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Oct 13

DataFlow-Harness: A Grounded Code-Agent Platform for Constructing Editable LLM Data Pipelines

Large language models (LLMs) are increasingly used to automate data-processing workflows, yet coding agents typically produce scripts that are not automatically materialized as persistent, editable platform artifacts. We call this disconnect the NL2Pipeline gap. To bridge it, we introduce DataFlow-Harness, a platform that guides an LLM agent to construct platform-native directed acyclic graphs (DAGs) through typed, incremental mutations rather than free-form scripts. The platform combines DataFlow-Skills for procedural guidance, a Model Context Protocol (MCP) layer that exposes the live operator registry and current pipeline state, and DataFlow-WebUI, which synchronizes conversational authoring with a visual DAG editor. On a 12-task data-engineering benchmark, DataFlow-Harness achieves a 93.3\% observed end-to-end pass rate. Relative to Vanilla Claude Code, it reduces measured monetary cost by 72.5\% and generation latency by 49.9\%; its observed pass rate is within 0.9 percentage points of the Context-Aware Claude Code baseline while its cost is 42.8\% lower. Per-task analysis indicates that Skills are most useful when construction depends on implicit procedural knowledge. These results show that live platform grounding can produce persistent, editable workflow artifacts with an observed reliability close to script-generation baselines and with lower measured construction cost and latency.

CellForge: Agentic Design of Virtual Cell Models

Virtual cell modeling represents an emerging frontier at the intersection of artificial intelligence and biology, aiming to predict quantities such as responses to diverse perturbations quantitatively. However, autonomously building computational models for virtual cells is challenging due to the complexity of biological systems, the heterogeneity of data modalities, and the need for domain-specific expertise across multiple disciplines. Here, we introduce CellForge, an agentic system that leverages a multi-agent framework that transforms presented biological datasets and research objectives directly into optimized computational models for virtual cells. More specifically, given only raw single-cell multi-omics data and task descriptions as input, CellForge outputs both an optimized model architecture and executable code for training virtual cell models and inference. The framework integrates three core modules: Task Analysis for presented dataset characterization and relevant literature retrieval, Method Design, where specialized agents collaboratively develop optimized modeling strategies, and Experiment Execution for automated generation of code. The agents in the Design module are separated into experts with differing perspectives and a central moderator, and have to collaboratively exchange solutions until they achieve a reasonable consensus. We demonstrate CellForge's capabilities in single-cell perturbation prediction, using six diverse datasets that encompass gene knockouts, drug treatments, and cytokine stimulations across multiple modalities. CellForge consistently outperforms task-specific state-of-the-art methods. Overall, CellForge demonstrates how iterative interaction between LLM agents with differing perspectives provides better solutions than directly addressing a modeling challenge. Our code is publicly available at https://github.com/gersteinlab/CellForge.

  • 15 authors
·
Aug 4, 2025 2

RescueADI: Adaptive Disaster Interpretation in Remote Sensing Images with Autonomous Agents

Current methods for disaster scene interpretation in remote sensing images (RSIs) mostly focus on isolated tasks such as segmentation, detection, or visual question-answering (VQA). However, current interpretation methods often fail at tasks that require the combination of multiple perception methods and specialized tools. To fill this gap, this paper introduces Adaptive Disaster Interpretation (ADI), a novel task designed to solve requests by planning and executing multiple sequentially correlative interpretation tasks to provide a comprehensive analysis of disaster scenes. To facilitate research and application in this area, we present a new dataset named RescueADI, which contains high-resolution RSIs with annotations for three connected aspects: planning, perception, and recognition. The dataset includes 4,044 RSIs, 16,949 semantic masks, 14,483 object bounding boxes, and 13,424 interpretation requests across nine challenging request types. Moreover, we propose a new disaster interpretation method employing autonomous agents driven by large language models (LLMs) for task planning and execution, proving its efficacy in handling complex disaster interpretations. The proposed agent-based method solves various complex interpretation requests such as counting, area calculation, and path-finding without human intervention, which traditional single-task approaches cannot handle effectively. Experimental results on RescueADI demonstrate the feasibility of the proposed task and show that our method achieves an accuracy 9% higher than existing VQA methods, highlighting its advantages over conventional disaster interpretation approaches. The dataset will be publicly available.

  • 3 authors
·
Oct 17, 2024

Bridging the Novice-Expert Gap via Models of Decision-Making: A Case Study on Remediating Math Mistakes

Scaling high-quality tutoring remains a major challenge in education. Due to growing demand, many platforms employ novice tutors who, unlike experienced educators, struggle to address student mistakes and thus fail to seize prime learning opportunities. Our work explores the potential of large language models (LLMs) to close the novice-expert knowledge gap in remediating math mistakes. We contribute Bridge, a method that uses cognitive task analysis to translate an expert's latent thought process into a decision-making model for remediation. This involves an expert identifying (A) the student's error, (B) a remediation strategy, and (C) their intention before generating a response. We construct a dataset of 700 real tutoring conversations, annotated by experts with their decisions. We evaluate state-of-the-art LLMs on our dataset and find that the expert's decision-making model is critical for LLMs to close the gap: responses from GPT4 with expert decisions (e.g., "simplify the problem") are +76% more preferred than without. Additionally, context-sensitive decisions are critical to closing pedagogical gaps: random decisions decrease GPT4's response quality by -97% than expert decisions. Our work shows the potential of embedding expert thought processes in LLM generations to enhance their capability to bridge novice-expert knowledge gaps. Our dataset and code can be found at: https://github.com/rosewang2008/bridge.

  • 5 authors
·
Oct 16, 2023

Unified Ultrasound Intelligence Toward an End-to-End Agentic System

Clinical ultrasound analysis demands models that generalize across heterogeneous organs, views, and devices, while supporting interpretable workflow-level analysis. Existing methods often rely on task-wise adaptation, and joint learning may be unstable due to cross-task interference, making it hard to deliver workflow-level outputs in practice. To address these challenges, we present USTri, a tri-stage ultrasound intelligence pipeline for unified multi-organ, multi-task analysis. Stage I trains a universal generalist USGen on different domains to learn broad, transferable priors that are robust to device and protocol variability. To better handle domain shifts and reach task-aligned performance while preserving ultrasound shared knowledge, Stage II builds USpec by keeping USGen frozen and finetuning dataset-specific heads. Stage III introduces USAgent, which mimics clinician workflows by orchestrating USpec specialists for multi-step inference and deterministic structured reports. On the FMC\_UIA validation set, our model achieves the best overall performance across 4 task types and 27 datasets, outperforming state-of-the-art methods. Moreover, qualitative results show that USAgent produces clinically structured reports with high accuracy and interpretability. Our study suggests a scalable path to ultrasound intelligence that generalizes across heterogeneous ultrasound tasks and supports consistent end-to-end clinical workflows. The code is publicly available at: https://github.com/MacDunno/USTri.

  • 6 authors
·
Apr 21

Agentic AI and Occupational Displacement: A Multi-Regional Task Exposure Analysis of Emerging Labor Market Disruption

This paper extends the Acemoglu-Restrepo task exposure framework to address the labor market effects of agentic artificial intelligence systems: autonomous AI agents capable of completing entire occupational workflows rather than discrete tasks. Unlike prior automation technologies that substitute for individual subtasks, agentic AI systems execute end-to-end workflows involving multi-step reasoning, tool invocation, and autonomous decision-making, substantially expanding occupational displacement risk beyond what existing task-level analyses capture. We introduce the Agentic Task Exposure (ATE) score, a composite measure computed algorithmically from O*NET task data using calibrated adoption parameters--not a regression estimate--incorporating AI capability scores, workflow coverage factors, and logistic adoption velocity. Applying the ATE framework across five major US technology regions (Seattle-Tacoma, San Francisco Bay Area, Austin, New York, and Boston) over a 2025-2030 horizon, we find that 93.2% of the 236 analyzed occupations across six information-intensive SOC groups (financial, legal, healthcare, healthcare support, sales, and administrative/clerical) cross the moderate-risk threshold (ATE >= 0.35) in Tier 1 regions by 2030, with credit analysts, judges, and sustainability specialists reaching ATE scores of 0.43-0.47. We simultaneously identify seventeen emerging occupational categories benefiting from reinstatement effects, concentrated in human-AI collaboration, AI governance, and domain-specific AI operations roles. Our findings carry implications for workforce transition policy, regional economic planning, and the temporal dynamics of labor market adjustment

  • 2 authors
·
Mar 30

SentZero: An Enhanced Sentence-Centric Vision-Language Pretraining for Multi-Task Zero-Shot Chest X-Ray Analysis

Vision-language (VL) pretraining using paired chest X-ray (CXR) images and radiology reports has shown strong potential for medical image understanding. However, existing methods often remain dependent on task-specific finetuning because radiology reports are lengthy, clinically dense, and difficult to align with simple zero-shot prompts. Recent sentence-level approaches partially address this limitation using clinical phrases extracted by large language models (LLMs), but they largely overlook the intrinsic characteristics of radiology discourse. In particular, limited positive-pair diversity constrains further gains, while clinically equivalent sentences frequently recur across patients, creating false negatives in contrastive learning. To address these issues, we propose SentZero, an enhanced sentence-centric VL pretraining framework for zero-shot, multi-task CXR analysis. SentZero introduces LLM-based abstract-level sentence structuring and mapping to expand positive-pair diversity, together with an additional loss term to mitigate false negatives. We further introduce sentence-conditioned residual modulation of visual embeddings, enabling visual features to adapt to the semantic characteristics of each input sentence. Across diverse downstream tasks and datasets, SentZero improves zero-shot generalization and outperforms prior multi-task zero-shot methods.

