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Dec 12

MIRROR: Multi-Modal Pathological Self-Supervised Representation Learning via Modality Alignment and Retention

Histopathology and transcriptomics are fundamental modalities in oncology, encapsulating the morphological and molecular aspects of the disease. Multi-modal self-supervised learning has demonstrated remarkable potential in learning pathological representations by integrating diverse data sources. Conventional multi-modal integration methods primarily emphasize modality alignment, while paying insufficient attention to retaining the modality-specific structures. However, unlike conventional scenarios where multi-modal inputs share highly overlapping features, histopathology and transcriptomics exhibit pronounced heterogeneity, offering orthogonal yet complementary insights. Histopathology provides morphological and spatial context, elucidating tissue architecture and cellular topology, whereas transcriptomics delineates molecular signatures through gene expression patterns. This inherent disparity introduces a major challenge in aligning them while maintaining modality-specific fidelity. To address these challenges, we present MIRROR, a novel multi-modal representation learning method designed to foster both modality alignment and retention. MIRROR employs dedicated encoders to extract comprehensive features for each modality, which is further complemented by a modality alignment module to achieve seamless integration between phenotype patterns and molecular profiles. Furthermore, a modality retention module safeguards unique attributes from each modality, while a style clustering module mitigates redundancy and enhances disease-relevant information by modeling and aligning consistent pathological signatures within a clustering space. Extensive evaluations on TCGA cohorts for cancer subtyping and survival analysis highlight MIRROR's superior performance, demonstrating its effectiveness in constructing comprehensive oncological feature representations and benefiting the cancer diagnosis.

  • 7 authors
·
Mar 1

The Evolution of Multimodal Model Architectures

This work uniquely identifies and characterizes four prevalent multimodal model architectural patterns in the contemporary multimodal landscape. Systematically categorizing models by architecture type facilitates monitoring of developments in the multimodal domain. Distinct from recent survey papers that present general information on multimodal architectures, this research conducts a comprehensive exploration of architectural details and identifies four specific architectural types. The types are distinguished by their respective methodologies for integrating multimodal inputs into the deep neural network model. The first two types (Type A and B) deeply fuses multimodal inputs within the internal layers of the model, whereas the following two types (Type C and D) facilitate early fusion at the input stage. Type-A employs standard cross-attention, whereas Type-B utilizes custom-designed layers for modality fusion within the internal layers. On the other hand, Type-C utilizes modality-specific encoders, while Type-D leverages tokenizers to process the modalities at the model's input stage. The identified architecture types aid the monitoring of any-to-any multimodal model development. Notably, Type-C and Type-D are currently favored in the construction of any-to-any multimodal models. Type-C, distinguished by its non-tokenizing multimodal model architecture, is emerging as a viable alternative to Type-D, which utilizes input-tokenizing techniques. To assist in model selection, this work highlights the advantages and disadvantages of each architecture type based on data and compute requirements, architecture complexity, scalability, simplification of adding modalities, training objectives, and any-to-any multimodal generation capability.

  • 4 authors
·
May 28, 2024

Open World Object Detection in the Era of Foundation Models

Object detection is integral to a bevy of real-world applications, from robotics to medical image analysis. To be used reliably in such applications, models must be capable of handling unexpected - or novel - objects. The open world object detection (OWD) paradigm addresses this challenge by enabling models to detect unknown objects and learn discovered ones incrementally. However, OWD method development is hindered due to the stringent benchmark and task definitions. These definitions effectively prohibit foundation models. Here, we aim to relax these definitions and investigate the utilization of pre-trained foundation models in OWD. First, we show that existing benchmarks are insufficient in evaluating methods that utilize foundation models, as even naive integration methods nearly saturate these benchmarks. This result motivated us to curate a new and challenging benchmark for these models. Therefore, we introduce a new benchmark that includes five real-world application-driven datasets, including challenging domains such as aerial and surgical images, and establish baselines. We exploit the inherent connection between classes in application-driven datasets and introduce a novel method, Foundation Object detection Model for the Open world, or FOMO, which identifies unknown objects based on their shared attributes with the base known objects. FOMO has ~3x unknown object mAP compared to baselines on our benchmark. However, our results indicate a significant place for improvement - suggesting a great research opportunity in further scaling object detection methods to real-world domains. Our code and benchmark are available at https://orrzohar.github.io/projects/fomo/.

  • 5 authors
·
Dec 9, 2023

BoostDream: Efficient Refining for High-Quality Text-to-3D Generation from Multi-View Diffusion

Witnessing the evolution of text-to-image diffusion models, significant strides have been made in text-to-3D generation. Currently, two primary paradigms dominate the field of text-to-3D: the feed-forward generation solutions, capable of swiftly producing 3D assets but often yielding coarse results, and the Score Distillation Sampling (SDS) based solutions, known for generating high-fidelity 3D assets albeit at a slower pace. The synergistic integration of these methods holds substantial promise for advancing 3D generation techniques. In this paper, we present BoostDream, a highly efficient plug-and-play 3D refining method designed to transform coarse 3D assets into high-quality. The BoostDream framework comprises three distinct processes: (1) We introduce 3D model distillation that fits differentiable representations from the 3D assets obtained through feed-forward generation. (2) A novel multi-view SDS loss is designed, which utilizes a multi-view aware 2D diffusion model to refine the 3D assets. (3) We propose to use prompt and multi-view consistent normal maps as guidance in refinement.Our extensive experiment is conducted on different differentiable 3D representations, revealing that BoostDream excels in generating high-quality 3D assets rapidly, overcoming the Janus problem compared to conventional SDS-based methods. This breakthrough signifies a substantial advancement in both the efficiency and quality of 3D generation processes.

