Plant phenotyping increasingly relies on (semi-)automated image-based analysis workflows to improve its accuracy and scalability. However, many existing solutions remain overly complex, difficult to reimplement and maintain, and pose high barriers for users without substantial computational expertise. To address these challenges, we introduce PhenoAssistant: a pioneering AI-driven system that streamlines plant phenotyping via intuitive natural language interaction. PhenoAssistant leverages a large language model to orchestrate a curated toolkit supporting tasks including automated phenotype extraction, data visualisation and automated model training. We validate PhenoAssistant through several representative case studies and a set of evaluation tasks. By significantly lowering technical hurdles, PhenoAssistant underscores the promise of AI-driven methodologies to democratising AI adoption in plant biology.
We introduce RegionFocus, a visual test-time scaling approach for Vision Language Model Agents. Understanding webpages is challenging due to the visual complexity of GUI images and the large number of interface elements, making accurate action selection difficult. Our approach dynamically zooms in on relevant regions, reducing background clutter and improving grounding accuracy. To support this process, we propose an image-as-map mechanism that visualizes key landmarks at each step, providing a transparent action record and enables the agent to effectively choose among action candidates. Even with a simple region selection strategy, we observe significant performance gains of 28+\% on Screenspot-pro and 24+\% on WebVoyager benchmarks on top of two state-of-the-art open vision language model agents, UI-TARS and Qwen2.5-VL, highlighting the effectiveness of visual test-time scaling in interactive settings. We achieve a new state-of-the-art grounding performance of 61.6\% on the ScreenSpot-Pro benchmark by applying RegionFocus to a Qwen2.5-VL-72B model. Our code will be released publicly at https://github.com/tiangeluo/RegionFocus.
Prompt engineering for large language models is challenging, as even small prompt perturbations or model changes can significantly impact the generated output texts. Existing evaluation methods of LLM outputs, either automated metrics or human evaluation, have limitations, such as providing limited insights or being labor-intensive. We propose Spotlight, a new approach that combines both automation and human analysis. Based on data mining techniques, we automatically distinguish between random (decoding) variations and systematic differences in language model outputs. This process provides token patterns that describe the systematic differences and guide the user in manually analyzing the effects of their prompts and changes in models efficiently. We create three benchmarks to quantitatively test the reliability of token pattern extraction methods and demonstrate that our approach provides new insights into established prompt data. From a human-centric perspective, through demonstration studies and a user study, we show that our token pattern approach helps users understand the systematic differences of language model outputs. We are further able to discover relevant differences caused by prompt and model changes (e.g. related to gender or culture), thus supporting the prompt engineering process and human-centric model behavior research.
Antenna modeling is a time-consuming and complex process, decreasing the speed of antenna analysis and design. In this paper, a large language model (LLM)- enabled antenna modeling method, called LEAM, is presented to address this challenge. LEAM enables automatic antenna model generation based on language descriptions via prompt input, images, descriptions from academic papers, patents, and technical reports (either one or multiple). The effectiveness of LEAM is demonstrated by three examples: a Vivaldi antenna generated from a complete user description, a slotted patch antenna generated from an incomplete user description and the operating frequency, and a monopole slotted antenna generated from images and descriptions scanned from the literature. For all the examples, correct antenna models are generated in a few minutes. The code can be accessed via https://github.com/TaoWu974/LEAM.
Pipeline Parallelism (PP) enables large neural network training on small, interconnected devices by splitting the model into multiple stages. To maximize pipeline utilization, asynchronous optimization is appealing as it offers 100% pipeline utilization by construction. However, it is inherently challenging as the weights and gradients are no longer synchronized, leading to stale (or delayed) gradients. To alleviate this, we introduce a variant of Nesterov Accelerated Gradient (NAG) for asynchronous optimization in PP. Specifically, we modify the look-ahead step in NAG to effectively address the staleness in gradients. We theoretically prove that our approach converges at a sublinear rate in the presence of fixed delay in gradients. Our experiments on large-scale language modelling tasks using decoder-only architectures with up to 1B parameters, demonstrate that our approach significantly outperforms existing asynchronous methods, even surpassing the synchronous baseline.
Recently, large language model based (LLM-based) agents have been widely applied across various fields. As a critical part, their memory capabilities have captured significant interest from both industrial and academic communities. Despite the proposal of many advanced memory models in recent research, however, there remains a lack of unified implementations under a general framework. To address this issue, we develop a unified and modular library for developing advanced memory models of LLM-based agents, called MemEngine. Based on our framework, we implement abundant memory models from recent research works. Additionally, our library facilitates convenient and extensible memory development, and offers user-friendly and pluggable memory usage. For benefiting our community, we have made our project publicly available at https://github.com/nuster1128/MemEngine.