  • 4 authors
·
Sep 27 1

The Imperative of Conversation Analysis in the Era of LLMs: A Survey of Tasks, Techniques, and Trends

In the era of large language models (LLMs), a vast amount of conversation logs will be accumulated thanks to the rapid development trend of language UI. Conversation Analysis (CA) strives to uncover and analyze critical information from conversation data, streamlining manual processes and supporting business insights and decision-making. The need for CA to extract actionable insights and drive empowerment is becoming increasingly prominent and attracting widespread attention. However, the lack of a clear scope for CA leads to a dispersion of various techniques, making it difficult to form a systematic technical synergy to empower business applications. In this paper, we perform a thorough review and systematize CA task to summarize the existing related work. Specifically, we formally define CA task to confront the fragmented and chaotic landscape in this field, and derive four key steps of CA from conversation scene reconstruction, to in-depth attribution analysis, and then to performing targeted training, finally generating conversations based on the targeted training for achieving the specific goals. In addition, we showcase the relevant benchmarks, discuss potential challenges and point out future directions in both industry and academia. In view of current advancements, it is evident that the majority of efforts are still concentrated on the analysis of shallow conversation elements, which presents a considerable gap between the research and business, and with the assist of LLMs, recent work has shown a trend towards research on causality and strategic tasks which are sophisticated and high-level. The analyzed experiences and insights will inevitably have broader application value in business operations that target conversation logs.

  • 6 authors
·
Sep 21, 2024 2

AI-Facilitated Analysis of Abstracts and Conclusions: Flagging Unsubstantiated Claims and Ambiguous Pronouns

We present and evaluate a suite of proof-of-concept (PoC), structured workflow prompts designed to elicit human-like hierarchical reasoning while guiding Large Language Models (LLMs) in the high-level semantic and linguistic analysis of scholarly manuscripts. The prompts target two non-trivial analytical tasks within academic summaries (abstracts and conclusions): identifying unsubstantiated claims (informational integrity) and flagging semantically confusing ambiguous pronoun references (linguistic clarity). We conducted a systematic, multi-run evaluation on two frontier models (Gemini Pro 2.5 Pro and ChatGPT Plus o3) under varied context conditions. Our results for the informational integrity task reveal a significant divergence in model performance: while both models successfully identified an unsubstantiated head of a noun phrase (95% success), ChatGPT consistently failed (0% success) to identify an unsubstantiated adjectival modifier that Gemini correctly flagged (95% success), raising a question regarding the potential influence of the target's syntactic role. For the linguistic analysis task, both models performed well (80-90% success) with full manuscript context. Surprisingly, in a summary-only setting, Gemini's performance was substantially degraded, while ChatGPT achieved a perfect (100%) success rate. Our findings suggest that while structured prompting is a viable methodology for complex textual analysis, prompt performance may be highly dependent on the interplay between the model, task type, and context, highlighting the need for rigorous, model-specific testing.

  • 1 authors
·
Jun 16, 2025 2

A Contrastive Cross-Channel Data Augmentation Framework for Aspect-based Sentiment Analysis

Aspect-based sentiment analysis (ABSA) is a fine-grained sentiment analysis task, which focuses on detecting the sentiment polarity towards the aspect in a sentence. However, it is always sensitive to the multi-aspect challenge, where features of multiple aspects in a sentence will affect each other. To mitigate this issue, we design a novel training framework, called Contrastive Cross-Channel Data Augmentation (C3 DA), which leverages an in-domain generator to construct more multi-aspect samples and then boosts the robustness of ABSA models via contrastive learning on these generated data. In practice, given a generative pretrained language model and some limited ABSA labeled data, we first employ some parameter-efficient approaches to perform the in-domain fine-tuning. Then, the obtained in-domain generator is used to generate the synthetic sentences from two channels, i.e., Aspect Augmentation Channel and Polarity Augmentation Channel, which generate the sentence condition on a given aspect and polarity respectively. Specifically, our C3 DA performs the sentence generation in a cross-channel manner to obtain more sentences, and proposes an Entropy-Minimization Filter to filter low-quality generated samples. Extensive experiments show that our C3 DA can outperform those baselines without any augmentations by about 1% on accuracy and Macro- F1. Code and data are released in https://github.com/wangbing1416/C3DA.

  • 5 authors
·
Apr 16, 2022

ImageRAG: Enhancing Ultra High Resolution Remote Sensing Imagery Analysis with ImageRAG

Ultra High Resolution (UHR) remote sensing imagery (RSI) (e.g. 100,000 times 100,000 pixels or more) poses a significant challenge for current Remote Sensing Multimodal Large Language Models (RSMLLMs). If choose to resize the UHR image to standard input image size, the extensive spatial and contextual information that UHR images contain will be neglected. Otherwise, the original size of these images often exceeds the token limits of standard RSMLLMs, making it difficult to process the entire image and capture long-range dependencies to answer the query based on the abundant visual context. In this paper, we introduce ImageRAG for RS, a training-free framework to address the complexities of analyzing UHR remote sensing imagery. By transforming UHR remote sensing image analysis task to image's long context selection task, we design an innovative image contextual retrieval mechanism based on the Retrieval-Augmented Generation (RAG) technique, denoted as ImageRAG. ImageRAG's core innovation lies in its ability to selectively retrieve and focus on the most relevant portions of the UHR image as visual contexts that pertain to a given query. Fast path and slow path are proposed in this framework to handle this task efficiently and effectively. ImageRAG allows RSMLLMs to manage extensive context and spatial information from UHR RSI, ensuring the analysis is both accurate and efficient. Codebase will be released in https://github.com/om-ai-lab/ImageRAG

  • 10 authors
·
Nov 12, 2024

SwinFace: A Multi-task Transformer for Face Recognition, Expression Recognition, Age Estimation and Attribute Estimation

In recent years, vision transformers have been introduced into face recognition and analysis and have achieved performance breakthroughs. However, most previous methods generally train a single model or an ensemble of models to perform the desired task, which ignores the synergy among different tasks and fails to achieve improved prediction accuracy, increased data efficiency, and reduced training time. This paper presents a multi-purpose algorithm for simultaneous face recognition, facial expression recognition, age estimation, and face attribute estimation (40 attributes including gender) based on a single Swin Transformer. Our design, the SwinFace, consists of a single shared backbone together with a subnet for each set of related tasks. To address the conflicts among multiple tasks and meet the different demands of tasks, a Multi-Level Channel Attention (MLCA) module is integrated into each task-specific analysis subnet, which can adaptively select the features from optimal levels and channels to perform the desired tasks. Extensive experiments show that the proposed model has a better understanding of the face and achieves excellent performance for all tasks. Especially, it achieves 90.97% accuracy on RAF-DB and 0.22 epsilon-error on CLAP2015, which are state-of-the-art results on facial expression recognition and age estimation respectively. The code and models will be made publicly available at https://github.com/lxq1000/SwinFace.

  • 7 authors
·
Aug 22, 2023

AdaptiveLog: An Adaptive Log Analysis Framework with the Collaboration of Large and Small Language Model

Automated log analysis is crucial to ensure high availability and reliability of complex systems. The advent of LLMs in NLP has ushered in a new era of language model-driven automated log analysis, garnering significant interest. Within this field, two primary paradigms based on language models for log analysis have become prominent. Small Language Models (SLMs) follow the pre-train and fine-tune paradigm, focusing on the specific log analysis task through fine-tuning on supervised datasets. On the other hand, LLMs following the in-context learning paradigm, analyze logs by providing a few examples in prompt contexts without updating parameters. Despite their respective strengths, we notice that SLMs are more cost-effective but less powerful, whereas LLMs with large parameters are highly powerful but expensive and inefficient. To trade-off between the performance and inference costs of both models in automated log analysis, this paper introduces an adaptive log analysis framework known as AdaptiveLog, which effectively reduces the costs associated with LLM while ensuring superior results. This framework collaborates an LLM and a small language model, strategically allocating the LLM to tackle complex logs while delegating simpler logs to the SLM. Specifically, to efficiently query the LLM, we propose an adaptive selection strategy based on the uncertainty estimation of the SLM, where the LLM is invoked only when the SLM is uncertain. In addition, to enhance the reasoning ability of the LLM in log analysis tasks, we propose a novel prompt strategy by retrieving similar error-prone cases as the reference, enabling the model to leverage past error experiences and learn solutions from these cases. Extensive experiments demonstrate that AdaptiveLog achieves state-of-the-art results across different tasks, elevating the overall accuracy of log analysis while maintaining cost efficiency.