  • 4 authors
·
Jan 30, 2024

Safe LLM-Controlled Robots with Formal Guarantees via Reachability Analysis

The deployment of Large Language Models (LLMs) in robotic systems presents unique safety challenges, particularly in unpredictable environments. Although LLMs, leveraging zero-shot learning, enhance human-robot interaction and decision-making capabilities, their inherent probabilistic nature and lack of formal guarantees raise significant concerns for safety-critical applications. Traditional model-based verification approaches often rely on precise system models, which are difficult to obtain for real-world robotic systems and may not be fully trusted due to modeling inaccuracies, unmodeled dynamics, or environmental uncertainties. To address these challenges, this paper introduces a safety assurance framework for LLM-controlled robots based on data-driven reachability analysis, a formal verification technique that ensures all possible system trajectories remain within safe operational limits. Our framework specifically investigates the problem of instructing an LLM to navigate the robot to a specified goal and assesses its ability to generate low-level control actions that successfully guide the robot safely toward that goal. By leveraging historical data to construct reachable sets of states for the robot-LLM system, our approach provides rigorous safety guarantees against unsafe behaviors without relying on explicit analytical models. We validate the framework through experimental case studies in autonomous navigation and task planning, demonstrating its effectiveness in mitigating risks associated with LLM-generated commands. This work advances the integration of formal methods into LLM-based robotics, offering a principled and practical approach to ensuring safety in next-generation autonomous systems.

  • 4 authors
·
Mar 5

Addressing Negative Transfer in Diffusion Models

Diffusion-based generative models have achieved remarkable success in various domains. It trains a shared model on denoising tasks that encompass different noise levels simultaneously, representing a form of multi-task learning (MTL). However, analyzing and improving diffusion models from an MTL perspective remains under-explored. In particular, MTL can sometimes lead to the well-known phenomenon of negative transfer, which results in the performance degradation of certain tasks due to conflicts between tasks. In this paper, we first aim to analyze diffusion training from an MTL standpoint, presenting two key observations: (O1) the task affinity between denoising tasks diminishes as the gap between noise levels widens, and (O2) negative transfer can arise even in diffusion training. Building upon these observations, we aim to enhance diffusion training by mitigating negative transfer. To achieve this, we propose leveraging existing MTL methods, but the presence of a huge number of denoising tasks makes this computationally expensive to calculate the necessary per-task loss or gradient. To address this challenge, we propose clustering the denoising tasks into small task clusters and applying MTL methods to them. Specifically, based on (O2), we employ interval clustering to enforce temporal proximity among denoising tasks within clusters. We show that interval clustering can be solved using dynamic programming, utilizing signal-to-noise ratio, timestep, and task affinity for clustering objectives. Through this, our approach addresses the issue of negative transfer in diffusion models by allowing for efficient computation of MTL methods. We validate the proposed clustering and its integration with MTL methods through various experiments, demonstrating improved sample quality of diffusion models. Our project page is available at https://gohyojun15.github.io/ANT_diffusion/{url}.

  • 7 authors
·
Jun 1, 2023

KiloNeuS: A Versatile Neural Implicit Surface Representation for Real-Time Rendering

NeRF-based techniques fit wide and deep multi-layer perceptrons (MLPs) to a continuous radiance field that can be rendered from any unseen viewpoint. However, the lack of surface and normals definition and high rendering times limit their usage in typical computer graphics applications. Such limitations have recently been overcome separately, but solving them together remains an open problem. We present KiloNeuS, a neural representation reconstructing an implicit surface represented as a signed distance function (SDF) from multi-view images and enabling real-time rendering by partitioning the space into thousands of tiny MLPs fast to inference. As we learn the implicit surface locally using independent models, resulting in a globally coherent geometry is non-trivial and needs to be addressed during training. We evaluate rendering performance on a GPU-accelerated ray-caster with in-shader neural network inference, resulting in an average of 46 FPS at high resolution, proving a satisfying tradeoff between storage costs and rendering quality. In fact, our evaluation for rendering quality and surface recovery shows that KiloNeuS outperforms its single-MLP counterpart. Finally, to exhibit the versatility of KiloNeuS, we integrate it into an interactive path-tracer taking full advantage of its surface normals. We consider our work a crucial first step toward real-time rendering of implicit neural representations under global illumination.

  • 5 authors
·
Jun 22, 2022

UUKG: Unified Urban Knowledge Graph Dataset for Urban Spatiotemporal Prediction

Accurate Urban SpatioTemporal Prediction (USTP) is of great importance to the development and operation of the smart city. As an emerging building block, multi-sourced urban data are usually integrated as urban knowledge graphs (UrbanKGs) to provide critical knowledge for urban spatiotemporal prediction models. However, existing UrbanKGs are often tailored for specific downstream prediction tasks and are not publicly available, which limits the potential advancement. This paper presents UUKG, the unified urban knowledge graph dataset for knowledge-enhanced urban spatiotemporal predictions. Specifically, we first construct UrbanKGs consisting of millions of triplets for two metropolises by connecting heterogeneous urban entities such as administrative boroughs, POIs, and road segments. Moreover, we conduct qualitative and quantitative analysis on constructed UrbanKGs and uncover diverse high-order structural patterns, such as hierarchies and cycles, that can be leveraged to benefit downstream USTP tasks. To validate and facilitate the use of UrbanKGs, we implement and evaluate 15 KG embedding methods on the KG completion task and integrate the learned KG embeddings into 9 spatiotemporal models for five different USTP tasks. The extensive experimental results not only provide benchmarks of knowledge-enhanced USTP models under different task settings but also highlight the potential of state-of-the-art high-order structure-aware UrbanKG embedding methods. We hope the proposed UUKG fosters research on urban knowledge graphs and broad smart city applications. The dataset and source code are available at https://github.com/usail-hkust/UUKG/.

  • 5 authors
·
Jun 20, 2023

Towards domain-invariant Self-Supervised Learning with Batch Styles Standardization

In Self-Supervised Learning (SSL), models are typically pretrained, fine-tuned, and evaluated on the same domains. However, they tend to perform poorly when evaluated on unseen domains, a challenge that Unsupervised Domain Generalization (UDG) seeks to address. Current UDG methods rely on domain labels, which are often challenging to collect, and domain-specific architectures that lack scalability when confronted with numerous domains, making the current methodology impractical and rigid. Inspired by contrastive-based UDG methods that mitigate spurious correlations by restricting comparisons to examples from the same domain, we hypothesize that eliminating style variability within a batch could provide a more convenient and flexible way to reduce spurious correlations without requiring domain labels. To verify this hypothesis, we introduce Batch Styles Standardization (BSS), a relatively simple yet powerful Fourier-based method to standardize the style of images in a batch specifically designed for integration with SSL methods to tackle UDG. Combining BSS with existing SSL methods offers serious advantages over prior UDG methods: (1) It eliminates the need for domain labels or domain-specific network components to enhance domain-invariance in SSL representations, and (2) offers flexibility as BSS can be seamlessly integrated with diverse contrastive-based but also non-contrastive-based SSL methods. Experiments on several UDG datasets demonstrate that it significantly improves downstream task performances on unseen domains, often outperforming or rivaling with UDG methods. Finally, this work clarifies the underlying mechanisms contributing to BSS's effectiveness in improving domain-invariance in SSL representations and performances on unseen domain.