Evaluating the quality of slide-based multimedia instruction is challenging. Existing methods like manual assessment, reference-based metrics, and large language model evaluators face limitations in scalability, context capture, or bias. In this paper, we introduce LecEval, an automated metric grounded in Mayer's Cognitive Theory of Multimedia Learning, to evaluate multimodal knowledge acquisition in slide-based learning. LecEval assesses effectiveness using four rubrics: Content Relevance (CR), Expressive Clarity (EC), Logical Structure (LS), and Audience Engagement (AE). We curate a large-scale dataset of over 2,000 slides from more than 50 online course videos, annotated with fine-grained human ratings across these rubrics. A model trained on this dataset demonstrates superior accuracy and adaptability compared to existing metrics, bridging the gap between automated and human assessments. We release our dataset and toolkits at https://github.com/JoylimJY/LecEval.
Transformer models have established new benchmarks in natural language processing; however, their increasing depth results in substantial growth in parameter counts. While existing recurrent transformer methods address this issue by reprocessing layers multiple times, they often apply recurrence indiscriminately across entire blocks of layers. In this work, we investigate Intra-Layer Recurrence (ILR), a more targeted approach that applies recurrence selectively to individual layers within a single forward pass. Our experiments show that allocating more iterations to earlier layers yields optimal results. These findings suggest that ILR offers a promising direction for optimizing recurrent structures in transformer architectures.
Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize advanced neural networks, ranging from convolutional and recurrent models to Transformer-based models, to capture contextual information of gene sequence, with the primary goal of obtaining effective gene sequence representations and thus enhance the models' understanding of various running gene samples. However, these approaches often directly apply language modeling techniques to gene sequences and do not fully consider the intrinsic information organization in them, where they do not consider how units at different granularities contribute to representation. In this paper, we propose DNAZEN, an enhanced genomic representation framework designed to learn from various granularities in gene sequences, including small polymers and G-grams that are combinations of several contiguous polymers. Specifically, we extract the G-grams from large-scale genomic corpora through an unsupervised approach to construct the G-gram vocabulary, which is used to provide G-grams in the learning process of DNA sequences through dynamically matching from running gene samples. A Transformer-based G-gram encoder is also proposed and the matched G-grams are fed into it to compute their representations and integrated into the encoder for basic unit (E4BU), which is responsible for encoding small units and maintaining the learning and inference process. To further enhance the learning process, we propose whole G-gram masking to train DNAZEN, where the model largely favors the selection of each entire G-gram to mask rather than an ordinary masking mechanism performed on basic units. Experiments on benchmark datasets demonstrate the effectiveness of DNAZEN on various downstream tasks.
Target-specific peptides, such as conotoxins, exhibit exceptional binding affinity and selectivity toward ion channels and receptors. However, their therapeutic potential remains underutilized due to the limited diversity of natural variants and the labor-intensive nature of traditional optimization strategies. Here, we present CreoPep, a deep learning-based conditional generative framework that integrates masked language modeling with a progressive masking scheme to design high-affinity peptide mutants while uncovering novel structural motifs. CreoPep employs an integrative augmentation pipeline, combining FoldX-based energy screening with temperature-controlled multinomial sampling, to generate structurally and functionally diverse peptides that retain key pharmacological properties. We validate this approach by designing conotoxin inhibitors targeting the $\alpha$7 nicotinic acetylcholine receptor, achieving submicromolar potency in electrophysiological assays. Structural analysis reveals that CreoPep-generated variants engage in both conserved and novel binding modes, including disulfide-deficient forms, thus expanding beyond conventional design paradigms. Overall, CreoPep offers a robust and generalizable platform that bridges computational peptide design with experimental validation, accelerating the discovery of next-generation peptide therapeutics.
Large language models (LLMs) excel at generating code from natural language instructions, yet they often lack an understanding of security vulnerabilities. This limitation makes it difficult for LLMs to avoid security risks in generated code, particularly in high-security programming tasks such as smart contract development for blockchain. Researchers have attempted to enhance the vulnerability awareness of these models by training them to differentiate between vulnerable and fixed code snippets. However, this approach relies heavily on manually labeled vulnerability data, which is only available for popular languages like Python and C++. For low-resource languages like Solidity, used in smart contracts, large-scale annotated datasets are scarce and difficult to obtain. To address this challenge, we introduce CodeBC, a code generation model specifically designed for generating secure smart contracts in blockchain. CodeBC employs a three-stage fine-tuning approach based on CodeLlama, distinguishing itself from previous methods by not relying on pairwise vulnerability location annotations. Instead, it leverages vulnerability and security tags to teach the model the differences between vulnerable and secure code. During the inference phase, the model leverages security tags to generate secure and robust code. Experimental results demonstrate that CodeBC outperforms baseline models in terms of BLEU, CodeBLEU, and compilation pass rates, while significantly reducing vulnerability rates. These findings validate the effectiveness and cost-efficiency of our three-stage fine-tuning strategy, making CodeBC a promising solution for generating secure smart contract code.