  • 9 authors
·
Jan 19, 2025

EmoLLMs: A Series of Emotional Large Language Models and Annotation Tools for Comprehensive Affective Analysis

Sentiment analysis and emotion detection are important research topics in natural language processing (NLP) and benefit many downstream tasks. With the widespread application of LLMs, researchers have started exploring the application of LLMs based on instruction-tuning in the field of sentiment analysis. However, these models only focus on single aspects of affective classification tasks (e.g. sentimental polarity or categorical emotions), and overlook the regression tasks (e.g. sentiment strength or emotion intensity), which leads to poor performance in downstream tasks. The main reason is the lack of comprehensive affective instruction tuning datasets and evaluation benchmarks, which cover various affective classification and regression tasks. Moreover, although emotional information is useful for downstream tasks, existing downstream datasets lack high-quality and comprehensive affective annotations. In this paper, we propose EmoLLMs, the first series of open-sourced instruction-following LLMs for comprehensive affective analysis based on fine-tuning various LLMs with instruction data, the first multi-task affective analysis instruction dataset (AAID) with 234K data samples based on various classification and regression tasks to support LLM instruction tuning, and a comprehensive affective evaluation benchmark (AEB) with 14 tasks from various sources and domains to test the generalization ability of LLMs. We propose a series of EmoLLMs by fine-tuning LLMs with AAID to solve various affective instruction tasks. We compare our model with a variety of LLMs on AEB, where our models outperform all other open-sourced LLMs, and surpass ChatGPT and GPT-4 in most tasks, which shows that the series of EmoLLMs achieve the ChatGPT-level and GPT-4-level generalization capabilities on affective analysis tasks, and demonstrates our models can be used as affective annotation tools.

  • 6 authors
·
Jan 16, 2024

Class-Agnostic Region-of-Interest Matching in Document Images

Document understanding and analysis have received a lot of attention due to their widespread application. However, existing document analysis solutions, such as document layout analysis and key information extraction, are only suitable for fixed category definitions and granularities, and cannot achieve flexible applications customized by users. Therefore, this paper defines a new task named ``Class-Agnostic Region-of-Interest Matching'' (``RoI-Matching'' for short), which aims to match the customized regions in a flexible, efficient, multi-granularity, and open-set manner. The visual prompt of the reference document and target document images are fed into our model, while the output is the corresponding bounding boxes in the target document images. To meet the above requirements, we construct a benchmark RoI-Matching-Bench, which sets three levels of difficulties following real-world conditions, and propose the macro and micro metrics to evaluate. Furthermore, we also propose a new framework RoI-Matcher, which employs a siamese network to extract multi-level features both in the reference and target domains, and cross-attention layers to integrate and align similar semantics in different domains. Experiments show that our method with a simple procedure is effective on RoI-Matching-Bench, and serves as the baseline for further research. The code is available at https://github.com/pd162/RoI-Matching.

  • 4 authors
·
Jun 25, 2025

Trackastra: Transformer-based cell tracking for live-cell microscopy

Cell tracking is a ubiquitous image analysis task in live-cell microscopy. Unlike multiple object tracking (MOT) for natural images, cell tracking typically involves hundreds of similar-looking objects that can divide in each frame, making it a particularly challenging problem. Current state-of-the-art approaches follow the tracking-by-detection paradigm, i.e. first all cells are detected per frame and successively linked in a second step to form biologically consistent cell tracks. Linking is commonly solved via discrete optimization methods, which require manual tuning of hyperparameters for each dataset and are therefore cumbersome to use in practice. Here we propose Trackastra, a general purpose cell tracking approach that uses a simple transformer architecture to directly learn pairwise associations of cells within a temporal window from annotated data. Importantly, unlike existing transformer-based MOT pipelines, our learning architecture also accounts for dividing objects such as cells and allows for accurate tracking even with simple greedy linking, thus making strides towards removing the requirement for a complex linking step. The proposed architecture operates on the full spatio-temporal context of detections within a time window by avoiding the computational burden of processing dense images. We show that our tracking approach performs on par with or better than highly tuned state-of-the-art cell tracking algorithms for various biological datasets, such as bacteria, cell cultures and fluorescent particles. We provide code at https://github.com/weigertlab/trackastra.

  • 2 authors
·
Jul 23, 2024

BiomechGPT: Extending Motion-Language Models to Clinical Motion Understanding

Advances in markerless motion capture are making high-quality biomechanical data increasingly accessible, creating a growing need for scalable downstream analytics. Building a bespoke pipeline for each analysis task is time-consuming, motivating models that can flexibly handle diverse clinical questions within a single framework. Recent work has shown that fine-tuning language models to accept tokenized motion as an additional modality enables descriptive captioning of movement, raising the question of whether these models are also capable of clinically relevant motion understanding, where diverse tasks and annotations provide a natural testbed. We investigate whether such a multimodal motion--language model can answer detailed, clinically meaningful questions about movement. We collected 71 hours of biomechanical data from 750 participants, many with movement impairments, performing tasks commonly used in clinical assessment. To further expand the training dataset, we designed a cross-format tokenizer that directly encodes motion data from heterogeneous formats into a shared latent space without paired data, allowing a second dataset to be incorporated and enabling pooling annotations across datasets. From these tokenized representations, we constructed a multimodal dataset of motion-related question--answer pairs and used it to train BiomechGPT, a multimodal biomechanics--language model. BiomechGPT achieves competitive performance across a range of clinically relevant tasks, with performance scaling with both dataset and model size. It offers a new way for clinicians and researchers to interact with biomechanical data and represents a promising direction for rehabilitation-focused movement analysis. Project page: https://intelligentsensingandrehabilitation.github.io/BiomechGPT/

  • 3 authors
·
Jul 9

TunBERT: Pretrained Contextualized Text Representation for Tunisian Dialect

Pretrained contextualized text representation models learn an effective representation of a natural language to make it machine understandable. After the breakthrough of the attention mechanism, a new generation of pretrained models have been proposed achieving good performances since the introduction of the Transformer. Bidirectional Encoder Representations from Transformers (BERT) has become the state-of-the-art model for language understanding. Despite their success, most of the available models have been trained on Indo-European languages however similar research for under-represented languages and dialects remains sparse. In this paper, we investigate the feasibility of training monolingual Transformer-based language models for under represented languages, with a specific focus on the Tunisian dialect. We evaluate our language model on sentiment analysis task, dialect identification task and reading comprehension question-answering task. We show that the use of noisy web crawled data instead of structured data (Wikipedia, articles, etc.) is more convenient for such non-standardized language. Moreover, results indicate that a relatively small web crawled dataset leads to performances that are as good as those obtained using larger datasets. Finally, our best performing TunBERT model reaches or improves the state-of-the-art in all three downstream tasks. We release the TunBERT pretrained model and the datasets used for fine-tuning.

  • 9 authors
·
Nov 25, 2021

MolSpectLLM: A Molecular Foundation Model Bridging Spectroscopy, Molecule Elucidation, and 3D Structure Generation

Recent advances in molecular foundation models have shown impressive performance in molecular property prediction and de novo molecular design, with promising applications in areas such as drug discovery and reaction prediction. Nevertheless, most existing approaches rely exclusively on SMILES representations and overlook both experimental spectra and 3D structural information-two indispensable sources for capturing molecular behavior in real-world scenarios. This limitation reduces their effectiveness in tasks where stereochemistry, spatial conformation, and experimental validation are critical. To overcome these challenges, we propose MolSpectLLM, a molecular foundation model pretrained on Qwen2.5-7B that unifies experimental spectroscopy with molecular 3D structure. By explicitly modeling molecular spectra, MolSpectLLM achieves state-of-the-art performance on spectrum-related tasks, with an average accuracy of 0.53 across NMR, IR, and MS benchmarks. MolSpectLLM also shows strong performance on the spectra analysis task, obtaining 15.5% sequence accuracy and 41.7% token accuracy on Spectra-to-SMILES, substantially outperforming large general-purpose LLMs. More importantly, MolSpectLLM not only achieves strong performance on molecular elucidation tasks, but also generates accurate 3D molecular structures directly from SMILES or spectral inputs, bridging spectral analysis, molecular elucidation, and molecular design. Code are available at https://github.com/Eurekashen/MolSpectLLM{https://github.com/Eurekashen/MolSpectLLM}.