  • 3 authors
·
Mar 10, 2023

Enabling Flexible Multi-LLM Integration for Scalable Knowledge Aggregation

Large language models (LLMs) have shown remarkable promise but remain challenging to continually improve through traditional finetuning, particularly when integrating capabilities from other specialized LLMs. Popular methods like ensemble and weight merging require substantial memory and struggle to adapt to changing data environments. Recent efforts have transferred knowledge from multiple LLMs into a single target model; however, they suffer from interference and degraded performance among tasks, largely due to limited flexibility in candidate selection and training pipelines. To address these issues, we propose a framework that adaptively selects and aggregates knowledge from diverse LLMs to build a single, stronger model, avoiding the high memory overhead of ensemble and inflexible weight merging. Specifically, we design an adaptive selection network that identifies the most relevant source LLMs based on their scores, thereby reducing knowledge interference. We further propose a dynamic weighted fusion strategy that accounts for the inherent strengths of candidate LLMs, along with a feedback-driven loss function that prevents the selector from converging on a single subset of sources. Experimental results demonstrate that our method can enable a more stable and scalable knowledge aggregation process while reducing knowledge interference by up to 50% compared to existing approaches. Code is avaliable at https://github.com/ZLKong/LLM_Integration

Multimodal Data Integration for Oncology in the Era of Deep Neural Networks: A Review

Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the accuracy and reliability of cancer diagnosis and treatment. There can be disease-related information that is too subtle for humans or existing technological tools to discern visually. Traditional methods typically focus on partial or unimodal information about biological systems at individual scales and fail to encapsulate the complete spectrum of the heterogeneous nature of data. Deep neural networks have facilitated the development of sophisticated multimodal data fusion approaches that can extract and integrate relevant information from multiple sources. Recent deep learning frameworks such as Graph Neural Networks (GNNs) and Transformers have shown remarkable success in multimodal learning. This review article provides an in-depth analysis of the state-of-the-art in GNNs and Transformers for multimodal data fusion in oncology settings, highlighting notable research studies and their findings. We also discuss the foundations of multimodal learning, inherent challenges, and opportunities for integrative learning in oncology. By examining the current state and potential future developments of multimodal data integration in oncology, we aim to demonstrate the promising role that multimodal neural networks can play in cancer prevention, early detection, and treatment through informed oncology practices in personalized settings.

  • 5 authors
·
Mar 11, 2023

FUSION: Fully Integration of Vision-Language Representations for Deep Cross-Modal Understanding

We introduce FUSION, a family of multimodal large language models (MLLMs) with a fully vision-language alignment and integration paradigm. Unlike existing methods that primarily rely on late-stage modality interaction during LLM decoding, our approach achieves deep, dynamic integration throughout the entire processing pipeline. To this end, we propose Text-Guided Unified Vision Encoding, incorporating textual information in vision encoding to achieve pixel-level integration. We further design Context-Aware Recursive Alignment Decoding that recursively aggregates visual features conditioned on textual context during decoding, enabling fine-grained, question-level semantic integration. To guide feature mapping and mitigate modality discrepancies, we develop Dual-Supervised Semantic Mapping Loss. Additionally, we construct a Synthesized Language-Driven Question-Answer (QA) dataset through a new data synthesis method, prioritizing high-quality QA pairs to optimize text-guided feature integration. Building on these foundations, we train FUSION at two scales-3B, 8B-and demonstrate that our full-modality integration approach significantly outperforms existing methods with only 630 vision tokens. Notably, FUSION 3B surpasses Cambrian-1 8B and Florence-VL 8B on most benchmarks. FUSION 3B continues to outperform Cambrian-1 8B even when limited to 300 vision tokens. Our ablation studies show that FUSION outperforms LLaVA-NeXT on over half of the benchmarks under same configuration without dynamic resolution, highlighting the effectiveness of our approach. We release our code, model weights, and dataset. https://github.com/starriver030515/FUSION

  • 7 authors
·
Apr 14 3

Twin-Merging: Dynamic Integration of Modular Expertise in Model Merging

In the era of large language models, model merging is a promising way to combine multiple task-specific models into a single multitask model without extra training. However, two challenges remain: (a) interference between different models and (b) heterogeneous data during testing. Traditional model merging methods often show significant performance gaps compared to fine-tuned models due to these issues. Additionally, a one-size-fits-all model lacks flexibility for diverse test data, leading to performance degradation. We show that both shared and exclusive task-specific knowledge are crucial for merging performance, but directly merging exclusive knowledge hinders overall performance. In view of this, we propose Twin-Merging, a method that encompasses two principal stages: (1) modularizing knowledge into shared and exclusive components, with compression to reduce redundancy and enhance efficiency; (2) dynamically merging shared and task-specific knowledge based on the input. This approach narrows the performance gap between merged and fine-tuned models and improves adaptability to heterogeneous data. Extensive experiments on 12 datasets for both discriminative and generative tasks demonstrate the effectiveness of our method, showing an average improvement of 28.34% in absolute normalized score for discriminative tasks and even surpassing the fine-tuned upper bound on the generative tasks. (Our implementation is available in https://github.com/LZY-the-boys/Twin-Mergin.)

