Daily Papers

Recent advances in protein structure prediction have achieved near-atomic accuracy for well-folded proteins. However, current benchmarks inadequately assess model performance in biologically challenging contexts, especially those involving intrinsically disordered regions (IDRs), limiting their utility in applications such as drug discovery, disease variant interpretation, and protein interface design. We introduce DisProtBench, a comprehensive benchmark for evaluating protein structure prediction models (PSPMs) under structural disorder and complex biological conditions. DisProtBench spans three key axes: (1) Data complexity, covering disordered regions, G protein-coupled receptor (GPCR) ligand pairs, and multimeric complexes; (2) Task diversity, benchmarking twelve leading PSPMs across structure-based tasks with unified classification, regression, and interface metrics; and (3) Interpretability, via the DisProtBench Portal, which provides precomputed 3D structures and visual error analyses. Our results reveal significant variability in model robustness under disorder, with low-confidence regions linked to functional prediction failures. Notably, global accuracy metrics often fail to predict task performance in disordered settings, emphasizing the need for function-aware evaluation. DisProtBench establishes a reproducible, extensible, and biologically grounded framework for assessing next-generation PSPMs in realistic biomedical scenarios.

Code-recommendation systems, such as Copilot and CodeWhisperer, have the potential to improve programmer productivity by suggesting and auto-completing code. However, to fully realize their potential, we must understand how programmers interact with these systems and identify ways to improve that interaction. To make progress, we studied GitHub Copilot, a code-recommendation system used by millions of programmers daily. We developed CUPS, a taxonomy of common programmer activities when interacting with Copilot. Our study of 21 programmers, who completed coding tasks and retrospectively labeled their sessions with CUPS, showed that CUPS can help us understand how programmers interact with code-recommendation systems, revealing inefficiencies and time costs. Our insights reveal how programmers interact with Copilot and motivate new interface designs and metrics.

Integrating Large Language Models (LLMs) with Knowledge Graphs (KGs) results in complex systems with numerous hyperparameters that directly affect performance. While such systems are increasingly common in retrieval-augmented generation, the role of systematic hyperparameter optimization remains underexplored. In this paper, we study this problem in the context of Cognee, a modular framework for end-to-end KG construction and retrieval. Using three multi-hop QA benchmarks (HotPotQA, TwoWikiMultiHop, and MuSiQue) we optimize parameters related to chunking, graph construction, retrieval, and prompting. Each configuration is scored using established metrics (exact match, F1, and DeepEval's LLM-based correctness metric). Our results demonstrate that meaningful gains can be achieved through targeted tuning. While the gains are consistent, they are not uniform, with performance varying across datasets and metrics. This variability highlights both the value of tuning and the limitations of standard evaluation measures. While demonstrating the immediate potential of hyperparameter tuning, we argue that future progress will depend not only on architectural advances but also on clearer frameworks for optimization and evaluation in complex, modular systems.

We introduce gec-metrics, a library for using and developing grammatical error correction (GEC) evaluation metrics through a unified interface. Our library enables fair system comparisons by ensuring that everyone conducts evaluations using a consistent implementation. Moreover, it is designed with a strong focus on API usage, making it highly extensible. It also includes meta-evaluation functionalities and provides analysis and visualization scripts, contributing to developing GEC evaluation metrics. Our code is released under the MIT license and is also distributed as an installable package. The video is available on YouTube.

Automating the conversion of UI images into web code is a critical task for front-end development and rapid prototyping. Advances in multimodal large language models (MLLMs) have made WebUI-to-Code increasingly feasible, yet existing benchmarks remain limited in data diversity and evaluation reliability. To address these issues, we present WebRenderBench, a large-scale benchmark of 22.5k webpages collected from real-world portal sites, offering greater diversity, complexity, and realism than prior benchmarks. We further propose a novel evaluation metric that measures layout and style consistency from the final rendered pages. Unlike vision-based methods that rely on costly LLM reasoning or structure-based comparisons vulnerable to noise and asymmetry, our approach enables more efficient, objective, and reliable UI quality assessment. Finally, we introduce the Automated Layout and Style Inspection Agent (ALISA), which integrates this metric into reinforcement learning as a reward signal to enhance training on crawled asymmetric webpages. Experiments show that ALISA significantly boosts generation performance, achieving state-of-the-art results across multiple metrics.