Financial sectors are rapidly adopting language model technologies, yet evaluating specialized RAG systems in this domain remains challenging. This paper introduces SMARTFinRAG, addressing three critical gaps in financial RAG assessment: (1) a fully modular architecture where components can be dynamically interchanged during runtime; (2) a document-centric evaluation paradigm generating domain-specific QA pairs from newly ingested financial documents; and (3) an intuitive interface bridging research-implementation divides. Our evaluation quantifies both retrieval efficacy and response quality, revealing significant performance variations across configurations. The platform's open-source architecture supports transparent, reproducible research while addressing practical deployment challenges faced by financial institutions implementing RAG systems.
With the growing requirement for natural human-computer interaction, speech-based systems receive increasing attention as speech is one of the most common forms of daily communication. However, the existing speech models still experience high latency when generating the first audio token during streaming, which poses a significant bottleneck for deployment. To address this issue, we propose VITA-Audio, an end-to-end large speech model with fast audio-text token generation. Specifically, we introduce a lightweight Multiple Cross-modal Token Prediction (MCTP) module that efficiently generates multiple audio tokens within a single model forward pass, which not only accelerates the inference but also significantly reduces the latency for generating the first audio in streaming scenarios. In addition, a four-stage progressive training strategy is explored to achieve model acceleration with minimal loss of speech quality. To our knowledge, VITA-Audio is the first multi-modal large language model capable of generating audio output during the first forward pass, enabling real-time conversational capabilities with minimal latency. VITA-Audio is fully reproducible and is trained on open-source data only. Experimental results demonstrate that our model achieves an inference speedup of 3~5x at the 7B parameter scale, but also significantly outperforms open-source models of similar model size on multiple benchmarks for automatic speech recognition (ASR), text-to-speech (TTS), and spoken question answering (SQA) tasks.
Learning discriminative 3D representations that generalize well to unknown testing categories is an emerging requirement for many real-world 3D applications. Existing well-established methods often struggle to attain this goal due to insufficient 3D training data from broader concepts. Meanwhile, pre-trained large vision-language models (e.g., CLIP) have shown remarkable zero-shot generalization capabilities. Yet, they are limited in extracting suitable 3D representations due to substantial gaps between their 2D training and 3D testing distributions. To address these challenges, we propose Testing-time Distribution Alignment (TeDA), a novel framework that adapts a pretrained 2D vision-language model CLIP for unknown 3D object retrieval at test time. To our knowledge, it is the first work that studies the test-time adaptation of a vision-language model for 3D feature learning. TeDA projects 3D objects into multi-view images, extracts features using CLIP, and refines 3D query embeddings with an iterative optimization strategy by confident query-target sample pairs in a self-boosting manner. Additionally, TeDA integrates textual descriptions generated by a multimodal language model (InternVL) to enhance 3D object understanding, leveraging CLIP's aligned feature space to fuse visual and textual cues. Extensive experiments on four open-set 3D object retrieval benchmarks demonstrate that TeDA greatly outperforms state-of-the-art methods, even those requiring extensive training. We also experimented with depth maps on Objaverse-LVIS, further validating its effectiveness. Code is available at https://github.com/wangzhichuan123/TeDA.
Recent advances in large language models (LLMs) have sparked growing interest in building fully autonomous agents. However, fully autonomous LLM-based agents still face significant challenges, including limited reliability due to hallucinations, difficulty in handling complex tasks, and substantial safety and ethical risks, all of which limit their feasibility and trustworthiness in real-world applications. To overcome these limitations, LLM-based human-agent systems (LLM-HAS) incorporate human-provided information, feedback, or control into the agent system to enhance system performance, reliability and safety. This paper provides the first comprehensive and structured survey of LLM-HAS. It clarifies fundamental concepts, systematically presents core components shaping these systems, including environment & profiling, human feedback, interaction types, orchestration and communication, explores emerging applications, and discusses unique challenges and opportunities. By consolidating current knowledge and offering a structured overview, we aim to foster further research and innovation in this rapidly evolving interdisciplinary field. Paper lists and resources are available at https://github.com/HenryPengZou/Awesome-LLM-Based-Human-Agent-Systems.