  • 6 authors
·
Jun 16, 2024

ECON: Explicit Clothed humans Optimized via Normal integration

The combination of deep learning, artist-curated scans, and Implicit Functions (IF), is enabling the creation of detailed, clothed, 3D humans from images. However, existing methods are far from perfect. IF-based methods recover free-form geometry, but produce disembodied limbs or degenerate shapes for novel poses or clothes. To increase robustness for these cases, existing work uses an explicit parametric body model to constrain surface reconstruction, but this limits the recovery of free-form surfaces such as loose clothing that deviates from the body. What we want is a method that combines the best properties of implicit representation and explicit body regularization. To this end, we make two key observations: (1) current networks are better at inferring detailed 2D maps than full-3D surfaces, and (2) a parametric model can be seen as a "canvas" for stitching together detailed surface patches. Based on these, our method, ECON, has three main steps: (1) It infers detailed 2D normal maps for the front and back side of a clothed person. (2) From these, it recovers 2.5D front and back surfaces, called d-BiNI, that are equally detailed, yet incomplete, and registers these w.r.t. each other with the help of a SMPL-X body mesh recovered from the image. (3) It "inpaints" the missing geometry between d-BiNI surfaces. If the face and hands are noisy, they can optionally be replaced with the ones of SMPL-X. As a result, ECON infers high-fidelity 3D humans even in loose clothes and challenging poses. This goes beyond previous methods, according to the quantitative evaluation on the CAPE and Renderpeople datasets. Perceptual studies also show that ECON's perceived realism is better by a large margin. Code and models are available for research purposes at econ.is.tue.mpg.de

  • 5 authors
·
Dec 14, 2022

Towards integration of Privacy Enhancing Technologies in Explainable Artificial Intelligence

Explainable Artificial Intelligence (XAI) is a crucial pathway in mitigating the risk of non-transparency in the decision-making process of black-box Artificial Intelligence (AI) systems. However, despite the benefits, XAI methods are found to leak the privacy of individuals whose data is used in training or querying the models. Researchers have demonstrated privacy attacks that exploit explanations to infer sensitive personal information of individuals. Currently there is a lack of defenses against known privacy attacks targeting explanations when vulnerable XAI are used in production and machine learning as a service system. To address this gap, in this article, we explore Privacy Enhancing Technologies (PETs) as a defense mechanism against attribute inference on explanations provided by feature-based XAI methods. We empirically evaluate 3 types of PETs, namely synthetic training data, differentially private training and noise addition, on two categories of feature-based XAI. Our evaluation determines different responses from the mitigation methods and side-effects of PETs on other system properties such as utility and performance. In the best case, PETs integration in explanations reduced the risk of the attack by 49.47%, while maintaining model utility and explanation quality. Through our evaluation, we identify strategies for using PETs in XAI for maximizing benefits and minimizing the success of this privacy attack on sensitive personal information.

  • 4 authors
·
Jul 6

Step-wise Adaptive Integration of Supervised Fine-tuning and Reinforcement Learning for Task-Specific LLMs

Large language models (LLMs) excel at mathematical reasoning and logical problem-solving. The current popular training paradigms primarily use supervised fine-tuning (SFT) and reinforcement learning (RL) to enhance the models' reasoning abilities. However, when using SFT or RL alone, there are respective challenges: SFT may suffer from overfitting, while RL is prone to mode collapse. The state-of-the-art methods have proposed hybrid training schemes. However, static switching faces challenges such as poor generalization across different tasks and high dependence on data quality. In response to these challenges, inspired by the curriculum learning-quiz mechanism in human reasoning cultivation, We propose SASR, a step-wise adaptive hybrid training framework that theoretically unifies SFT and RL and dynamically balances the two throughout optimization. SASR uses SFT for initial warm-up to establish basic reasoning skills, and then uses an adaptive dynamic adjustment algorithm based on gradient norm and divergence relative to the original distribution to seamlessly integrate SFT with the online RL method GRPO. By monitoring the training status of LLMs and adjusting the training process in sequence, SASR ensures a smooth transition between training schemes, maintaining core reasoning abilities while exploring different paths. Experimental results demonstrate that SASR outperforms SFT, RL, and static hybrid training methods.

  • 10 authors
·
May 19

SPARKLE: Enhancing SPARQL Generation with Direct KG Integration in Decoding

Existing KBQA methods have traditionally relied on multi-stage methodologies, involving tasks such as entity linking, subgraph retrieval and query structure generation. However, multi-stage approaches are dependent on the accuracy of preceding steps, leading to cascading errors and increased inference time. Although a few studies have explored the use of end-to-end models, they often suffer from lower accuracy and generate inoperative query that is not supported by the underlying data. Furthermore, most prior approaches are limited to the static training data, potentially overlooking the evolving nature of knowledge bases over time. To address these challenges, we present a novel end-to-end natural language to SPARQL framework, SPARKLE. Notably SPARKLE leverages the structure of knowledge base directly during the decoding, effectively integrating knowledge into the query generation. Our study reveals that simply referencing knowledge base during inference significantly reduces the occurrence of inexecutable query generations. SPARKLE achieves new state-of-the-art results on SimpleQuestions-Wiki and highest F1 score on LCQuAD 1.0 (among models not using gold entities), while getting slightly lower result on the WebQSP dataset. Finally, we demonstrate SPARKLE's fast inference speed and its ability to adapt when the knowledge base differs between the training and inference stages.

  • 2 authors
·
Jun 29, 2024

Domain Terminology Integration into Machine Translation: Leveraging Large Language Models

This paper discusses the methods that we used for our submissions to the WMT 2023 Terminology Shared Task for German-to-English (DE-EN), English-to-Czech (EN-CS), and Chinese-to-English (ZH-EN) language pairs. The task aims to advance machine translation (MT) by challenging participants to develop systems that accurately translate technical terms, ultimately enhancing communication and understanding in specialised domains. To this end, we conduct experiments that utilise large language models (LLMs) for two purposes: generating synthetic bilingual terminology-based data, and post-editing translations generated by an MT model through incorporating pre-approved terms. Our system employs a four-step process: (i) using an LLM to generate bilingual synthetic data based on the provided terminology, (ii) fine-tuning a generic encoder-decoder MT model, with a mix of the terminology-based synthetic data generated in the first step and a randomly sampled portion of the original generic training data, (iii) generating translations with the fine-tuned MT model, and (iv) finally, leveraging an LLM for terminology-constrained automatic post-editing of the translations that do not include the required terms. The results demonstrate the effectiveness of our proposed approach in improving the integration of pre-approved terms into translations. The number of terms incorporated into the translations of the blind dataset increases from an average of 36.67% with the generic model to an average of 72.88% by the end of the process. In other words, successful utilisation of terms nearly doubles across the three language pairs.

