Large language models (LLMs) have large potential for molecular optimization, as they can gather external chemistry tools and enable collaborative interactions to iteratively refine molecular candidates. However, this potential remains underexplored, particularly in the context of structured reasoning, interpretability, and comprehensive tool-grounded molecular optimization. To address this gap, we introduce MT-Mol, a multi-agent framework for molecular optimization that leverages tool-guided reasoning and role-specialized LLM agents. Our system incorporates comprehensive RDKit tools, categorized into five distinct domains: structural descriptors, electronic and topological features, fragment-based functional groups, molecular representations, and miscellaneous chemical properties. Each category is managed by an expert analyst agent, responsible for extracting task-relevant tools and enabling interpretable, chemically grounded feedback. MT-Mol produces molecules with tool-aligned and stepwise reasoning through the interaction between the analyst agents, a molecule-generating scientist, a reasoning-output verifier, and a reviewer agent. As a result, we show that our framework shows the state-of-the-art performance of the PMO-1K benchmark on 17 out of 23 tasks.
Large Language Models (LLMs) for Generative AI have achieved remarkable progress, evolving into sophisticated and versatile tools widely adopted across various domains and applications. However, the substantial memory overhead caused by their vast number of parameters, combined with the high computational demands of the attention mechanism, poses significant challenges in achieving low latency and high throughput for LLM inference services. Recent advancements, driven by groundbreaking research, have significantly accelerated progress in this field. This paper provides a comprehensive survey of these methods, covering fundamental instance-level approaches, in-depth cluster-level strategies, emerging scenario directions, and other miscellaneous but important areas. At the instance level, we review model placement, request scheduling, decoding length prediction, storage management, and the disaggregation paradigm. At the cluster level, we explore GPU cluster deployment, multi-instance load balancing, and cloud service solutions. For emerging scenarios, we organize the discussion around specific tasks, modules, and auxiliary methods. To ensure a holistic overview, we also highlight several niche yet critical areas. Finally, we outline potential research directions to further advance the field of LLM inference serving.
ANCHOLIK-NER is a linguistically diverse dataset for Named Entity Recognition (NER) in Bangla regional dialects, capturing variations across Sylhet, Chittagong, and Barishal. The dataset has around 10,443 sentences, 3,481 sentences per region. The data was collected from two publicly available datasets and through web scraping from various online newspapers, articles. To ensure high-quality annotations, the BIO tagging scheme was employed, and professional annotators with expertise in regional dialects carried out the labeling process. The dataset is structured into separate subsets for each region and is available both in CSV format. Each entry contains textual data along with identified named entities and their corresponding annotations. Named entities are categorized into ten distinct classes: Person, Location, Organization, Food, Animal, Colour, Role, Relation, Object, and Miscellaneous. This dataset serves as a valuable resource for developing and evaluating NER models for Bangla dialectal variations, contributing to regional language processing and low-resource NLP applications. It can be utilized to enhance NER systems in Bangla dialects, improve regional language understanding, and support applications in machine translation, information retrieval, and conversational AI.
Out-of-distribution (OOD) detection is crucial for developing trustworthy and reliable machine learning systems. Recent advances in training with auxiliary OOD data demonstrate efficacy in enhancing detection capabilities. Nonetheless, these methods heavily rely on acquiring a large pool of high-quality natural outliers. Some prior methods try to alleviate this problem by synthesizing virtual outliers but suffer from either poor quality or high cost due to the monotonous sampling strategy and the heavy-parameterized generative models. In this paper, we overcome all these problems by proposing the Hamiltonian Monte Carlo Outlier Synthesis (HamOS) framework, which views the synthesis process as sampling from Markov chains. Based solely on the in-distribution data, the Markov chains can extensively traverse the feature space and generate diverse and representative outliers, hence exposing the model to miscellaneous potential OOD scenarios. The Hamiltonian Monte Carlo with sampling acceptance rate almost close to 1 also makes our framework enjoy great efficiency. By empirically competing with SOTA baselines on both standard and large-scale benchmarks, we verify the efficacy and efficiency of our proposed HamOS.