  • 9 authors
·
Sep 26, 2025

How to build the best medical image segmentation algorithm using foundation models: a comprehensive empirical study with Segment Anything Model

Automated segmentation is a fundamental medical image analysis task, which enjoys significant advances due to the advent of deep learning. While foundation models have been useful in natural language processing and some vision tasks for some time, the foundation model developed with image segmentation in mind - Segment Anything Model (SAM) - has been developed only recently and has shown similar promise. However, there are still no systematic analyses or "best-practice" guidelines for optimal fine-tuning of SAM for medical image segmentation. This work summarizes existing fine-tuning strategies with various backbone architectures, model components, and fine-tuning algorithms across 18 combinations, and evaluates them on 17 datasets covering all common radiology modalities. Our study reveals that (1) fine-tuning SAM leads to slightly better performance than previous segmentation methods, (2) fine-tuning strategies that use parameter-efficient learning in both the encoder and decoder are superior to other strategies, (3) network architecture has a small impact on final performance, (4) further training SAM with self-supervised learning can improve final model performance. We also demonstrate the ineffectiveness of some methods popular in the literature and further expand our experiments into few-shot and prompt-based settings. Lastly, we released our code and MRI-specific fine-tuned weights, which consistently obtained superior performance over the original SAM, at https://github.com/mazurowski-lab/finetune-SAM.

  • 4 authors
·
Apr 15, 2024

Swin UNETR: Swin Transformers for Semantic Segmentation of Brain Tumors in MRI Images

Semantic segmentation of brain tumors is a fundamental medical image analysis task involving multiple MRI imaging modalities that can assist clinicians in diagnosing the patient and successively studying the progression of the malignant entity. In recent years, Fully Convolutional Neural Networks (FCNNs) approaches have become the de facto standard for 3D medical image segmentation. The popular "U-shaped" network architecture has achieved state-of-the-art performance benchmarks on different 2D and 3D semantic segmentation tasks and across various imaging modalities. However, due to the limited kernel size of convolution layers in FCNNs, their performance of modeling long-range information is sub-optimal, and this can lead to deficiencies in the segmentation of tumors with variable sizes. On the other hand, transformer models have demonstrated excellent capabilities in capturing such long-range information in multiple domains, including natural language processing and computer vision. Inspired by the success of vision transformers and their variants, we propose a novel segmentation model termed Swin UNEt TRansformers (Swin UNETR). Specifically, the task of 3D brain tumor semantic segmentation is reformulated as a sequence to sequence prediction problem wherein multi-modal input data is projected into a 1D sequence of embedding and used as an input to a hierarchical Swin transformer as the encoder. The swin transformer encoder extracts features at five different resolutions by utilizing shifted windows for computing self-attention and is connected to an FCNN-based decoder at each resolution via skip connections. We have participated in BraTS 2021 segmentation challenge, and our proposed model ranks among the top-performing approaches in the validation phase. Code: https://monai.io/research/swin-unetr

  • 6 authors
·
Jan 4, 2022

Set2Seq Transformer: Temporal and Position-Aware Set Representations for Sequential Multiple-Instance Learning

In many real-world applications, modeling both the internal structure of sets and their temporal relationships is essential for capturing complex underlying patterns. Sequential multiple-instance learning aims to address this challenge by learning permutation-invariant representations of sets distributed across discrete timesteps. However, existing methods either focus on learning set representations at a static level, ignoring temporal dynamics, or treat sequences as ordered lists of individual elements, lacking explicit mechanisms for representing sets. Crucially, effective modeling of such sequences of sets often requires encoding both the positional ordering across timesteps and their absolute temporal values to jointly capture relative progression and temporal context. In this work, we propose Set2Seq Transformer, a novel architecture that jointly models permutation-invariant set structure and temporal dependencies by learning temporal and position-aware representations of sets within a sequence in an end-to-end multimodal manner. We evaluate our Set2Seq Transformer on two tasks that require modeling set structure alongside temporal and positional patterns, but differ significantly in domain, modality, and objective. First, we consider a fine art analysis task, modeling artists' oeuvres for predicting artistic success using a novel dataset, WikiArt-Seq2Rank. Second, we utilize our Set2Seq Transformer for short-term wildfire danger forecasting. Through extensive experimentation, we show that our Set2Seq Transformer consistently improves over traditional static multiple-instance learning methods by effectively learning permutation-invariant set, temporal, and position-aware representations across diverse domains, modalities, and tasks. We release all code and datasets at https://github.com/thefth/set2seq-transformer.

  • 5 authors
·
Aug 6, 2024

VipAct: Visual-Perception Enhancement via Specialized VLM Agent Collaboration and Tool-use

While vision-language models (VLMs) have demonstrated remarkable performance across various tasks combining textual and visual information, they continue to struggle with fine-grained visual perception tasks that require detailed pixel-level analysis. Effectively eliciting comprehensive reasoning from VLMs on such intricate visual elements remains an open challenge. In this paper, we present VipAct, an agent framework that enhances VLMs by integrating multi-agent collaboration and vision expert models, enabling more precise visual understanding and comprehensive reasoning. VipAct consists of an orchestrator agent, which manages task requirement analysis, planning, and coordination, along with specialized agents that handle specific tasks such as image captioning and vision expert models that provide high-precision perceptual information. This multi-agent approach allows VLMs to better perform fine-grained visual perception tasks by synergizing planning, reasoning, and tool use. We evaluate VipAct on benchmarks featuring a diverse set of visual perception tasks, with experimental results demonstrating significant performance improvements over state-of-the-art baselines across all tasks. Furthermore, comprehensive ablation studies reveal the critical role of multi-agent collaboration in eliciting more detailed System-2 reasoning and highlight the importance of image input for task planning. Additionally, our error analysis identifies patterns of VLMs' inherent limitations in visual perception, providing insights into potential future improvements. VipAct offers a flexible and extensible framework, paving the way for more advanced visual perception systems across various real-world applications.

  • 10 authors
·
Oct 21, 2024

DuPLUS: Dual-Prompt Vision-Language Framework for Universal Medical Image Segmentation and Prognosis

Deep learning for medical imaging is hampered by task-specific models that lack generalizability and prognostic capabilities, while existing 'universal' approaches suffer from simplistic conditioning and poor medical semantic understanding. To address these limitations, we introduce DuPLUS, a deep learning framework for efficient multi-modal medical image analysis. DuPLUS introduces a novel vision-language framework that leverages hierarchical semantic prompts for fine-grained control over the analysis task, a capability absent in prior universal models. To enable extensibility to other medical tasks, it includes a hierarchical, text-controlled architecture driven by a unique dual-prompt mechanism. For segmentation, DuPLUS is able to generalize across three imaging modalities, ten different anatomically various medical datasets, encompassing more than 30 organs and tumor types. It outperforms the state-of-the-art task specific and universal models on 8 out of 10 datasets. We demonstrate extensibility of its text-controlled architecture by seamless integration of electronic health record (EHR) data for prognosis prediction, and on a head and neck cancer dataset, DuPLUS achieved a Concordance Index (CI) of 0.69. Parameter-efficient fine-tuning enables rapid adaptation to new tasks and modalities from varying centers, establishing DuPLUS as a versatile and clinically relevant solution for medical image analysis. The code for this work is made available at: https://anonymous.4open.science/r/DuPLUS-6C52

  • 6 authors
·
Oct 3, 2025

Training Prompt Matters: State-Adaptive Optimization for Robust Fine-Tuning

While prompt engineering is instrumental in maximizing the capabilities of Large Language Models (LLMs) during inference, the role of prompts during training remains critically underexplored. Prevailing fine-tuning paradigms typically treat training prompts as mere surface forms, assuming that semantically equivalent instructions yield identical learning outcomes. However, we reveal that this equivalence is deceptive: while paraphrased prompts often lead to comparable in-task performance, they induce drastically different cross-task impacts regarding catastrophic forgetting and generalization. Crucially, these impacts are positively correlated across tasks, indicating the existence of superior prompts that consistently yield better performance. Furthermore, we discover that these superior prompts can be robustly identified by task loss prior to learning. Leveraging these insights, we introduce State-Adaptive Prompt Optimization (SAPO), a lightweight yet effective training strategy that shifts task formulation from a static input to a dynamic, state-adaptive variable. Comprehensive experiments on diverse benchmarks confirm its effectiveness, which significantly mitigates forgetting while improving generalization, achieving substantial performance gains over state-of-the-art methods. These results provide insights into how training prompts shape learning dynamics and offer a practical recipe for robust fine-tuning. Our code is available at https://github.com/Eric8932/SAPO.