  • 6 authors
·
Oct 22, 2023

Integrating Reinforcement Learning with Foundation Models for Autonomous Robotics: Methods and Perspectives

Foundation models (FMs), large deep learning models pre-trained on vast, unlabeled datasets, exhibit powerful capabilities in understanding complex patterns and generating sophisticated outputs. However, they often struggle to adapt to specific tasks. Reinforcement learning (RL), which allows agents to learn through interaction and feedback, offers a compelling solution. Integrating RL with FMs enables these models to achieve desired outcomes and excel at particular tasks. Additionally, RL can be enhanced by leveraging the reasoning and generalization capabilities of FMs. This synergy is revolutionizing various fields, including robotics. FMs, rich in knowledge and generalization, provide robots with valuable information, while RL facilitates learning and adaptation through real-world interactions. This survey paper comprehensively explores this exciting intersection, examining how these paradigms can be integrated to advance robotic intelligence. We analyze the use of foundation models as action planners, the development of robotics-specific foundation models, and the mutual benefits of combining FMs with RL. Furthermore, we present a taxonomy of integration approaches, including large language models, vision-language models, diffusion models, and transformer-based RL models. We also explore how RL can utilize world representations learned from FMs to enhance robotic task execution. Our survey aims to synthesize current research and highlight key challenges in robotic reasoning and control, particularly in the context of integrating FMs and RL--two rapidly evolving technologies. By doing so, we seek to spark future research and emphasize critical areas that require further investigation to enhance robotics. We provide an updated collection of papers based on our taxonomy, accessible on our open-source project website at: https://github.com/clmoro/Robotics-RL-FMs-Integration.

  • 8 authors
·
Oct 21, 2024

SCONE: Surface Coverage Optimization in Unknown Environments by Volumetric Integration

Next Best View computation (NBV) is a long-standing problem in robotics, and consists in identifying the next most informative sensor position(s) for reconstructing a 3D object or scene efficiently and accurately. Like most current methods, we consider NBV prediction from a depth sensor like Lidar systems. Learning-based methods relying on a volumetric representation of the scene are suitable for path planning, but have lower accuracy than methods using a surface-based representation. However, the latter do not scale well with the size of the scene and constrain the camera to a small number of poses. To obtain the advantages of both representations, we show that we can maximize surface metrics by Monte Carlo integration over a volumetric representation. In particular, we propose an approach, SCONE, that relies on two neural modules: The first module predicts occupancy probability in the entire volume of the scene. Given any new camera pose, the second module samples points in the scene based on their occupancy probability and leverages a self-attention mechanism to predict the visibility of the samples. Finally, we integrate the visibility to evaluate the gain in surface coverage for the new camera pose. NBV is selected as the pose that maximizes the gain in total surface coverage. Our method scales to large scenes and handles free camera motion: It takes as input an arbitrarily large point cloud gathered by a depth sensor as well as camera poses to predict NBV. We demonstrate our approach on a novel dataset made of large and complex 3D scenes.

  • 3 authors
·
Aug 22, 2022

AgentStore: Scalable Integration of Heterogeneous Agents As Specialized Generalist Computer Assistant

Digital agents capable of automating complex computer tasks have attracted considerable attention due to their immense potential to enhance human-computer interaction. However, existing agent methods exhibit deficiencies in their generalization and specialization capabilities, especially in handling open-ended computer tasks in real-world environments. Inspired by the rich functionality of the App store, we present AgentStore, a scalable platform designed to dynamically integrate heterogeneous agents for automating computer tasks. AgentStore empowers users to integrate third-party agents, allowing the system to continuously enrich its capabilities and adapt to rapidly evolving operating systems. Additionally, we propose a novel core MetaAgent with the AgentToken strategy to efficiently manage diverse agents and utilize their specialized and generalist abilities for both domain-specific and system-wide tasks. Extensive experiments on three challenging benchmarks demonstrate that AgentStore surpasses the limitations of previous systems with narrow capabilities, particularly achieving a significant improvement from 11.21\% to 23.85\% on the OSWorld benchmark, more than doubling the previous results. Comprehensive quantitative and qualitative results further demonstrate AgentStore's ability to enhance agent systems in both generalization and specialization, underscoring its potential for developing the specialized generalist computer assistant. All our codes will be made publicly available in https://chengyou-jia.github.io/AgentStore-Home.

  • 8 authors
·
Oct 24, 2024 2

Benchmarking Computational Methods for Emerging Drug-Drug Interaction Prediction

Motivation: Emerging drug-drug interaction (DDI) prediction is crucial for new drugs but is hindered by distribution changes between known and new drugs in real-world scenarios. Current evaluation often neglects these changes, relying on unrealistic i.i.d. split due to the absence of drug approval data. Results: We propose DDI-Ben, a benchmarking framework for emerging DDI prediction under distribution changes. DDI-Ben introduces a distribution change simulation framework that leverages distribution changes between drug sets as a surrogate for real-world distribution changes of DDIs, and is compatible with various drug split strategies. Through extensive benchmarking on ten representative methods, we show that most existing approaches suffer substantial performance degradation under distribution changes. Our analysis further indicates that large language model (LLM) based methods and the integration of drug-related textual information offer promising robustness against such degradation. To support future research, we release the benchmark datasets with simulated distribution changes. Overall, DDI-Ben highlights the importance of explicitly addressing distribution changes and provides a foundation for developing more resilient methods for emerging DDI prediction. Availability and implementation: Our code and data are available at https://github.com/LARS-research/DDI-Bench.

  • 4 authors
·
Oct 24, 2024

The order in speech disorder: a scoping review of state of the art machine learning methods for clinical speech classification

Background:Speech patterns have emerged as potential diagnostic markers for conditions with varying etiologies. Machine learning (ML) presents an opportunity to harness these patterns for accurate disease diagnosis. Objective: This review synthesized findings from studies exploring ML's capability in leveraging speech for the diagnosis of neurological, laryngeal and mental disorders. Methods: A systematic examination of 564 articles was conducted with 91 articles included in the study, which encompassed a wide spectrum of conditions, ranging from voice pathologies to mental and neurological disorders. Methods for speech classifications were assessed based on the relevant studies and scored between 0-10 based on the reported diagnostic accuracy of their ML models. Results: High diagnostic accuracies were consistently observed for laryngeal disorders, dysarthria, and changes related to speech in Parkinsons disease. These findings indicate the robust potential of speech as a diagnostic tool. Disorders like depression, schizophrenia, mild cognitive impairment and Alzheimers dementia also demonstrated high accuracies, albeit with some variability across studies. Meanwhile, disorders like OCD and autism highlighted the need for more extensive research to ascertain the relationship between speech patterns and the respective conditions. Conclusion: ML models utilizing speech patterns demonstrate promising potential in diagnosing a range of mental, laryngeal, and neurological disorders. However, the efficacy varies across conditions, and further research is needed. The integration of these models into clinical practice could potentially revolutionize the evaluation and diagnosis of a number of different medical conditions.