Visual question answering (VQA) refers to the problem where, given an image and a natural language question about the image, a correct natural language answer has to be generated. A VQA model has to demonstrate both the visual understanding of the image and the semantic understanding of the question, demonstrating reasoning capability. Since the inception of this field, a plethora of VQA datasets and models have been published. In this article, we meticulously analyze the current state of VQA datasets and models, while cleanly dividing them into distinct categories and then summarizing the methodologies and characteristics of each category. We divide VQA datasets into four categories: (1) available datasets that contain a rich collection of authentic images, (2) synthetic datasets that contain only synthetic images produced through artificial means, (3) diagnostic datasets that are specially designed to test model performance in a particular area, e.g., understanding the scene text, and (4) KB (Knowledge-Based) datasets that are designed to measure a model's ability to utilize outside knowledge. Concurrently, we explore six main paradigms of VQA models: fusion, where we discuss different methods of fusing information between visual and textual modalities; attention, the technique of using information from one modality to filter information from another; external knowledge base, where we discuss different models utilizing outside information; composition or reasoning, where we analyze techniques to answer advanced questions that require complex reasoning steps; explanation, which is the process of generating visual and textual descriptions to verify sound reasoning; and graph models, which encode and manipulate relationships through nodes in a graph. We also discuss some miscellaneous topics, such as scene text understanding, counting, and bias reduction.
Histopathology whole slide images (WSIs) are being widely used to develop deep learning-based diagnostic solutions, especially for precision oncology. Most of these diagnostic softwares are vulnerable to biases and impurities in the training and test data which can lead to inaccurate diagnoses. For instance, WSIs contain multiple types of tissue regions, at least some of which might not be relevant to the diagnosis. We introduce HistoROI, a robust yet lightweight deep learning-based classifier to segregate WSI into six broad tissue regions -- epithelium, stroma, lymphocytes, adipose, artifacts, and miscellaneous. HistoROI is trained using a novel human-in-the-loop and active learning paradigm that ensures variations in training data for labeling-efficient generalization. HistoROI consistently performs well across multiple organs, despite being trained on only a single dataset, demonstrating strong generalization. Further, we have examined the utility of HistoROI in improving the performance of downstream deep learning-based tasks using the CAMELYON breast cancer lymph node and TCGA lung cancer datasets. For the former dataset, the area under the receiver operating characteristic curve (AUC) for metastasis versus normal tissue of a neural network trained using weakly supervised learning increased from 0.88 to 0.92 by filtering the data using HistoROI. Similarly, the AUC increased from 0.88 to 0.93 for the classification between adenocarcinoma and squamous cell carcinoma on the lung cancer dataset. We also found that the performance of the HistoROI improves upon HistoQC for artifact detection on a test dataset of 93 annotated WSIs. The limitations of the proposed model are analyzed, and potential extensions are also discussed.
"Artificial Neural Network and Deep Learning: Fundamentals and Theory" offers a comprehensive exploration of the foundational principles and advanced methodologies in neural networks and deep learning. This book begins with essential concepts in descriptive statistics and probability theory, laying a solid groundwork for understanding data and probability distributions. As the reader progresses, they are introduced to matrix calculus and gradient optimization, crucial for training and fine-tuning neural networks. The book delves into multilayer feed-forward neural networks, explaining their architecture, training processes, and the backpropagation algorithm. Key challenges in neural network optimization, such as activation function saturation, vanishing and exploding gradients, and weight initialization, are thoroughly discussed. The text covers various learning rate schedules and adaptive algorithms, providing strategies to optimize the training process. Techniques for generalization and hyperparameter tuning, including Bayesian optimization and Gaussian processes, are also presented to enhance model performance and prevent overfitting. Advanced activation functions are explored in detail, categorized into sigmoid-based, ReLU-based, ELU-based, miscellaneous, non-standard, and combined types. Each activation function is examined for its properties and applications, offering readers a deep understanding of their impact on neural network behavior. The final chapter introduces complex-valued neural networks, discussing complex numbers, functions, and visualizations, as well as complex calculus and backpropagation algorithms. This book equips readers with the knowledge and skills necessary to design, and optimize advanced neural network models, contributing to the ongoing advancements in artificial intelligence.