  • 8 authors
·
Jun 1

Gaze Target Estimation Anywhere with Concepts

Estimating human gaze targets from images in-the-wild is an important and formidable task. Existing approaches primarily employ brittle, multi-stage pipelines that require explicit inputs, like head bounding boxes and human pose, in order to identify the subject of gaze analysis. As a result, detection errors can cascade and lead to failure. Moreover, these prior works lack the flexibility of specifying the gaze analysis task via natural language prompting, an approach which has been shown to have significant benefits in convenience and scalability for other image analysis tasks. To overcome these limitations, we introduce the Promptable Gaze Target Estimation (PGE) task, a new end-to-end, concept-driven paradigm for gaze analysis. PGE conditions gaze prediction on flexible user text or visual prompts (e.g., "the boy in the red shirt" or "person in point [0.52, 0.48]") to identify a specific subject for gaze analysis. This approach integrates subject localization with gaze estimation, and eliminates the rigid dependency on intermediate analysis stages. We develop a scalable data engine to generate Gaze-Co (Gaze Estimation with Concepts), a dataset and benchmark of 120K high-quality, prompt-annotated image pairs. We also propose GazeAnywhere, the first model designed for PGE. GazeAnywhere uses a transformer-based detector to fuse features from frozen encoders and simultaneously solves subject localization, in/out-of-frame presence, and gaze target heatmap estimation. GazeAnywhere achieves state-of-the-art performance on multiple PGE benchmarks, setting a strong baseline for this new problem even on a difficult out-of-domain, real-world clinical dataset. GazeAnywhere is open-sourced in github.com/IrohXu/GazeAnywhere.

google Google
·
Aug 10 2

TPS-Bench: Evaluating AI Agents' Tool Planning \& Scheduling Abilities in Compounding Tasks

Large language model (LLM) agents have exhibited strong problem-solving competence across domains like research and coding. Yet, it remains underexplored whether LLM agents can tackle compounding real-world problems that require a diverse set of tools to complete. Given a broad, heterogeneous tool repository, LLM agents must not only select appropriate tools based on task planning analysis but also strategically schedule the execution order to ensure efficiency. This paper introduces TPS-Bench to benchmark the ability of LLM agents in solving such problems that demand Tool Planning and Scheduling. TPS-Bench collects 200 compounding tasks of two difficulty levels, based on a tool repository containing hundreds of model context protocol (MCP) tools. In particular, each task is composed of multiple subtasks, such as web search, map navigation, calendar checking, etc., and each subtask can be completed by a basic tool. Our evaluation emphasizes both task completion rate and efficiency. The empirical studies on popular closed-source and open-source LLMs indicate that most models can perform reasonable tool planning, but differ in scheduling. For example, GLM-4.5 achieves an outperforming task completion rate of 64.72% with extensive sequential tool calls, hence suffering from significantly long execution time. By contrast, GPT-4o prioritizes parallel tool calls but achieves only a 45.08% completion rate. Considering reinforcement learning (RL) can be a viable way to improve the scheduling efficiency without compromising performance, we perform an initial study on Qwen3-1.7B and witness a 14% reduction in execution time alongside a 6% gain in task completion rate based on rarely 100 RL training samples. Our code is available https://github.com/hanwenxu1/mcp-agent.

  • 5 authors
·
Nov 2, 2025

WILLIE: A Unified Framework and Benchmark for Wound Classification, Segmentation, and Localization

Chronic wound management affects over 8.2 million patients in the United States and imposes substantial clinical and economic burden. Clinical wound assessment commonly involves three coupled tasks: identifying wound type, delineating wound boundaries, and localizing the wound region for measurement and monitoring. Despite this clinical coupling, existing machine learning approaches typically address wound classification, segmentation, and localization using separate models. We present WILLIE, a unified framework and benchmark for wound classification, segmentation and localization that enables systematic evaluation of multi-task wound analysis under a common protocol. WILLIE harmonizes three public wound datasets into a shared benchmark and compares unified models across three scaling configurations against 10 single-task baselines. The best model achieves 91.88% classification accuracy, 91.41% Dice, and 96.23% AP@0.5 while producing all three outputs in a single forward pass. Beyond aggregate performance, our results show that segmentation-derived localization outperforms dedicated detection baselines in this benchmark, suggesting that box-based localization may be unnecessary for spatially coherent wound targets. Our findings highlight that effective multi-task learning in healthcare imaging depends not only on shared representations, but also on task formulation, compatibility, and benchmark design.

  • 5 authors
·
Oct 3

Pre-training Data Quality and Quantity for a Low-Resource Language: New Corpus and BERT Models for Maltese

Multilingual language models such as mBERT have seen impressive cross-lingual transfer to a variety of languages, but many languages remain excluded from these models. In this paper, we analyse the effect of pre-training with monolingual data for a low-resource language that is not included in mBERT -- Maltese -- with a range of pre-training set ups. We conduct evaluations with the newly pre-trained models on three morphosyntactic tasks -- dependency parsing, part-of-speech tagging, and named-entity recognition -- and one semantic classification task -- sentiment analysis. We also present a newly created corpus for Maltese, and determine the effect that the pre-training data size and domain have on the downstream performance. Our results show that using a mixture of pre-training domains is often superior to using Wikipedia text only. We also find that a fraction of this corpus is enough to make significant leaps in performance over Wikipedia-trained models. We pre-train and compare two models on the new corpus: a monolingual BERT model trained from scratch (BERTu), and a further pre-trained multilingual BERT (mBERTu). The models achieve state-of-the-art performance on these tasks, despite the new corpus being considerably smaller than typically used corpora for high-resourced languages. On average, BERTu outperforms or performs competitively with mBERTu, and the largest gains are observed for higher-level tasks.

  • 5 authors
·
May 21, 2022

RouteJudge: An Open Platform for Reproducible and Preference-Aware LLM Routing

We present RouteJudge, an online pairwise preference evaluation framework for LLM routing systems, with a public platform available at https://routejudge.cn. Different from model-level response evaluation, RouteJudge focuses on router-level decision quality. For each user query, multiple routing strategies independently recommend candidate models under the same model pool and budget constraints. The selected model responses are then presented to users through anonymous pairwise comparisons, and the resulting user preferences are attributed back to the routing strategies behind the compared responses. Each evaluation record stores the query, routing decisions, model responses, preference labels, cost, latency, and task metadata, enabling preference-aware, cost-aware, and task-conditioned analysis of LLM routers. To support the continuous expansion of routing methods in RouteJudge, we further release ORBIT (Optimal Routing and Budgeted Inference Toolbox), a modular and extensible toolbox that standardizes the end-to-end workflow of LLM routing. ORBIT provides unified interfaces for benchmark loading, query representation, router implementation, budget-aware evaluation, and method comparison, allowing researchers to develop and evaluate routing algorithms under consistent protocols. It also serves as the submission and integration layer for RouteJudge: researchers can implement routing methods within ORBIT, validate them on existing routing benchmarks, and submit compatible routers for online preference-based evaluation. The code of ORBIT is available at https://github.com/LAMDA-Model-Reuse/ORBIT.

  • 3 authors
·
Jun 18

TAP-SLF: Parameter-Efficient Adaptation of Vision Foundation Models for Multi-Task Ultrasound Image Analysis

Executing multiple tasks simultaneously in medical image analysis, including segmentation, classification, detection, and regression, often introduces significant challenges regarding model generalizability and the optimization of shared feature representations. While Vision Foundation Models (VFMs) provide powerful general representations, full fine-tuning on limited medical data is prone to overfitting and incurs high computational costs. Moreover, existing parameter-efficient fine-tuning approaches typically adopt task-agnostic adaptation protocols, overlooking both task-specific mechanisms and the varying sensitivity of model layers during fine-tuning. In this work, we propose Task-Aware Prompting and Selective Layer Fine-Tuning (TAP-SLF), a unified framework for multi-task ultrasound image analysis. TAP-SLF incorporates task-aware soft prompts to encode task-specific priors into the input token sequence and applies LoRA to selected specific top layers of the encoder. This strategy updates only a small fraction of the VFM parameters while keeping the pre-trained backbone frozen. By combining task-aware prompts with selective high-layer fine-tuning, TAP-SLF enables efficient VFM adaptation to diverse medical tasks within a shared backbone. Results on the FMC_UIA 2026 Challenge test set, where TAP-SLF wins fifth place, combined with evaluations on the officially released training dataset using an 8:2 train-test split, demonstrate that task-aware prompting and selective layer tuning are effective strategies for efficient VFM adaptation.

  • 2 authors
·
Feb 27

MT-Depth: Multi-task Instance feature analysis for the Depth Completion

Depth completion plays a vital role in 3D perception systems, especially in scenarios where sparse depth data must be densified for tasks such as autonomous driving, robotics, and augmented reality. While many existing approaches rely on semantic segmentation to guide depth completion, they often overlook the benefits of object-level understanding. In this work, we introduce an instance-aware depth completion framework that explicitly integrates binary instance masks as spatial priors to refine depth predictions. Our model combines four main components: a frozen YOLO V11 instance segmentation branch, a U-Net-based depth completion backbone, a cross-attention fusion module, and an attention-guided prediction head. The instance segmentation branch generates per-image foreground masks that guide the depth branch via cross-attention, allowing the network to focus on object-centric regions during refinement. We validate our method on the Virtual KITTI 2 dataset, showing that it achieves lower Root Mean Squared Error (RMSE) compared to both a U-Net-only baseline and previous semantic-guided methods, while maintaining competitive Mean Absolute Error (MAE). Qualitative and quantitative results demonstrate that the proposed model effectively enhances depth accuracy near object boundaries, occlusions, and thin structures. Our findings suggest that incorporating instance-aware cues offers a promising direction for improving depth completion without relying on dense semantic labels.

