluate this phenomenon. We present evaluation results from multiple representative models, addressing the gap in sycophancy research for VLMs. To mitigate sycophancy, we propose a synthetic dataset for training and employ methods based on prompts, supervised fine-tuning, and DPO. Our experiments demonstrate that these methods effectively alleviate sycophancy in VLMs. Additionally, we probe VLMs to assess the semantic impact of sycophancy and analyze the attention distribution of visual tokens. Our findings indicate that the ability to prevent sycophancy is predominantly observed in higher layers of the model. The lack of attention to image knowledge in these higher layers may contribute to sycophancy, and enhancing image attention at high layers proves beneficial in mitigating this issue.

cs.CV↗

arXiv2024

Generation with Dynamic Vocabulary

We introduce a new dynamic vocabulary for language models. It can involve arbitrary text spans during generation. These text spans act as basic generation bricks, akin to tokens in the traditional static vocabularies. We show that, the ability to generate multi-tokens atomically improve both generation quality and efficiency (compared to the standard language model, the MAUVE metric is increased by 25%, the latency is decreased by 20%). The dynamic vocabulary can be deployed in a plug-and-play way, thus is attractive for various downstream applications. For example, we demonstrate that dynamic vocabulary can be applied to different domains in a training-free manner. It also helps to generate reliable citations in question answering tasks (substantially enhancing citation results without compromising answer accuracy).

cs.CL↗

arXiv2024

Investigating and Mitigating Object Hallucinations in Pretrained Vision-Language (CLIP) Models

Large Vision-Language Models (LVLMs) have achieved impressive performance, yet research has pointed out a serious issue with object hallucinations within these models. However, there is no clear conclusion as to which part of the model these hallucinations originate from. In this paper, we present an in-depth investigation into the object hallucination problem specifically within the CLIP model, which serves as the backbone for many state-of-the-art vision-language systems. We unveil that even in isolation, the CLIP model is prone to object hallucinations, suggesting that the hallucination problem is not solely due to the interaction between vision and language modalities. To address this, we propose a counterfactual data augmentation method by creating negative samples with a variety of hallucination issues. We demonstrate that our method can effectively mitigate object hallucinations for CLIP model, and we show the the enhanced model can be employed as a visual encoder, effectively alleviating the object hallucination issue in LVLMs.

cs.CV↗

arXiv2024

FOSS: A Self-Learned Doctor for Query Optimizer

Various works have utilized deep learning to address the query optimization problem in database system. They either learn to construct plans from scratch in a bottom-up manner or steer the plan generation behavior of traditional optimizer using hints. While these methods have achieved some success, they face challenges in either low training efficiency or limited plan search space. To address these challenges, we introduce FOSS, a novel framework for query optimization based on deep reinforcement learning. FOSS initiates optimization from the original plan generated by a traditional optimizer and incrementally refines suboptimal nodes of the plan through a sequence of actions. Additionally, we devise an asymmetric advantage model to evaluate the advantage between two plans. We integrate it with a traditional optimizer to form a simulated environment. Leveraging this simulated environment, FOSS can bootstrap itself to rapidly generate a large amount of high-quality simulated experiences. FOSS then learns from these experiences to improve its optimization capability. We evaluate the performance of FOSS on Join Order Benchmark, TPC-DS, and Stack Overflow. The experimental results demonstrate that FOSS outperforms the state-of-the-art methods in terms of latency performance. Compared to PostgreSQL, FOSS achieves speedup ranging from 1.15x to 8.33x in total latency across different benchmarks.

cs.DB↗

arXiv2024

Is Large Language Model Good at Database Knob Tuning? A Comprehensive Experimental Evaluation

Knob tuning plays a crucial role in optimizing databases by adjusting knobs to enhance database performance. However, traditional tuning methods often follow a Try-Collect-Adjust approach, proving inefficient and database-specific. Moreover, these methods are often opaque, making it challenging for DBAs to grasp the underlying decision-making process. The emergence of large language models (LLMs) like GPT-4 and Claude-3 has excelled in complex natural language tasks, yet their potential in database knob tuning remains largely unexplored. This study harnesses LLMs as experienced DBAs for knob-tuning tasks with carefully designed prompts. We identify three key subtasks in the tuning system: knob pruning, model initialization, and knob recommendation, proposing LLM-driven solutions to replace conventional methods for each subtask. We conduct extensive experiments to compare LLM-driven approaches against traditional methods across the subtasks to evaluate LLMs' efficacy in the knob tuning domain. Furthermore, we explore the adaptability of LLM-based solutions in diverse evaluation settings, encompassing new benchmarks, database engines, and hardware environments. Our findings reveal that LLMs not only match or surpass traditional methods but also exhibit notable interpretability by generating responses in a coherent ``chain-of-thought'' manner. We further observe that LLMs exhibit remarkable generalizability through simple adjustments in prompts, eliminating the necessity for additional training or extensive code modifications. Drawing insights from our experimental findings, we identify several opportunities for future research aimed at advancing the utilization of LLMs in the realm of database management.

cs.DB↗