Large language models (LLMs) power many state-of-the-art systems in natural language processing. However, these models are extremely computationally expensive, even at inference time, raising the natural question: when is the extra cost of deploying a larger model worth the anticipated boost in capabilities? Better understanding this tradeoff fundamentally could benefit from an inference efficiency metric that is both (i) easily comparable across models from different providers, and (ii) representative of the true cost of running queries in an isolated performance environment. Unfortunately, access to LLMs today is largely restricted to black-box text generation APIs and raw runtimes measured through this interface do not satisfy these desiderata: model providers can apply various software and hardware optimizations orthogonal to the model, and models served on shared infrastructure are susceptible to performance contention. To circumvent these problems, we propose a new metric for comparing inference efficiency across models. This metric puts models on equal footing as though they were served (i) on uniform hardware and software, and (ii) without performance contention. We call this metric the idealized runtime, and we propose a methodology to efficiently estimate this metric for autoregressive Transformer models. We also propose cost-aware variants that incorporate the number of accelerators needed to serve the model. Using these metrics, we compare ten state-of-the-art LLMs to provide the first analysis of inference efficiency-capability tradeoffs; we make several observations from this analysis, including the fact that the superior inference runtime performance of certain APIs is often a byproduct of optimizations within the API rather than the underlying model. Our methodology also facilitates the efficient comparison of different software and hardware stacks.

We aim to evaluate Large Language Models (LLMs) for embodied decision making. While a significant body of work has been leveraging LLMs for decision making in embodied environments, we still lack a systematic understanding of their performance because they are usually applied in different domains, for different purposes, and built based on different inputs and outputs. Furthermore, existing evaluations tend to rely solely on a final success rate, making it difficult to pinpoint what ability is missing in LLMs and where the problem lies, which in turn blocks embodied agents from leveraging LLMs effectively and selectively. To address these limitations, we propose a generalized interface (Embodied Agent Interface) that supports the formalization of various types of tasks and input-output specifications of LLM-based modules. Specifically, it allows us to unify 1) a broad set of embodied decision-making tasks involving both state and temporally extended goals, 2) four commonly-used LLM-based modules for decision making: goal interpretation, subgoal decomposition, action sequencing, and transition modeling, and 3) a collection of fine-grained metrics which break down evaluation into various types of errors, such as hallucination errors, affordance errors, various types of planning errors, etc. Overall, our benchmark offers a comprehensive assessment of LLMs' performance for different subtasks, pinpointing the strengths and weaknesses in LLM-powered embodied AI systems, and providing insights for effective and selective use of LLMs in embodied decision making.

Large language models (LLMs) struggle to consistently generate UI code that compiles and produces visually relevant designs. Existing approaches to improve generation rely on expensive human feedback or distilling a proprietary model. In this paper, we explore the use of automated feedback (compilers and multi-modal models) to guide LLMs to generate high-quality UI code. Our method starts with an existing LLM and iteratively produces improved models by self-generating a large synthetic dataset using an original model, applying automated tools to aggressively filter, score, and de-duplicate the data into a refined higher quality dataset. The original LLM is improved by finetuning on this refined dataset. We applied our approach to several open-source LLMs and compared the resulting performance to baseline models with both automated metrics and human preferences. Our evaluation shows the resulting models outperform all other downloadable baselines and approach the performance of larger proprietary models.

