Datasets used for molecular docking, such as PDBBind, contain technical variability - they are noisy. Although the origins of the noise have been discussed, a comprehensive analysis of the physical, chemical, and bioactivity characteristics of the datasets is still lacking. To address this gap, we introduce the Comprehensive Accurate Assessment (Compass). Compass integrates two key components: PoseCheck, which examines ligand strain energy, protein-ligand steric clashes, and interactions, and AA-Score, a new empirical scoring function for calculating binding affinity energy. Together, these form a unified workflow that assesses both the physical/chemical properties and bioactivity favorability of ligands and protein-ligand interactions. Our analysis of the PDBBind dataset using Compass reveals substantial noise in the ground truth data. Additionally, we propose CompassDock, which incorporates the Compass module with DiffDock, the state-of-the-art deep learning-based molecular docking method, to enable accurate assessment of docked ligands during inference. Finally, we present a new paradigm for enhancing molecular docking model performance by fine-tuning with Compass Scores, which encompass binding affinity energy, strain energy, and the number of steric clashes identified by Compass. Our results show that, while fine-tuning without Compass improves the percentage of docked poses with RMSD < 2{\AA}, it leads to a decrease in physical/chemical and bioactivity favorability. In contrast, fine-tuning with Compass shows a limited improvement in RMSD < 2{\AA} but enhances the physical/chemical and bioactivity favorability of the ligand conformation. The source code is available publicly at //github.com/BIMSBbioinfo/CompassDock.
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Large language models (LLMs) are increasingly being used in materials science. However, little attention has been given to benchmarking and standardized evaluation for LLM-based materials property prediction, which hinders progress. We present LLM4Mat-Bench, the largest benchmark to date for evaluating the performance of LLMs in predicting the properties of crystalline materials. LLM4Mat-Bench contains about 1.9M crystal structures in total, collected from 10 publicly available materials data sources, and 45 distinct properties. LLM4Mat-Bench features different input modalities: crystal composition, CIF, and crystal text description, with 4.7M, 615.5M, and 3.1B tokens in total for each modality, respectively. We use LLM4Mat-Bench to fine-tune models with different sizes, including LLM-Prop and MatBERT, and provide zero-shot and few-shot prompts to evaluate the property prediction capabilities of LLM-chat-like models, including Llama, Gemma, and Mistral. The results highlight the challenges of general-purpose LLMs in materials science and the need for task-specific predictive models and task-specific instruction-tuned LLMs in materials property prediction.
Users typically engage with LLMs interactively, yet most existing benchmarks evaluate them in a static, single-turn format, posing reliability concerns in interactive scenarios. We identify a key obstacle towards reliability: LLMs are trained to answer any question, even with incomplete context or insufficient knowledge. In this paper, we propose to change the static paradigm to an interactive one, develop systems that proactively ask questions to gather more information and respond reliably, and introduce an benchmark - MediQ - to evaluate question-asking ability in LLMs. MediQ simulates clinical interactions consisting of a Patient System and an adaptive Expert System; with potentially incomplete initial information, the Expert refrains from making diagnostic decisions when unconfident, and instead elicits missing details via follow-up questions. We provide a pipeline to convert single-turn medical benchmarks into an interactive format. Our results show that directly prompting state-of-the-art LLMs to ask questions degrades performance, indicating that adapting LLMs to proactive information-seeking settings is nontrivial. We experiment with abstention strategies to better estimate model confidence and decide when to ask questions, improving diagnostic accuracy by 22.3%; however, performance still lags compared to an (unrealistic in practice) upper bound with complete information upfront. Further analyses show improved interactive performance with filtering irrelevant contexts and reformatting conversations. Overall, we introduce a novel problem towards LLM reliability, an interactive MediQ benchmark and a novel question-asking system, and highlight directions to extend LLMs' information-seeking abilities in critical domains.
Training robot policies in simulation is becoming increasingly popular; nevertheless, a precise, reliable, and easy-to-use tactile simulator for contact-rich manipulation tasks is still missing. To close this gap, we develop TacEx -- a modular tactile simulation framework. We embed a state-of-the-art soft-body simulator for contacts named GIPC and vision-based tactile simulators Taxim and FOTS into Isaac Sim to achieve robust and plausible simulation of the visuotactile sensor GelSight Mini. We implement several Isaac Lab environments for Reinforcement Learning (RL) leveraging our TacEx simulation, including object pushing, lifting, and pole balancing. We validate that the simulation is stable and that the high-dimensional observations, such as the gel deformation and the RGB images from the GelSight camera, can be used for training. The code, videos, and additional results will be released online //sites.google.com/view/tacex.
Speech is the most natural way of expressing ourselves as humans. Identifying emotion from speech is a nontrivial task due to the ambiguous definition of emotion itself. Speaker Emotion Recognition (SER) is essential for understanding human emotional behavior. The SER task is challenging due to the variety of speakers, background noise, complexity of emotions, and speaking styles. It has many applications in education, healthcare, customer service, and Human-Computer Interaction (HCI). Previously, conventional machine learning methods such as SVM, HMM, and KNN have been used for the SER task. In recent years, deep learning methods have become popular, with convolutional neural networks and recurrent neural networks being used for SER tasks. The input of these methods is mostly spectrograms and hand-crafted features. In this work, we study the use of self-supervised transformer-based models, Wav2Vec2 and HuBERT, to determine the emotion of speakers from their voice. The models automatically extract features from raw audio signals, which are then used for the classification task. The proposed solution is evaluated on reputable datasets, including RAVDESS, SHEMO, SAVEE, AESDD, and Emo-DB. The results show the effectiveness of the proposed method on different datasets. Moreover, the model has been used for real-world applications like call center conversations, and the results demonstrate that the model accurately predicts emotions.