Bayesian learning provides a unified skeleton to solve the electrophysiological source imaging task. From this perspective, existing source imaging algorithms utilize the Gaussian assumption for the observation noise to build the likelihood function for Bayesian inference. However, the electromagnetic measurements of brain activity are usually affected by miscellaneous artifacts, leading to a potentially non-Gaussian distribution for the observation noise. Hence the conventional Gaussian likelihood model is a suboptimal choice for the real-world source imaging task. In this study, we aim to solve this problem by proposing a new likelihood model which is robust with respect to non-Gaussian noises. Motivated by the robust maximum correntropy criterion, we propose a new improper distribution model concerning the noise assumption. This new noise distribution is leveraged to structure a robust likelihood function and integrated with hierarchical prior distributions to estimate source activities by variational inference. In particular, the score matching is adopted to determine the hyperparameters for the improper likelihood model. A comprehensive performance evaluation is performed to compare the proposed noise assumption to the conventional Gaussian model. Simulation results show that, the proposed method can realize more precise source reconstruction by designing known ground-truth. The real-world dataset also demonstrates the superiority of our new method with the visual perception task. This study provides a new backbone for Bayesian source imaging, which would facilitate its application using real-world noisy brain signal.
Recent generative models produce images with a level of authenticity that makes them nearly indistinguishable from real photos and artwork. Potential harmful use cases of these models, necessitate the creation of robust synthetic image detectors. However, current datasets in the field contain generated images with questionable quality or have examples from one predominant content type which leads to poor generalizability of the underlying detectors. We find that the curation of a balanced amount of high-resolution generated images across various content types is crucial for the generalizability of detectors, and introduce ImagiNet, a dataset of 200K examples, spanning four categories: photos, paintings, faces, and miscellaneous. Synthetic images in ImagiNet are produced with both open-source and proprietary generators, whereas real counterparts for each content type are collected from public datasets. The structure of ImagiNet allows for a two-track evaluation system: i) classification as real or synthetic and ii) identification of the generative model. To establish a strong baseline, we train a ResNet-50 model using a self-supervised contrastive objective (SelfCon) for each track which achieves evaluation AUC of up to 0.99 and balanced accuracy ranging from 86% to 95%, even under conditions that involve compression and resizing. The provided model is generalizable enough to achieve zero-shot state-of-the-art performance on previous synthetic detection benchmarks. We provide ablations to demonstrate the importance of content types and publish code and data.
Recent years have witnessed a thriving growth of computing facilities connected at the network edge, cultivating edge networks as a fundamental infrastructure for supporting miscellaneous intelligent services.Meanwhile, Artificial Intelligence (AI) frontiers have extrapolated to the graph domain and promoted Graph Intelligence (GI). Given the inherent relation between graphs and networks, the interdiscipline of graph learning and edge networks, i.e., Edge GI or EGI, has revealed a novel interplay between them -- GI aids in optimizing edge networks, while edge networks facilitate GI model deployment. Driven by this delicate closed-loop, EGI is recognized as a promising solution to fully unleash the potential of edge computing power and is garnering growing attention. Nevertheless, research on EGI remains nascent, and there is a soaring demand within both the communications and AI communities for a dedicated venue to share recent advancements. To this end, this paper promotes the concept of EGI, explores its scope and core principles, and conducts a comprehensive survey concerning recent research efforts on this emerging field. Specifically, this paper introduces and discusses: 1) fundamentals of edge computing and graph learning,2) emerging techniques centering on the closed loop between graph intelligence and edge networks, and 3) open challenges and research opportunities of future EGI. By bridging the gap across communication, networking, and graph learning areas, we believe that this survey can garner increased attention, foster meaningful discussions, and inspire further research ideas in EGI.