  • 3 authors
·
Dec 8, 2025

RoboLab: A High-Fidelity Simulation Benchmark for Analysis of Task Generalist Policies

The pursuit of general-purpose robotics has yielded impressive foundation models, yet simulation-based benchmarking remains a bottleneck due to rapid performance saturation and a lack of true generalization testing. Existing benchmarks often exhibit significant domain overlap between training and evaluation, trivializing success rates and obscuring insights into robustness. We introduce RoboLab, a simulation benchmarking framework designed to address these challenges. Concretely, our framework is designed to answer two questions: (1) to what extent can we understand the performance of a real-world policy by analyzing its behavior in simulation, and (2) which external factors most strongly affect that behavior under controlled perturbations. First, RoboLab enables human-authored and LLM-enabled generation of scenes and tasks in a robot- and policy-agnostic manner within a physically realistic and photorealistic simulation. With this, we propose the RoboLab-120 benchmark, consisting of 120 tasks categorized into three competency axes: visual, procedural, relational competency, across three difficulty levels. Second, we introduce a systematic analysis of real-world policies that quantify both their performance and the sensitivity of their behavior to controlled perturbations, indicating that high-fidelity simulation can serve as a proxy for analyzing performance and its dependence on external factors. Evaluation with RoboLab exposes significant performance gap in current state-of-the-art models. By providing granular metrics and a scalable toolset, RoboLab offers a scalable framework for evaluating the true generalization capabilities of task-generalist robotic policies.

nvidia NVIDIA
·
Apr 13 2

Knowledge Graph Augmented Network Towards Multiview Representation Learning for Aspect-based Sentiment Analysis

Aspect-based sentiment analysis (ABSA) is a fine-grained task of sentiment analysis. To better comprehend long complicated sentences and obtain accurate aspect-specific information, linguistic and commonsense knowledge are generally required in this task. However, most current methods employ complicated and inefficient approaches to incorporate external knowledge, e.g., directly searching the graph nodes. Additionally, the complementarity between external knowledge and linguistic information has not been thoroughly studied. To this end, we propose a knowledge graph augmented network KGAN, which aims to effectively incorporate external knowledge with explicitly syntactic and contextual information. In particular, KGAN captures the sentiment feature representations from multiple different perspectives, i.e., context-, syntax- and knowledge-based. First, KGAN learns the contextual and syntactic representations in parallel to fully extract the semantic features. Then, KGAN integrates the knowledge graphs into the embedding space, based on which the aspect-specific knowledge representations are further obtained via an attention mechanism. Last, we propose a hierarchical fusion module to complement these multi-view representations in a local-to-global manner. Extensive experiments on five popular ABSA benchmarks demonstrate the effectiveness and robustness of our KGAN. Notably, with the help of the pretrained model of RoBERTa, KGAN achieves a new record of state-of-the-art performance among all datasets.

  • 6 authors
·
Jan 13, 2022

TFM Dataset: A Novel Multi-task Dataset and Integrated Pipeline for Automated Tear Film Break-Up Segmentation

Tear film break-up (TFBU) analysis is critical for diagnosing dry eye syndrome, but automated TFBU segmentation remains challenging due to the lack of annotated datasets and integrated solutions. This paper introduces the Tear Film Multi-task (TFM) Dataset, the first comprehensive dataset for multi-task tear film analysis, comprising 15 high-resolution videos (totaling 6,247 frames) annotated with three vision tasks: frame-level classification ('clear', 'closed', 'broken', 'blur'), Placido Ring detection, and pixel-wise TFBU area segmentation. Leveraging this dataset, we first propose TF-Net, a novel and efficient baseline segmentation model. TF-Net incorporates a MobileOne-mini backbone with re-parameterization techniques and an enhanced feature pyramid network to achieve a favorable balance between accuracy and computational efficiency for real-time clinical applications. We further establish benchmark performance on the TFM segmentation subset by comparing TF-Net against several state-of-the-art medical image segmentation models. Furthermore, we design TF-Collab, a novel integrated real-time pipeline that synergistically leverages models trained on all three tasks of the TFM dataset. By sequentially orchestrating frame classification for BUT determination, pupil region localization for input standardization, and TFBU segmentation, TF-Collab fully automates the analysis. Experimental results demonstrate the effectiveness of the proposed TF-Net and TF-Collab, providing a foundation for future research in ocular surface diagnostics. Our code and the TFM datasets are available at https://github.com/glory-wan/TF-Net

  • 7 authors
·
Oct 7, 2025

Beyond Activation Alignment:The Alignment-Diversity Tradeoff in Task-Aware LLM Quantization

Mixed-precision quantization (MPQ) has become a key technique for deploying large language models under stringent memory and compute constraints. We first identify a phenomenon that we term the Perplexity Illusion: layers ranked as important by perplexity-based sensitivity show little rank correlation with those that are most influential for complex reasoning performance, with Kendall τapprox 0 in our analysis. We further reveal an Alignment-Diversity Tradeoff: using only target-task calibration data can degrade post-quantization performance, whereas incorporating general-domain data stabilizes sensitivity estimation and improves robustness across tasks. Based on these observations, we propose TASA (Task-Aware Sensitivity Analysis), a two-level framework that jointly optimizes calibration-data composition and mixed-precision bit allocation. Specifically, TASA searches for a calibration-data mixture using a training-free gradient-trace alignment criterion, and then aggregates perplexity and reasoning-oriented sensitivity signals to guide both inter-layer and intra-layer bit allocation. Experiments on LLaMA-3-8B and Qwen2.5-7B reveal a precision inversion: appropriately allocated 3.5-bit models can match or surpass less task-aware 4-bit baselines. At an average precision of 3.5 bits, TASA matches or outperforms several competitive 4-bit uniform baselines in aggregate accuracy, and improves over the strongest W3 baseline on GSM8K by more than 20 absolute points on LLaMA-3-8B. These results show that calibration-data composition substantially affects task-sensitive quantization, a factor underexplored in prior work.

  • 6 authors
·
Jun 30

Comet: Fine-grained Computation-communication Overlapping for Mixture-of-Experts

Mixture-of-experts (MoE) has been extensively employed to scale large language models to trillion-plus parameters while maintaining a fixed computational cost. The development of large MoE models in the distributed scenario encounters the problem of large communication overhead. The inter-device communication of a MoE layer can occupy 47% time of the entire model execution with popular models and frameworks. Therefore, existing methods suggest the communication in a MoE layer to be pipelined with the computation for overlapping. However, these coarse grained overlapping schemes introduce a notable impairment of computational efficiency and the latency concealing is sub-optimal. To this end, we present COMET, an optimized MoE system with fine-grained communication-computation overlapping. Leveraging data dependency analysis and task rescheduling, COMET achieves precise fine-grained overlapping of communication and computation. Through adaptive workload assignment, COMET effectively eliminates fine-grained communication bottlenecks and enhances its adaptability across various scenarios. Our evaluation shows that COMET accelerates the execution of a single MoE layer by 1.96times and for end-to-end execution, COMET delivers a 1.71times speedup on average. COMET has been adopted in the production environment of clusters with ten-thousand-scale of GPUs, achieving savings of millions of GPU hours.

  • 12 authors
·
Feb 27, 2025

DrafterBench: Benchmarking Large Language Models for Tasks Automation in Civil Engineering

Large Language Model (LLM) agents have shown great potential for solving real-world problems and promise to be a solution for tasks automation in industry. However, more benchmarks are needed to systematically evaluate automation agents from an industrial perspective, for example, in Civil Engineering. Therefore, we propose DrafterBench for the comprehensive evaluation of LLM agents in the context of technical drawing revision, a representation task in civil engineering. DrafterBench contains twelve types of tasks summarized from real-world drawing files, with 46 customized functions/tools and 1920 tasks in total. DrafterBench is an open-source benchmark to rigorously test AI agents' proficiency in interpreting intricate and long-context instructions, leveraging prior knowledge, and adapting to dynamic instruction quality via implicit policy awareness. The toolkit comprehensively assesses distinct capabilities in structured data comprehension, function execution, instruction following, and critical reasoning. DrafterBench offers detailed analysis of task accuracy and error statistics, aiming to provide deeper insight into agent capabilities and identify improvement targets for integrating LLMs in engineering applications. Our benchmark is available at https://github.com/Eason-Li-AIS/DrafterBench, with the test set hosted at https://huggingface.co/datasets/Eason666/DrafterBench.