  • 4 authors
·
Mar 3

Multi-Stage Knowledge Integration of Vision-Language Models for Continual Learning

Vision Language Models (VLMs), pre-trained on large-scale image-text datasets, enable zero-shot predictions for unseen data but may underperform on specific unseen tasks. Continual learning (CL) can help VLMs effectively adapt to new data distributions without joint training, but faces challenges of catastrophic forgetting and generalization forgetting. Although significant progress has been achieved by distillation-based methods, they exhibit two severe limitations. One is the popularly adopted single-teacher paradigm fails to impart comprehensive knowledge, The other is the existing methods inadequately leverage the multimodal information in the original training dataset, instead they rely on additional data for distillation, which increases computational and storage overhead. To mitigate both limitations, by drawing on Knowledge Integration Theory (KIT), we propose a Multi-Stage Knowledge Integration network (MulKI) to emulate the human learning process in distillation methods. MulKI achieves this through four stages, including Eliciting Ideas, Adding New Ideas, Distinguishing Ideas, and Making Connections. During the four stages, we first leverage prototypes to align across modalities, eliciting cross-modal knowledge, then adding new knowledge by constructing fine-grained intra- and inter-modality relationships with prototypes. After that, knowledge from two teacher models is adaptively distinguished and re-weighted. Finally, we connect between models from intra- and inter-task, integrating preceding and new knowledge. Our method demonstrates significant improvements in maintaining zero-shot capabilities while supporting continual learning across diverse downstream tasks, showcasing its potential in adapting VLMs to evolving data distributions.

  • 5 authors
·
Nov 11, 2024

Zero-Shot Dual-Path Integration Framework for Open-Vocabulary 3D Instance Segmentation

Open-vocabulary 3D instance segmentation transcends traditional closed-vocabulary methods by enabling the identification of both previously seen and unseen objects in real-world scenarios. It leverages a dual-modality approach, utilizing both 3D point clouds and 2D multi-view images to generate class-agnostic object mask proposals. Previous efforts predominantly focused on enhancing 3D mask proposal models; consequently, the information that could come from 2D association to 3D was not fully exploited. This bias towards 3D data, while effective for familiar indoor objects, limits the system's adaptability to new and varied object types, where 2D models offer greater utility. Addressing this gap, we introduce Zero-Shot Dual-Path Integration Framework that equally values the contributions of both 3D and 2D modalities. Our framework comprises three components: 3D pathway, 2D pathway, and Dual-Path Integration. 3D pathway generates spatially accurate class-agnostic mask proposals of common indoor objects from 3D point cloud data using a pre-trained 3D model, while 2D pathway utilizes pre-trained open-vocabulary instance segmentation model to identify a diverse array of object proposals from multi-view RGB-D images. In Dual-Path Integration, our Conditional Integration process, which operates in two stages, filters and merges the proposals from both pathways adaptively. This process harmonizes output proposals to enhance segmentation capabilities. Our framework, utilizing pre-trained models in a zero-shot manner, is model-agnostic and demonstrates superior performance on both seen and unseen data, as evidenced by comprehensive evaluations on the ScanNet200 and qualitative results on ARKitScenes datasets.

  • 6 authors
·
Aug 16, 2024

KIND: Knowledge Integration and Diversion in Diffusion Models

Pre-trained models have become the preferred backbone due to the expansion of model parameters, with techniques like Parameter-Efficient Fine-Tuning (PEFTs) typically fixing the parameters of these models. However, pre-trained models may not always be optimal, especially when there are discrepancies between training tasks and target tasks, potentially resulting in negative transfer. To address this, we introduce KIND, which performs Knowledge INtegration and Diversion in diffusion models. KIND first integrates knowledge by decomposing parameter matrices of models using U, Sigma, and V matrices, formally inspired by singular value decomposition (SVD). Then it explicitly partitions the components of these matrices into learngenes and tailors to condense common and class-specific knowledge, respectively, through a class gate. In this way, KIND redefines traditional pre-training methods by adjusting training objectives from maximizing model performance on current tasks to condensing transferable common knowledge, leveraging the Learngene framework. We conduct experiments on ImageNet-1K and compare KIND with PEFT and other learngene methods. Results indicate that KIND achieves state-of-the-art performance compared to other PEFT and learngene methods. Specifically, the images generated by KIND achieves more than 6.54 and 1.07 decrease in FID and sFID on DiT-L/2, utilizing only 45.4M trainable parameters and saving at least 35.4G FLOPs in computational cost.

  • 5 authors
·
Aug 14, 2024

Prompting is not Enough: Exploring Knowledge Integration and Controllable Generation

Open-domain question answering (OpenQA) represents a cornerstone in natural language processing (NLP), primarily focused on extracting answers from unstructured textual data. With the rapid advancements in Large Language Models (LLMs), LLM-based OpenQA methods have reaped the benefits of emergent understanding and answering capabilities enabled by massive parameters compared to traditional methods. However, most of these methods encounter two critical challenges: how to integrate knowledge into LLMs effectively and how to adaptively generate results with specific answer formats for various task situations. To address these challenges, we propose a novel framework named GenKI, which aims to improve the OpenQA performance by exploring Knowledge Integration and controllable Generation on LLMs simultaneously. Specifically, we first train a dense passage retrieval model to retrieve associated knowledge from a given knowledge base. Subsequently, we introduce a novel knowledge integration model that incorporates the retrieval knowledge into instructions during fine-tuning to intensify the model. Furthermore, to enable controllable generation in LLMs, we leverage a certain fine-tuned LLM and an ensemble based on text consistency incorporating all coherence, fluency, and answer format assurance. Finally, extensive experiments conducted on the TriviaQA, MSMARCO, and CMRC2018 datasets, featuring diverse answer formats, have demonstrated the effectiveness of GenKI with comparison of state-of-the-art baselines. Moreover, ablation studies have disclosed a linear relationship between the frequency of retrieved knowledge and the model's ability to recall knowledge accurately against the ground truth. Our code of GenKI is available at https://github.com/USTC-StarTeam/GenKI