The deployment of deep neural networks on resource-constrained devices necessitates effective model com- pression strategies that judiciously balance the reduction of model size with the preservation of performance. This study introduces a novel safety-driven quantization framework that leverages preservation sets to systematically prune and quantize neural network weights, thereby optimizing model complexity without compromising accuracy. The proposed methodology is rigorously evaluated on both a convolutional neural network (CNN) and an attention-based language model, demonstrating its applicability across diverse architectural paradigms. Experimental results reveal that our framework achieves up to a 2.5% enhancement in test accuracy relative to the original unquantized models while maintaining 60% of the initial model size. In comparison to conventional quantization techniques, our approach not only augments generalization by eliminating parameter noise and retaining essential weights but also reduces variance, thereby ensuring the retention of critical model features. These findings underscore the efficacy of safety-driven quantization as a robust and reliable strategy for the efficient optimization of deep learn- ing models. The implementation and comprehensive experimental evaluations of our framework are publicly accessible at GitHub.
Large language models (LLMs) are capable of generating plausible explanations of how they arrived at an answer to a question. However, these explanations can misrepresent the model's "reasoning" process, i.e., they can be unfaithful. This, in turn, can lead to over-trust and misuse. We introduce a new approach for measuring the faithfulness of LLM explanations. First, we provide a rigorous definition of faithfulness. Since LLM explanations mimic human explanations, they often reference high-level concepts in the input question that purportedly influenced the model. We define faithfulness in terms of the difference between the set of concepts that LLM explanations imply are influential and the set that truly are. Second, we present a novel method for estimating faithfulness that is based on: (1) using an auxiliary LLM to modify the values of concepts within model inputs to create realistic counterfactuals, and (2) using a Bayesian hierarchical model to quantify the causal effects of concepts at both the example- and dataset-level. Our experiments show that our method can be used to quantify and discover interpretable patterns of unfaithfulness. On a social bias task, we uncover cases where LLM explanations hide the influence of social bias. On a medical question answering task, we uncover cases where LLM explanations provide misleading claims about which pieces of evidence influenced the model's decisions.
In this paper, we introduce EasyEdit2, a framework designed to enable plug-and-play adjustability for controlling Large Language Model (LLM) behaviors. EasyEdit2 supports a wide range of test-time interventions, including safety, sentiment, personality, reasoning patterns, factuality, and language features. Unlike its predecessor, EasyEdit2 features a new architecture specifically designed for seamless model steering. It comprises key modules such as the steering vector generator and the steering vector applier, which enable automatic generation and application of steering vectors to influence the model's behavior without modifying its parameters. One of the main advantages of EasyEdit2 is its ease of use-users do not need extensive technical knowledge. With just a single example, they can effectively guide and adjust the model's responses, making precise control both accessible and efficient. Empirically, we report model steering performance across different LLMs, demonstrating the effectiveness of these techniques. We have released the source code on GitHub at https://github.com/zjunlp/EasyEdit along with a demonstration notebook. In addition, we provide a demo video at https://zjunlp.github.io/project/EasyEdit2/video for a quick introduction.
Retrieval-Augmented Generation (RAG) systems often struggle to handle multi-hop question-answering tasks accurately due to irrelevant context retrieval and limited complex reasoning capabilities. We introduce Collab-RAG, a collaborative training framework that leverages mutual enhancement between a white-box small language model (SLM) and a blackbox large language model (LLM) for RAG. Specifically, the SLM decomposes complex queries into simpler sub-questions, thus enhancing the accuracy of the retrieval and facilitating more effective reasoning by the black-box LLM. Concurrently, the black-box LLM provides feedback signals to improve the SLM's decomposition capability. We observe that Collab-RAG relies solely on supervision from an affordable black-box LLM without additional distillation from frontier LLMs, yet demonstrates strong generalization across multiple black-box LLMs. Experimental evaluations across five multi-hop QA datasets demonstrate that Collab-RAG substantially outperforms existing black-box-only and SLM fine-tuning baselines by 1.8%-14.2% on average. In particular, our fine-tuned 3B SLM surpasses a frozen 32B LLM in question decomposition, highlighting the efficiency of Collab-RAG in improving reasoning and retrieval for complex questions. The code of Collab-RAG is available on https://github.com/ritaranx/Collab-RAG/.
Given a sequence of tokens generated by a language model, we may want to identify the preceding tokens that influence the model to generate this sequence. Performing such token attribution is expensive; a common approach is to ablate preceding tokens and directly measure their effects. To reduce the cost of token attribution, we revisit attention weights as a heuristic for how a language model uses previous tokens. Naive approaches to attribute model behavior with attention (e.g., averaging attention weights across attention heads to estimate a token's influence) have been found to be unreliable. To attain faithful attributions, we propose treating the attention weights of different attention heads as features. This way, we can learn how to effectively leverage attention weights for attribution (using signal from ablations). Our resulting method, Attribution with Attention (AT2), reliably performs on par with approaches that involve many ablations, while being significantly more efficient. To showcase the utility of AT2, we use it to prune less important parts of a provided context in a question answering setting, improving answer quality. We provide code for AT2 at https://github.com/MadryLab/AT2 .