  • 3 authors
·
Jul 15, 2025 1

LongBench Pro: A More Realistic and Comprehensive Bilingual Long-Context Evaluation Benchmark

The rapid expansion of context length in large language models (LLMs) has outpaced existing evaluation benchmarks. Current long-context benchmarks often trade off scalability and realism: synthetic tasks underrepresent real-world complexity, while fully manual annotation is costly to scale to extreme lengths and diverse scenarios. We present LongBench Pro, a more realistic and comprehensive bilingual benchmark of 1,500 naturally occurring long-context samples in English and Chinese spanning 11 primary tasks and 25 secondary tasks, with input lengths from 8k to 256k tokens. LongBench Pro supports fine-grained analysis with task-specific metrics and a multi-dimensional taxonomy of context requirement (full vs. partial dependency), length (six levels), and difficulty (four levels calibrated by model performance). To balance quality with scalability, we propose a Human-Model Collaborative Construction pipeline: frontier LLMs draft challenging questions and reference answers, along with design rationales and solution processes, to reduce the cost of expert verification. Experts then rigorously validate correctness and refine problematic cases. Evaluating 46 widely used long-context LLMs on LongBench Pro yields three findings: (1) long-context optimization contributes more to long-context comprehension than parameter scaling; (2) effective context length is typically shorter than the claimed context length, with pronounced cross-lingual misalignment; and (3) the "thinking" paradigm helps primarily models trained with native reasoning, while mixed-thinking designs offer a promising Pareto trade-off. In summary, LongBench Pro provides a robust testbed for advancing long-context understanding.

  • 7 authors
·
Jan 6

MolDeTox: Evaluating Language Model's Stepwise Fragment Editing for Molecular Detoxification

Large Language Models (LLMs) and Vision Language Models (VLMs) have recently shown promising capabilities in various scientific domain. In particular, these advances have opened new opportunities in drug discovery, where the ability to understand and modify molecular structures is critical for optimizing drug properties such as efficacy and toxicity. However, existing models and benchmarks often overlook toxicity-related challenges, focusing primarily on general property optimization without adequately addressing safety concerns. In addition, even existing toxicity repair benchmarks suffer from limited data diversity, low structural validity of generated molecules, and heavy reliance on proxy models for toxicity assessment. To address these limitations, we propose MolDeTox, a novel benchmark for molecular detoxification, designed to enable fine-grained and reliable evaluation of toxicity-aware molecular optimization across stepwise tasks. We evaluate a wide range of general-purpose LLMs and VLMs under diverse settings, and demonstrate that understanding and generating molecules at the fragment-level improves structural validity and enhances the quality of generated molecules. Moreover, through detailed task-level performance analysis, MolDeTox provides an interpretable benchmark that enables a deeper understanding of the detoxification process. Our dataset is available at : https://huggingface.co/datasets/MolDeTox/MolDeTox

  • 5 authors
·
May 11

A Sublinear Algorithm for Approximate Shortest Paths in Large Networks

Computing distances and finding shortest paths in massive real-world networks is a fundamental algorithmic task in network analysis. There are two main approaches to solving this task. On one hand are traversal-based algorithms like bidirectional breadth-first search (BiBFS) with no preprocessing step and slow individual distance inquiries. On the other hand are indexing-based approaches, which maintain a large index. This allows for answering individual inquiries very fast; however, index creation is prohibitively expensive. We seek to bridge these two extremes: quickly answer distance inquiries without the need for costly preprocessing. In this work, we propose a new algorithm and data structure, WormHole, for approximate shortest path computations. WormHole leverages structural properties of social networks to build a sublinearly sized index, drawing upon the explicit core-periphery decomposition of Ben-Eliezer et al. Empirically, the preprocessing time of WormHole improves upon index-based solutions by orders of magnitude, and individual inquiries are consistently much faster than in BiBFS. The acceleration comes at the cost of a minor accuracy trade-off. Nonetheless, our empirical evidence demonstrates that WormHole accurately answers essentially all inquiries within a maximum additive error of 2. We complement these empirical results with provable theoretical guarantees, showing that WormHole requires n^{o(1)} node queries per distance inquiry in random power-law networks. In contrast, any approach without a preprocessing step requires n^{Ω(1)} queries for the same task. WormHole does not require reading the whole graph. Unlike the vast majority of index-based algorithms, it returns paths, not just distances. For faster inquiry times, it can be combined effectively with other index-based solutions, by running them only on the sublinear core.

  • 5 authors
·
Jun 11, 2024

Can Large Language Models Explain Themselves? A Study of LLM-Generated Self-Explanations

Large language models (LLMs) such as ChatGPT have demonstrated superior performance on a variety of natural language processing (NLP) tasks including sentiment analysis, mathematical reasoning and summarization. Furthermore, since these models are instruction-tuned on human conversations to produce "helpful" responses, they can and often will produce explanations along with the response, which we call self-explanations. For example, when analyzing the sentiment of a movie review, the model may output not only the positivity of the sentiment, but also an explanation (e.g., by listing the sentiment-laden words such as "fantastic" and "memorable" in the review). How good are these automatically generated self-explanations? In this paper, we investigate this question on the task of sentiment analysis and for feature attribution explanation, one of the most commonly studied settings in the interpretability literature (for pre-ChatGPT models). Specifically, we study different ways to elicit the self-explanations, evaluate their faithfulness on a set of evaluation metrics, and compare them to traditional explanation methods such as occlusion or LIME saliency maps. Through an extensive set of experiments, we find that ChatGPT's self-explanations perform on par with traditional ones, but are quite different from them according to various agreement metrics, meanwhile being much cheaper to produce (as they are generated along with the prediction). In addition, we identified several interesting characteristics of them, which prompt us to rethink many current model interpretability practices in the era of ChatGPT(-like) LLMs.

  • 5 authors
·
Oct 17, 2023

Geometrically-Constrained Agent for Spatial Reasoning

Vision Language Models (VLMs) exhibit a fundamental semantic-to-geometric gap in spatial reasoning: they excel at qualitative semantic inference but their reasoning operates within a lossy semantic space, misaligned with high-fidelity geometry. Current paradigms fail to bridge this gap. Training-based methods suffer from an ``oracle paradox,'' learning flawed spatial logic from imperfect oracles. Tool-integrated methods constrain the final computation but critically leave the VLM's planning process unconstrained, resulting in geometrically flawed plans. In this work, we propose Geometrically-Constrained Agent (GCA), a training-free agentic paradigm that resolves this gap by introducing a formal task constraint. Specifically, we strategically decouples the VLM's role into two stages. First, acting as a semantic analyst, the VLM translates the user's ambiguous query into the formal, verifiable task constraint, which defines the reference frame and objective. Second, acting as a task solver, the VLM generates and executes tool calls strictly within the deterministic bounds defined by the constraint. This geometrically-constrained reasoning strategy successfully resolve the semantic-to-geometric gap, yielding a robust and verifiable reasoning pathway for spatial reasoning. Comprehensive experiments demonstrate that GCA achieves SOTA performance on multiple spatial reasoning benchmarks, surpassing existing training-based and tool-integrated methods by ~27%. Please see our homepage at https://gca-spatial-reasoning.github.io.

  • 9 authors
·
Nov 27, 2025 2

MM-OPERA: Benchmarking Open-ended Association Reasoning for Large Vision-Language Models

Large Vision-Language Models (LVLMs) have exhibited remarkable progress. However, deficiencies remain compared to human intelligence, such as hallucination and shallow pattern matching. In this work, we aim to evaluate a fundamental yet underexplored intelligence: association, a cornerstone of human cognition for creative thinking and knowledge integration. Current benchmarks, often limited to closed-ended tasks, fail to capture the complexity of open-ended association reasoning vital for real-world applications. To address this, we present MM-OPERA, a systematic benchmark with 11,497 instances across two open-ended tasks: Remote-Item Association (RIA) and In-Context Association (ICA), aligning association intelligence evaluation with human psychometric principles. It challenges LVLMs to resemble the spirit of divergent thinking and convergent associative reasoning through free-form responses and explicit reasoning paths. We deploy tailored LLM-as-a-Judge strategies to evaluate open-ended outputs, applying process-reward-informed judgment to dissect reasoning with precision. Extensive empirical studies on state-of-the-art LVLMs, including sensitivity analysis of task instances, validity analysis of LLM-as-a-Judge strategies, and diversity analysis across abilities, domains, languages, cultures, etc., provide a comprehensive and nuanced understanding of the limitations of current LVLMs in associative reasoning, paving the way for more human-like and general-purpose AI. The dataset and code are available at https://github.com/MM-OPERA-Bench/MM-OPERA.