  • 8 authors
·
May 26

Exact Diffusion Inversion via Bi-directional Integration Approximation

Recently, various methods have been proposed to address the inconsistency issue of DDIM inversion to enable image editing, such as EDICT [36] and Null-text inversion [22]. However, the above methods introduce considerable computational overhead. In this paper, we propose a new technique, named bi-directional integration approximation (BDIA), to perform exact diffusion inversion with neglible computational overhead. Suppose we would like to estimate the next diffusion state z_{i-1} at timestep t_i with the historical information (i,z_i) and (i+1,z_{i+1}). We first obtain the estimated Gaussian noise boldsymbol{epsilon}(z_i,i), and then apply the DDIM update procedure twice for approximating the ODE integration over the next time-slot [t_i, t_{i-1}] in the forward manner and the previous time-slot [t_i, t_{t+1}] in the backward manner. The DDIM step for the previous time-slot is used to refine the integration approximation made earlier when computing z_i. A nice property of BDIA-DDIM is that the update expression for z_{i-1} is a linear combination of (z_{i+1}, z_i, boldsymbol{epsilon}(z_i,i)). This allows for exact backward computation of z_{i+1} given (z_i, z_{i-1}), thus leading to exact diffusion inversion. It is demonstrated with experiments that (round-trip) BDIA-DDIM is particularly effective for image editing. Our experiments further show that BDIA-DDIM produces markedly better image sampling qualities than DDIM for text-to-image generation. BDIA can also be applied to improve the performance of other ODE solvers in addition to DDIM. In our work, it is found that applying BDIA to the EDM sampling procedure produces consistently better performance over four pre-trained models.

  • 3 authors
·
Jul 10, 2023

Categorical semiotics: Foundations for Knowledge Integration

The integration of knowledge extracted from diverse models, whether described by domain experts or generated by machine learning algorithms, has historically been challenged by the absence of a suitable framework for specifying and integrating structures, learning processes, data transformations, and data models or rules. In this work, we extend algebraic specification methods to address these challenges within such a framework. In our work, we tackle the challenging task of developing a comprehensive framework for defining and analyzing deep learning architectures. We believe that previous efforts have fallen short by failing to establish a clear connection between the constraints a model must adhere to and its actual implementation. Our methodology employs graphical structures that resemble Ehresmann's sketches, interpreted within a universe of fuzzy sets. This approach offers a unified theory that elegantly encompasses both deterministic and non-deterministic neural network designs. Furthermore, we highlight how this theory naturally incorporates fundamental concepts from computer science and automata theory. Our extended algebraic specification framework, grounded in graphical structures akin to Ehresmann's sketches, offers a promising solution for integrating knowledge across disparate models and domains. By bridging the gap between domain-specific expertise and machine-generated insights, we pave the way for more comprehensive, collaborative, and effective approaches to knowledge integration and modeling.

  • 1 authors
·
Apr 1, 2024

Trusta: Reasoning about Assurance Cases with Formal Methods and Large Language Models

Assurance cases can be used to argue for the safety of products in safety engineering. In safety-critical areas, the construction of assurance cases is indispensable. Trustworthiness Derivation Trees (TDTs) enhance assurance cases by incorporating formal methods, rendering it possible for automatic reasoning about assurance cases. We present Trustworthiness Derivation Tree Analyzer (Trusta), a desktop application designed to automatically construct and verify TDTs. The tool has a built-in Prolog interpreter in its backend, and is supported by the constraint solvers Z3 and MONA. Therefore, it can solve constraints about logical formulas involving arithmetic, sets, Horn clauses etc. Trusta also utilizes large language models to make the creation and evaluation of assurance cases more convenient. It allows for interactive human examination and modification. We evaluated top language models like ChatGPT-3.5, ChatGPT-4, and PaLM 2 for generating assurance cases. Our tests showed a 50%-80% similarity between machine-generated and human-created cases. In addition, Trusta can extract formal constraints from text in natural languages, facilitating an easier interpretation and validation process. This extraction is subject to human review and correction, blending the best of automated efficiency with human insight. To our knowledge, this marks the first integration of large language models in automatic creating and reasoning about assurance cases, bringing a novel approach to a traditional challenge. Through several industrial case studies, Trusta has proven to quickly find some subtle issues that are typically missed in manual inspection, demonstrating its practical value in enhancing the assurance case development process.

  • 3 authors
·
Sep 22, 2023

LayerCraft: Enhancing Text-to-Image Generation with CoT Reasoning and Layered Object Integration

Text-to-image generation (T2I) has become a key area of research with broad applications. However, existing methods often struggle with complex spatial relationships and fine-grained control over multiple concepts. Many existing approaches require significant architectural modifications, extensive training, or expert-level prompt engineering. To address these challenges, we introduce LayerCraft, an automated framework that leverages large language models (LLMs) as autonomous agents for structured procedural generation. LayerCraft enables users to customize objects within an image and supports narrative-driven creation with minimal effort. At its core, the system includes a coordinator agent that directs the process, along with two specialized agents: ChainArchitect, which employs chain-of-thought (CoT) reasoning to generate a dependency-aware 3D layout for precise instance-level control, and the Object-Integration Network (OIN), which utilizes LoRA fine-tuning on pre-trained T2I models to seamlessly blend objects into specified regions of an image based on textual prompts without requiring architectural changes. Extensive evaluations demonstrate LayerCraft's versatility in applications ranging from multi-concept customization to storytelling. By providing non-experts with intuitive, precise control over T2I generation, our framework democratizes creative image creation. Our code will be released upon acceptance at github.com/PeterYYZhang/LayerCraft

  • 3 authors
·
Mar 25

GBT-SAM: Adapting a Foundational Deep Learning Model for Generalizable Brain Tumor Segmentation via Efficient Integration of Multi-Parametric MRI Data

Gliomas are aggressive brain tumors that require accurate imaging-based diagnosis, with segmentation playing a critical role in evaluating morphology and treatment decisions. Manual delineation of gliomas is time-consuming and prone to variability, motivating the use of deep learning to improve consistency and alleviate clinical workload. However, existing methods often fail to fully exploit the information available in multi-parametric MRI (mp-MRI), particularly inter-slice contextual features, and typically require considerable computational resources while lacking robustness across tumor type variations. We present GBT-SAM, a parameter-efficient deep learning framework that adapts the Segment Anything Model (SAM), a large-scale vision model, to volumetric mp-MRI data. GBT-SAM reduces input complexity by selecting fewer than 2.6\% of slices per scan while incorporating all four MRI modalities, preserving essential tumor-related information with minimal cost. Furthermore, our model is trained by a two-step fine-tuning strategy that incorporates a depth-aware module to capture inter-slice correlations and lightweight adaptation layers, resulting in just 6.5M trainable parameters, which is the lowest among SAM-based approaches. GBT-SAM achieves a Dice Score of 93.54 on the BraTS Adult Glioma dataset and demonstrates robust performance on Meningioma, Pediatric Glioma, and Sub-Saharan Glioma datasets. These results highlight GBT-SAM's potential as a computationally efficient and domain-robust framework for brain tumor segmentation using mp-MRI. Our code and models are available at https://github.com/vpulab/med-sam-brain .