Cellular nuclei recognition serves as a fundamental and essential step in the workflow of digital pathology. However, with disparate source organs and staining procedures among histology image clusters, the scanned tiles inherently conform to a non-uniform data distribution, which induces deteriorated promises for general cross-cohort usages. Despite the latest efforts leveraging domain adaptation to mitigate distributional discrepancy, those methods are subjected to modeling the morphological characteristics of each cell individually, disregarding the hierarchical latent structure and intrinsic contextual correspondences across the tumor micro-environment. In this work, we identify the importance of implicit correspondences across biological contexts for exploiting domain-invariant pathological composition and thereby propose to exploit the dependence over various biological structures for domain adaptive cellular recognition. We discover those high-level correspondences via unsupervised contextual modeling and use them as bridges to facilitate adaptation over diverse organs and stains. In addition, to further exploit the rich spatial contexts embedded amongst nuclear communities, we propose self-adaptive dynamic distillation to secure instance-aware trade-offs across different model constituents. The proposed method is extensively evaluated on a broad spectrum of cross-domain settings under miscellaneous data distribution shifts and outperforms the state-of-the-art methods by a substantial margin. Code is available at https://github.com/camwew/CellularRecognition_DA_CC.
In the architecture of deep learning models, inspired by biological neurons, activation functions (AFs) play a pivotal role. They significantly influence the performance of artificial neural networks. By modulating the non-linear properties essential for learning complex patterns, AFs are fundamental in both classification and regression tasks. This paper presents a comprehensive review of various types of AFs, including fixed-shape, parametric, adaptive, stochastic/probabilistic, non-standard, and ensemble/combining types. We begin with a systematic taxonomy and detailed classification frameworks that delineates the principal characteristics of AFs and organizes them based on their structural and functional distinctions. Our in-depth analysis covers primary groups such as sigmoid-based, ReLU-based, and ELU-based AFs, discussing their theoretical foundations, mathematical formulations, and specific benefits and limitations in different contexts. We also highlight key attributes of AFs such as output range, monotonicity, and smoothness. Furthermore, we explore miscellaneous AFs that do not conform to these categories but have shown unique advantages in specialized applications. Non-standard AFs are also explored, showcasing cutting-edge variations that challenge traditional paradigms and offer enhanced adaptability and model performance. We examine strategies for combining multiple AFs to leverage complementary properties. The paper concludes with a comparative evaluation of 12 state-of-the-art AFs, using rigorous statistical and experimental methodologies to assess their efficacy. This analysis not only aids practitioners in selecting and designing the most appropriate AFs for their specific deep learning tasks but also encourages continued innovation in AF development within the machine learning community.
Chronotype compares individuals' circadian phase to others. It contextualizes mental health risk assessments and detection of social jet lag, which can hamper mental health and cognitive performance. Existing ways of determining chronotypes, such as Dim Light Melatonin Onset (DLMO) or the Morningness-Eveningness Questionnaire (MEQ), are limited by being discrete in time and time-intensive to update, meaning they rarely capture real-world variability across time. Chronotyping users based on a daily planner app might augment existing methods to enable assessment continuously and at scale. This paper reports the construction of a supervised binary classifier that attempts to demonstrate the feasibility of this approach. 1,460 registered users from the Owaves app opted in by filling out the MEQ survey between July 14, 2022, and May 1, 2023. 142 met the eligibility criteria. We used multimodal app data from individuals identified as morning and evening types from MEQ data, basing the classifier on app time series data. This included daily timing for 8 main lifestyle activity types: exercise, sleep, social interactions, meal times, relaxation, work, play, and miscellaneous, as defined in the app. The timing of activities showed substantial change across time, as well as heterogeneity by activity type. Our novel chronotyping classifier was able to predict the morningness and eveningness of its users with an ROC AUC of 0.70. Our findings demonstrate the feasibility of chronotype classification from multimodal, real-world app data, while highlighting fundamental challenges to applying discrete and fixed labels to complex, dynamic, multimodal behaviors. Our findings suggest a potential for real-time monitoring of shifts in chronotype specific to different causes (i.e. types of activity), which could feasibly be used to support future, prospective mental health support research.