Metamaterials, engineered materials with architected structures across multiple length scales, offer unprecedented and tunable mechanical properties that surpass those of conventional materials. However, leveraging advanced machine learning (ML) for metamaterial discovery is hindered by three fundamental challenges: (C1) Data Heterogeneity Challenge arises from heterogeneous data sources, heterogeneous composition scales, and heterogeneous structure categories; (C2) Model Complexity Challenge stems from the intricate geometric constraints of ML models, which complicate their adaptation to metamaterial structures; and (C3) Human-AI Collaboration Challenge comes from the "dual black-box'' nature of sophisticated ML models and the need for intuitive user interfaces. To tackle these challenges, we introduce a unified framework, named MetamatBench, that operates on three levels. (1) At the data level, we integrate and standardize 5 heterogeneous, multi-modal metamaterial datasets. (2) The ML level provides a comprehensive toolkit that adapts 17 state-of-the-art ML methods for metamaterial discovery. It also includes a comprehensive evaluation suite with 12 novel performance metrics with finite element-based assessments to ensure accurate and reliable model validation. (3) The user level features a visual-interactive interface that bridges the gap between complex ML techniques and non-ML researchers, advancing property prediction and inverse design of metamaterials for research and applications. MetamatBench offers a unified platform deployed at http://zhoulab-1.cs.vt.edu:5550 that enables machine learning researchers and practitioners to develop and evaluate new methodologies in metamaterial discovery. For accessibility and reproducibility, we open-source our benchmark and the codebase at https://github.com/cjpcool/Metamaterial-Benchmark.

Sparse autoencoders (SAEs) are a popular technique for interpreting language model activations, and there is extensive recent work on improving SAE effectiveness. However, most prior work evaluates progress using unsupervised proxy metrics with unclear practical relevance. We introduce SAEBench, a comprehensive evaluation suite that measures SAE performance across seven diverse metrics, spanning interpretability, feature disentanglement and practical applications like unlearning. To enable systematic comparison, we open-source a suite of over 200 SAEs across eight recently proposed SAE architectures and training algorithms. Our evaluation reveals that gains on proxy metrics do not reliably translate to better practical performance. For instance, while Matryoshka SAEs slightly underperform on existing proxy metrics, they substantially outperform other architectures on feature disentanglement metrics; moreover, this advantage grows with SAE scale. By providing a standardized framework for measuring progress in SAE development, SAEBench enables researchers to study scaling trends and make nuanced comparisons between different SAE architectures and training methodologies. Our interactive interface enables researchers to flexibly visualize relationships between metrics across hundreds of open-source SAEs at: https://saebench.xyz

The evaluation of Natural Language Generation (NLG) models has gained increased attention, urging the development of metrics that evaluate various aspects of generated text. LUNA addresses this challenge by introducing a unified interface for 20 NLG evaluation metrics. These metrics are categorized based on their reference-dependence and the type of text representation they employ, from string-based n-gram overlap to the utilization of static embeddings and pre-trained language models. The straightforward design of LUNA allows for easy extension with novel metrics, requiring just a few lines of code. LUNA offers a user-friendly tool for evaluating generated texts.

This paper introduces a large collection of time series data derived from Twitter, postprocessed using word embedding techniques, as well as specialized fine-tuned language models. This data comprises the past five years and captures changes in n-gram frequency, similarity, sentiment and topic distribution. The interface built on top of this data enables temporal analysis for detecting and characterizing shifts in meaning, including complementary information to trending metrics, such as sentiment and topic association over time. We release an online demo for easy experimentation, and we share code and the underlying aggregated data for future work. In this paper, we also discuss three case studies unlocked thanks to our platform, showcasing its potential for temporal linguistic analysis.

With the emerging trend of GPT models, we have established a framework called AutoML-GPT that integrates a comprehensive set of tools and libraries. This framework grants users access to a wide range of data preprocessing techniques, feature engineering methods, and model selection algorithms. Through a conversational interface, users can specify their requirements, constraints, and evaluation metrics. Throughout the process, AutoML-GPT employs advanced techniques for hyperparameter optimization and model selection, ensuring that the resulting model achieves optimal performance. The system effectively manages the complexity of the machine learning pipeline, guiding users towards the best choices without requiring deep domain knowledge. Through our experimental results on diverse datasets, we have demonstrated that AutoML-GPT significantly reduces the time and effort required for machine learning tasks. Its ability to leverage the vast knowledge encoded in large language models enables it to provide valuable insights, identify potential pitfalls, and suggest effective solutions to common challenges faced during model training.