Owing to advancements in deep learning technology, Vision Transformers (ViTs) have demonstrated impressive performance in various computer vision tasks. Nonetheless, ViTs still face some challenges, such as high computational complexity and the absence of desirable inductive biases. To alleviate these issues, {the potential advantages of combining eagle vision with ViTs are explored. We summarize a Bi-Fovea Visual Interaction (BFVI) structure inspired by the unique physiological and visual characteristics of eagle eyes. A novel Bi-Fovea Self-Attention (BFSA) mechanism and Bi-Fovea Feedforward Network (BFFN) are proposed based on this structural design approach, which can be used to mimic the hierarchical and parallel information processing scheme of the biological visual cortex, enabling networks to learn feature representations of targets in a coarse-to-fine manner. Furthermore, a Bionic Eagle Vision (BEV) block is designed as the basic building unit based on the BFSA mechanism and BFFN. By stacking BEV blocks, a unified and efficient family of pyramid backbone networks called Eagle Vision Transformers (EViTs) is developed. Experimental results show that EViTs exhibit highly competitive performance in various computer vision tasks, such as image classification, object detection and semantic segmentation. Compared with other approaches, EViTs have significant advantages, especially in terms of performance and computational efficiency. Code is available at //github.com/nkusyl/EViT
With the recent rise of Large Language Models (LLMs), Vision-Language Models (VLMs), and other general foundation models, there is growing potential for multimodal, multi-task embodied agents that can operate in diverse environments given only natural language as input. One such application area is indoor navigation using natural language instructions. However, despite recent progress, this problem remains challenging due to the spatial reasoning and semantic understanding required, particularly in arbitrary scenes that may contain many objects belonging to fine-grained classes. To address this challenge, we curate the largest real-world dataset for Vision and Language-guided Action in 3D Scenes (VLA-3D), consisting of over 11.5K scanned 3D indoor rooms from existing datasets, 23.5M heuristically generated semantic relations between objects, and 9.7M synthetically generated referential statements. Our dataset consists of processed 3D point clouds, semantic object and room annotations, scene graphs, navigable free space annotations, and referential language statements that specifically focus on view-independent spatial relations for disambiguating objects. The goal of these features is to aid the downstream task of navigation, especially on real-world systems where some level of robustness must be guaranteed in an open world of changing scenes and imperfect language. We benchmark our dataset with current state-of-the-art models to obtain a performance baseline. All code to generate and visualize the dataset is publicly released, see //github.com/HaochenZ11/VLA-3D. With the release of this dataset, we hope to provide a resource for progress in semantic 3D scene understanding that is robust to changes and one which will aid the development of interactive indoor navigation systems.
Obelia improves upon structured DAG-based consensus protocols used in proof-of-stake systems, allowing them to effectively scale to accommodate hundreds of validators. Obelia implements a two-tier validator system. A core group of high-stake validators that propose blocks as in current protocols and a larger group of lower-stake auxiliary validators that occasionally author blocks. Obelia incentivizes auxiliary validators to assist recovering core validators and integrates seamlessly with existing protocols. We show that Obelia does not introduce visible overhead compared to the original protocol, even when scaling to hundreds of validators, or when a large number of auxiliary validators are unreliable.
Ensuring alignment, which refers to making models behave in accordance with human intentions [1,2], has become a critical task before deploying large language models (LLMs) in real-world applications. For instance, OpenAI devoted six months to iteratively aligning GPT-4 before its release [3]. However, a major challenge faced by practitioners is the lack of clear guidance on evaluating whether LLM outputs align with social norms, values, and regulations. This obstacle hinders systematic iteration and deployment of LLMs. To address this issue, this paper presents a comprehensive survey of key dimensions that are crucial to consider when assessing LLM trustworthiness. The survey covers seven major categories of LLM trustworthiness: reliability, safety, fairness, resistance to misuse, explainability and reasoning, adherence to social norms, and robustness. Each major category is further divided into several sub-categories, resulting in a total of 29 sub-categories. Additionally, a subset of 8 sub-categories is selected for further investigation, where corresponding measurement studies are designed and conducted on several widely-used LLMs. The measurement results indicate that, in general, more aligned models tend to perform better in terms of overall trustworthiness. However, the effectiveness of alignment varies across the different trustworthiness categories considered. This highlights the importance of conducting more fine-grained analyses, testing, and making continuous improvements on LLM alignment. By shedding light on these key dimensions of LLM trustworthiness, this paper aims to provide valuable insights and guidance to practitioners in the field. Understanding and addressing these concerns will be crucial in achieving reliable and ethically sound deployment of LLMs in various applications.
With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.
Many tasks in natural language processing can be viewed as multi-label classification problems. However, most of the existing models are trained with the standard cross-entropy loss function and use a fixed prediction policy (e.g., a threshold of 0.5) for all the labels, which completely ignores the complexity and dependencies among different labels. In this paper, we propose a meta-learning method to capture these complex label dependencies. More specifically, our method utilizes a meta-learner to jointly learn the training policies and prediction policies for different labels. The training policies are then used to train the classifier with the cross-entropy loss function, and the prediction policies are further implemented for prediction. Experimental results on fine-grained entity typing and text classification demonstrate that our proposed method can obtain more accurate multi-label classification results.
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