Multi-modal object tracking (MMOT) is an emerging field that combines data from various modalities, \eg vision (RGB), depth, thermal infrared, event, language and audio, to estimate the state of an arbitrary object in a video sequence. It is of great significance for many applications such as autonomous driving and intelligent surveillance. In recent years, MMOT has received more and more attention. However, existing MMOT algorithms mainly focus on two modalities (\eg RGB+depth, RGB+thermal infrared, and RGB+language). To leverage more modalities, some recent efforts have been made to learn a unified visual object tracking model for any modality. Additionally, some large-scale multi-modal tracking benchmarks have been established by simultaneously providing more than two modalities, such as vision-language-audio (\eg WebUAV-3M) and vision-depth-language (\eg UniMod1K). To track the latest progress in MMOT, we conduct a comprehensive investigation in this report. Specifically, we first divide existing MMOT tasks into five main categories, \ie RGBL tracking, RGBE tracking, RGBD tracking, RGBT tracking, and miscellaneous (RGB+X), where X can be any modality, such as language, depth, and event. Then, we analyze and summarize each MMOT task, focusing on widely used datasets and mainstream tracking algorithms based on their technical paradigms (\eg self-supervised learning, prompt learning, knowledge distillation, generative models, and state space models). Finally, we maintain a continuously updated paper list for MMOT at https://github.com/983632847/Awesome-Multimodal-Object-Tracking.
Large language models (LLMs) have garnered significant attention and widespread usage due to their impressive performance in various tasks. However, they are not without their own set of challenges, including issues such as hallucinations, factual inconsistencies, and limitations in numerical-quantitative reasoning. Evaluating LLMs in miscellaneous reasoning tasks remains an active area of research. Prior to the breakthrough of LLMs, Transformers had already proven successful in the medical domain, effectively employed for various natural language understanding (NLU) tasks. Following this trend, LLMs have also been trained and utilized in the medical domain, raising concerns regarding factual accuracy, adherence to safety protocols, and inherent limitations. In this paper, we focus on evaluating the natural language inference capabilities of popular open-source and closed-source LLMs using clinical trial reports as the dataset. We present the performance results of each LLM and further analyze their performance on a development set, particularly focusing on challenging instances that involve medical abbreviations and require numerical-quantitative reasoning. Gemini, our leading LLM, achieved a test set F1-score of 0.748, securing the ninth position on the task scoreboard. Our work is the first of its kind, offering a thorough examination of the inference capabilities of LLMs within the medical domain.
Existing X-ray based pre-trained vision models are usually conducted on a relatively small-scale dataset (less than 500k samples) with limited resolution (e.g., 224 $\times$ 224). However, the key to the success of self-supervised pre-training large models lies in massive training data, and maintaining high resolution in the field of X-ray images is the guarantee of effective solutions to difficult miscellaneous diseases. In this paper, we address these issues by proposing the first high-definition (1280 $\times$ 1280) X-ray based pre-trained foundation vision model on our newly collected large-scale dataset which contains more than 1 million X-ray images. Our model follows the masked auto-encoder framework which takes the tokens after mask processing (with a high rate) is used as input, and the masked image patches are reconstructed by the Transformer encoder-decoder network. More importantly, we introduce a novel context-aware masking strategy that utilizes the chest contour as a boundary for adaptive masking operations. We validate the effectiveness of our model on two downstream tasks, including X-ray report generation and disease recognition. Extensive experiments demonstrate that our pre-trained medical foundation vision model achieves comparable or even new state-of-the-art performance on downstream benchmark datasets. The source code and pre-trained models of this paper will be released on https://github.com/Event-AHU/Medical_Image_Analysis.