Graphical User Interface (GUI) agents, powered by Large Foundation Models, have emerged as a transformative approach to automating human-computer interaction. These agents autonomously interact with digital systems or software applications via GUIs, emulating human actions such as clicking, typing, and navigating visual elements across diverse platforms. Motivated by the growing interest and fundamental importance of GUI agents, we provide a comprehensive survey that categorizes their benchmarks, evaluation metrics, architectures, and training methods. We propose a unified framework that delineates their perception, reasoning, planning, and acting capabilities. Furthermore, we identify important open challenges and discuss key future directions. Finally, this work serves as a basis for practitioners and researchers to gain an intuitive understanding of current progress, techniques, benchmarks, and critical open problems that remain to be addressed.

Brain-Computer Interface (BCI) systems allow users to perform actions by translating their brain activity into commands. Such systems usually need a training phase, consisting in training a classification algorithm to discriminate between mental states using specific features from the recorded signals. This phase of feature selection and training is crucial for BCI performance and presents specific constraints to be met in a clinical context, such as post-stroke rehabilitation. In this paper, we present HappyFeat, a software making Motor Imagery (MI) based BCI experiments easier, by gathering all necessary manipulations and analysis in a single convenient GUI and via automation of experiment or analysis parameters. The resulting workflow allows for effortlessly selecting the best features, helping to achieve good BCI performance in time-constrained environments. Alternative features based on Functional Connectivity can be used and compared or combined with Power Spectral Density, allowing a network-oriented approach. We then give details of HappyFeat's main mechanisms, and a review of its performances in typical use cases. We also show that it can be used as an efficient tool for comparing different metrics extracted from the signals, to train the classification algorithm. To this end, we show a comparison between the commonly-used Power Spectral Density and network metrics based on Functional Connectivity. HappyFeat is available as an open-source project which can be freely downloaded on GitHub.

Large Language Models (LLMs) have demonstrated impressive capabilities across various domains, but their effectiveness in financial decision-making remains inadequately evaluated. Current benchmarks primarily assess LLMs' understanding on financial documents rather than the ability to manage assets or dig out trading opportunities in dynamic market conditions. Despite the release of new benchmarks for evaluating diversified tasks on the financial domain, we identified four major problems in these benchmarks, which are data leakage, navel-gazing, over-intervention, and maintenance-hard. To pave the research gap, we introduce DeepFund, a comprehensive arena platform for evaluating LLM-based trading strategies in a live environment. Our approach implements a multi-agent framework where they serve as multiple key roles that realize the real-world investment decision processes. Moreover, we provide a web interface that visualizes LLMs' performance with fund investment metrics across different market conditions, enabling detailed comparative analysis. Through DeepFund, we aim to provide a more realistic and fair assessment on LLM's capabilities in fund investment, offering diversified insights and revealing their potential applications in real-world financial markets. Our code is publicly available at https://github.com/HKUSTDial/DeepFund.

Existing methods for expressive music performance rendering rely on supervised learning over small labeled datasets, which limits scaling of both data volume and model size, despite the availability of vast unlabeled music, as in vision and language. To address this gap, we introduce Pianist Transformer, with four key contributions: 1) a unified Musical Instrument Digital Interface (MIDI) data representation for learning the shared principles of musical structure and expression without explicit annotation; 2) an efficient asymmetric architecture, enabling longer contexts and faster inference without sacrificing rendering quality; 3) a self-supervised pre-training pipeline with 10B tokens and 135M-parameter model, unlocking data and model scaling advantages for expressive performance rendering; 4) a state-of-the-art performance model, which achieves strong objective metrics and human-level subjective ratings. Overall, Pianist Transformer establishes a scalable path toward human-like performance synthesis in the music domain.