  • 12 authors
·
Oct 29, 2025

TDATR: Improving End-to-End Table Recognition via Table Detail-Aware Learning and Cell-Level Visual Alignment

Tables are pervasive in diverse documents, making table recognition (TR) a fundamental task in document analysis. Existing modular TR pipelines separately model table structure and content, leading to suboptimal integration and complex workflows. End-to-end approaches rely heavily on large-scale TR data and struggle in data-constrained scenarios. To address these issues, we propose TDATR (Table Detail-Aware Table Recognition) improves end-to-end TR through table detail-aware learning and cell-level visual alignment. TDATR adopts a ``perceive-then-fuse'' strategy. The model first performs table detail-aware learning to jointly perceive table structure and content through multiple structure understanding and content recognition tasks designed under a language modeling paradigm. These tasks can naturally leverage document data from diverse scenarios to enhance model robustness. The model then integrates implicit table details to generate structured HTML outputs, enabling more efficient TR modeling when trained with limited data. Furthermore, we design a structure-guided cell localization module integrated into the end-to-end TR framework, which efficiently locates cell and strengthens vision-language alignment. It enhances the interpretability and accuracy of TR. We achieve state-of-the-art or highly competitive performance on seven benchmarks without dataset-specific fine-tuning.

  • 7 authors
·
Mar 24

What Makes a Good Terminal-Agent Benchmark Task: A Guideline for Adversarial, Difficult, and Legible Evaluation Design

Terminal-agent benchmarks have become a primary signal for measuring the coding and system-administration capabilities of large language models. As the market for evaluation environments grows, so does the pressure to ship tasks quickly, often without thorough adversarial review of the verification logic. This paper is a guideline for writing good benchmark tasks, drawn from over a year of contributing to and reviewing tasks for Terminal Bench. Most people write benchmark tasks the way they write prompts. They shouldn't. A prompt is designed to help the agent succeed; a benchmark is designed to find out if it can. We argue that good tasks are adversarial, difficult, and legible, and that a large class of common failure modes -- AI-generated instructions, over-prescriptive specifications, clerical difficulty, oracle solutions that assume hidden knowledge, tests that validate the wrong things, and reward-hackable environments -- are predictable consequences of treating task authoring as prompt authoring. We catalog these failure modes, argue that real difficulty is conceptual rather than environmental, and discuss recent empirical evidence that over 15% of tasks in popular terminal-agent benchmarks are reward-hackable. We hope this serves as a useful reference for benchmark maintainers, task contributors, and researchers using benchmark scores as evidence.

  • 1 authors
·
Apr 29

WANDR: A Benchmark for Wide and Deep Research

WANDR (Wide ANd Deep Research) is a benchmark of 500 realistic, challenging data-collection tasks for research agents. Each task requires a system to discover a large set of entities that satisfy specified criteria (breadth), investigate each entity through multiple coordinated web searches (depth), and return independently verifiable records with supporting sources and excerpts. Tasks are represented as qualification key hierarchies that specify the entities, relationships, evidence, and required count at each level; a hierarchy with n companies, m employees per company, and k sources per employee requires n x m x k records. This structure supports diverse workflows such as market mapping, due diligence, literature review, product comparison, and talent sourcing, with targets ranging from dozens to thousands of records. WANDR replaces static gold answer sets with task-specific judges that refetch cited pages and verify each record against its evidence, allowing evaluation of current and changing facts. Record verdicts are aggregated into soft and hard precision, recall, and F1 scores that distinguish factual quality, coverage, and hierarchical completeness. The tasks are derived from de-identified product-usage logs and produced through a semi-automated pipeline with automated checks, empirical audits, and human review where needed. We evaluate six production research systems and find that the benchmark is far from saturated: at high effort, the strongest system reaches only 0.363 soft F1 and 0.133 hard F1. Performance degrades as target volume and hierarchy depth increase, with incomplete discovery, missing enrichment, and incomplete evidence construction remaining major bottlenecks. The benchmark and evaluation harness are available at https://github.com/perplexityai/wandr.

  • 10 authors
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Aug 13

A Comparative Analysis of Machine Learning Algorithms for Multi-Task Prediction of the Parameters of the Pectin Hydrolysis--Extraction Process

This study addresses the challenge of controlling a complex, multi-parameter technological process -- pectin hydrolysis--extraction -- using machine learning methods. The experimental foundation is a unique database comprising 1,000 laboratory experiments conducted under controlled conditions on seven types of plant raw material with four variable process factors (temperature 85--130 C, pressure 0.9--2.2 atm, holding time 3--10 min, pH 1.5--2.0). Four output characteristics were recorded: pectin yield, galacturonic acid content, molecular weight, and degree of esterification. To solve the multi-task regression problem, 11 algorithms were trained and compared: regularised linear models, ensemble methods (Random Forest, Gradient Boosting, XGBoost, CatBoost, Extra Trees), k-nearest neighbours, support vector regression, and a multilayer perceptron. The best results were demonstrated by CatBoost (average R-squared approximately 0.946 after hyperparameter optimisation). Feature importance analysis revealed the dominant role of the raw material type (63.6% of total importance), followed by temperature and holding time. The developed pipeline was exported in a production-ready format and deployed as an interactive web interface. The findings demonstrate that ensemble methods combined with rigorous statistical analysis and interpretable AI significantly reduce the need for physical experiments and form the basis for intelligent pectin production control.

  • 3 authors
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May 29

The Hard Part Comes After Search: Benchmarking Web Agents on Synthesizing, Organizing, and Displaying Knowledge

Existing computer-use agent benchmarks do not fully evaluate agents acting as assistants. A useful assistant retrieves information across complex, multi-step workflows, synthesizes it into artifacts (documents, presentations, spreadsheets), and navigates program interfaces to produce a coherent final product. Such workflows demand reasoning and synthesis, decomposition of complex tasks, as well as visual and spatial understanding. To study agents on workflows like these, we introduce KNOWS, a benchmark of open-ended, complex, browser-based tasks that jointly evaluate these capabilities, with each task culminating in a produced artifact. To write tasks, we develop a task design rubric and a protocol for ensuring that tasks meet the requirements. Each task is paired with an evaluator, a program that combines deterministic checks with LLM judgments to balance the richness, reliability, and automation tradeoff inherent to agent evaluation. We evaluate and analyze frontier computer-use agents and browser-based harnesses. They achieve moderate scores on partial-success metrics, but the best performer fully succeeds in fewer than 3% of our complex, long-horizon tasks. Failures on visual steps render the resulting artifacts unusable, even when agents complete more than 50% of other evaluation steps. Our results expose limitations of current agents acting as end-to-end assistants, and call for progress on tool use, visual understanding, and long-horizon reasoning.

  • 9 authors
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Sep 23

Entity-Level Sentiment Analysis (ELSA): An exploratory task survey

This paper explores the task of identifying the overall sentiment expressed towards volitional entities (persons and organizations) in a document -- what we refer to as Entity-Level Sentiment Analysis (ELSA). While identifying sentiment conveyed towards an entity is well researched for shorter texts like tweets, we find little to no research on this specific task for longer texts with multiple mentions and opinions towards the same entity. This lack of research would be understandable if ELSA can be derived from existing tasks and models. To assess this, we annotate a set of professional reviews for their overall sentiment towards each volitional entity in the text. We sample from data already annotated for document-level, sentence-level, and target-level sentiment in a multi-domain review corpus, and our results indicate that there is no single proxy task that provides this overall sentiment we seek for the entities at a satisfactory level of performance. We present a suite of experiments aiming to assess the contribution towards ELSA provided by document-, sentence-, and target-level sentiment analysis, and provide a discussion of their shortcomings. We show that sentiment in our dataset is expressed not only with an entity mention as target, but also towards targets with a sentiment-relevant relation to a volitional entity. In our data, these relations extend beyond anaphoric coreference resolution, and our findings call for further research of the topic. Finally, we also present a survey of previous relevant work.

  • 3 authors
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Apr 26, 2023

Enhancing Document Information Analysis with Multi-Task Pre-training: A Robust Approach for Information Extraction in Visually-Rich Documents

This paper introduces a deep learning model tailored for document information analysis, emphasizing document classification, entity relation extraction, and document visual question answering. The proposed model leverages transformer-based models to encode all the information present in a document image, including textual, visual, and layout information. The model is pre-trained and subsequently fine-tuned for various document image analysis tasks. The proposed model incorporates three additional tasks during the pre-training phase, including reading order identification of different layout segments in a document image, layout segments categorization as per PubLayNet, and generation of the text sequence within a given layout segment (text block). The model also incorporates a collective pre-training scheme where losses of all the tasks under consideration, including pre-training and fine-tuning tasks with all datasets, are considered. Additional encoder and decoder blocks are added to the RoBERTa network to generate results for all tasks. The proposed model achieved impressive results across all tasks, with an accuracy of 95.87% on the RVL-CDIP dataset for document classification, F1 scores of 0.9306, 0.9804, 0.9794, and 0.8742 on the FUNSD, CORD, SROIE, and Kleister-NDA datasets respectively for entity relation extraction, and an ANLS score of 0.8468 on the DocVQA dataset for visual question answering. The results highlight the effectiveness of the proposed model in understanding and interpreting complex document layouts and content, making it a promising tool for document analysis tasks.

  • 2 authors
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Oct 25, 2023