We introduce EXAMS-V, a new challenging multi-discipline multimodal multilingual exam benchmark for evaluating vision language models. It consists of 20,932 multiple-choice questions across 20 school disciplines covering natural science, social science, and other miscellaneous studies, e.g., religion, fine arts, business, etc. EXAMS-V includes a variety of multimodal features such as text, images, tables, figures, diagrams, maps, scientific symbols, and equations. The questions come in 11 languages from 7 language families. Unlike existing benchmarks, EXAMS-V is uniquely curated by gathering school exam questions from various countries, with a variety of education systems. This distinctive approach calls for intricate reasoning across diverse languages and relies on region-specific knowledge. Solving the problems in the dataset requires advanced perception and joint reasoning over the text and the visual content of the image. Our evaluation results demonstrate that this is a challenging dataset, which is difficult even for advanced vision-text models such as GPT-4V and Gemini; this underscores the inherent complexity of the dataset and its significance as a future benchmark.
Multimodal Named Entity Recognition (MNER) is a pivotal task designed to extract named entities from text with the support of pertinent images. Nonetheless, a notable paucity of data for Chinese MNER has considerably impeded the progress of this natural language processing task within the Chinese domain. Consequently, in this study, we compile a Chinese Multimodal NER dataset (CMNER) utilizing data sourced from Weibo, China's largest social media platform. Our dataset encompasses 5,000 Weibo posts paired with 18,326 corresponding images. The entities are classified into four distinct categories: person, location, organization, and miscellaneous. We perform baseline experiments on CMNER, and the outcomes underscore the effectiveness of incorporating images for NER. Furthermore, we conduct cross-lingual experiments on the publicly available English MNER dataset (Twitter2015), and the results substantiate our hypothesis that Chinese and English multimodal NER data can mutually enhance the performance of the NER model.
There has been increasing interest in exploring the capabilities of advanced large language models (LLMs) in the field of information extraction (IE), specifically focusing on tasks related to named entity recognition (NER) and relation extraction (RE). Although researchers are exploring the use of few-shot information extraction through in-context learning with LLMs, they tend to focus only on using correct or positive examples for demonstration, neglecting the potential value of incorporating incorrect or negative examples into the learning process. In this paper, we present c-ICL, a novel few-shot technique that leverages both correct and incorrect sample constructions to create in-context learning demonstrations. This approach enhances the ability of LLMs to extract entities and relations by utilizing prompts that incorporate not only the positive samples but also the reasoning behind them. This method allows for the identification and correction of potential interface errors. Specifically, our proposed method taps into the inherent contextual information and valuable information in hard negative samples and the nearest positive neighbors to the test and then applies the in-context learning demonstrations based on LLMs. Our experiments on various datasets indicate that c-ICL outperforms previous few-shot in-context learning methods, delivering substantial enhancements in performance across a broad spectrum of related tasks. These improvements are noteworthy, showcasing the versatility of our approach in miscellaneous scenarios.
Named Entity Recognition (NER) is a sequence classification Natural Language Processing task where entities are identified in the text and classified into predefined categories. It acts as a foundation for most information extraction systems. Dungeons and Dragons (D&D) is an open-ended tabletop fantasy game with its own diverse lore. DnD entities are domain-specific and are thus unrecognizable by even the state-of-the-art off-the-shelf NER systems as the NER systems are trained on general data for pre-defined categories such as: person (PERS), location (LOC), organization (ORG), and miscellaneous (MISC). For meaningful extraction of information from fantasy text, the entities need to be classified into domain-specific entity categories as well as the models be fine-tuned on a domain-relevant corpus. This work uses available lore of monsters in the D&D domain to fine-tune Trankit, which is a prolific NER framework that uses a pre-trained model for NER. Upon this training, the system acquires the ability to extract monster names from relevant domain documents under a novel NER tag. This work compares the accuracy of the monster name identification against; the zero-shot Trankit model and two FLAIR models. The fine-tuned Trankit model achieves an 87.86% F1 score surpassing all the other considered models.