  • 5 authors
·
Mar 6

Robust Table Integration in Data Lakes

In this paper, we investigate the challenge of integrating tables from data lakes, focusing on three core tasks: 1) pairwise integrability judgment, which determines whether a tuple pair in a table is integrable, accounting for any occurrences of semantic equivalence or typographical errors; 2) integrable set discovery, which aims to identify all integrable sets in a table based on pairwise integrability judgments established in the first task; 3) multi-tuple conflict resolution, which resolves conflicts among multiple tuples during integration. We train a binary classifier to address the task of pairwise integrability judgment. Given the scarcity of labeled data, we propose a self-supervised adversarial contrastive learning algorithm to perform classification, which incorporates data augmentation methods and adversarial examples to autonomously generate new training data. Upon the output of pairwise integrability judgment, each integrable set is considered as a community, a densely connected sub-graph where nodes and edges correspond to tuples in the table and their pairwise integrability, respectively. We proceed to investigate various community detection algorithms to address the integrable set discovery objective. Moving forward to tackle multi-tuple conflict resolution, we introduce an novel in-context learning methodology. This approach capitalizes on the knowledge embedded within pretrained large language models to effectively resolve conflicts that arise when integrating multiple tuples. Notably, our method minimizes the need for annotated data. Since no suitable test collections are available for our tasks, we develop our own benchmarks using two real-word dataset repositories: Real and Join. We conduct extensive experiments on these benchmarks to validate the robustness and applicability of our methodologies in the context of integrating tables within data lakes.

  • 4 authors
·
Nov 29, 2024

The Oxford Spires Dataset: Benchmarking Large-Scale LiDAR-Visual Localisation, Reconstruction and Radiance Field Methods

This paper introduces a large-scale multi-modal dataset captured in and around well-known landmarks in Oxford using a custom-built multi-sensor perception unit as well as a millimetre-accurate map from a Terrestrial LiDAR Scanner (TLS). The perception unit includes three synchronised global shutter colour cameras, an automotive 3D LiDAR scanner, and an inertial sensor - all precisely calibrated. We also establish benchmarks for tasks involving localisation, reconstruction, and novel-view synthesis, which enable the evaluation of Simultaneous Localisation and Mapping (SLAM) methods, Structure-from-Motion (SfM) and Multi-view Stereo (MVS) methods as well as radiance field methods such as Neural Radiance Fields (NeRF) and 3D Gaussian Splatting. To evaluate 3D reconstruction the TLS 3D models are used as ground truth. Localisation ground truth is computed by registering the mobile LiDAR scans to the TLS 3D models. Radiance field methods are evaluated not only with poses sampled from the input trajectory, but also from viewpoints that are from trajectories which are distant from the training poses. Our evaluation demonstrates a key limitation of state-of-the-art radiance field methods: we show that they tend to overfit to the training poses/images and do not generalise well to out-of-sequence poses. They also underperform in 3D reconstruction compared to MVS systems using the same visual inputs. Our dataset and benchmarks are intended to facilitate better integration of radiance field methods and SLAM systems. The raw and processed data, along with software for parsing and evaluation, can be accessed at https://dynamic.robots.ox.ac.uk/datasets/oxford-spires/.

  • 6 authors
·
Nov 15, 2024

Alt-MoE:A Scalable Framework for Bidirectional Multimodal Alignment and Efficient Knowledge Integration

Multimodal learning has advanced significantly by aligning different modalities within shared latent spaces, enabling tasks such as cross-modal understanding and generation. Current alignment strategies in multimodal learning primarily include direct alignment using pre-trained or unified encoders and single-directional alignment via modality-specific connectors. Direct alignment struggles to fully leverage rich intra-modal knowledge, often requiring extensive training data to achieve cross-modal representation. Meanwhile, single-directional alignment methods, despite leveraging pre-trained knowledge, restrict task adaptability and hinder the model's ability to capture bidirectional relationships, leading to incomplete knowledge fusion and underutilization of complementary modality-specific information. To address these limitations, we introduce Alt-MoE, a scalable multimodal alignment framework that employs a mixture of experts (MoE) model as a multi-directional connector across modalities. By utilizing a sequential alternating one-way alignment strategy, Alt-MoE iteratively refines the model to achieve bidirectional alignment. Alt-MoE operates in latent space, enabling efficient vector pre-storage and real-time retrieval via MoE, optimizing large-scale data processing. Extensive empirical studies demonstrate that Alt-MoE achieves competitive performance on cross-modal retrieval and visual question answering by integrating diverse modality-specific knowledge, generalizing to unseen data, and easily scaling to new tasks and modalities through dynamic adjustment of MoE capacity and expert activation.

  • 11 authors
·
Sep 9, 2024

Time Series Analysis for Education: Methods, Applications, and Future Directions

Recent advancements in the collection and analysis of sequential educational data have brought time series analysis to a pivotal position in educational research, highlighting its essential role in facilitating data-driven decision-making. However, there is a lack of comprehensive summaries that consolidate these advancements. To the best of our knowledge, this paper is the first to provide a comprehensive review of time series analysis techniques specifically within the educational context. We begin by exploring the landscape of educational data analytics, categorizing various data sources and types relevant to education. We then review four prominent time series methods-forecasting, classification, clustering, and anomaly detection-illustrating their specific application points in educational settings. Subsequently, we present a range of educational scenarios and applications, focusing on how these methods are employed to address diverse educational tasks, which highlights the practical integration of multiple time series methods to solve complex educational problems. Finally, we conclude with a discussion on future directions, including personalized learning analytics, multimodal data fusion, and the role of large language models (LLMs) in educational time series. The contributions of this paper include a detailed taxonomy of educational data, a synthesis of time series techniques with specific educational applications, and a forward-looking perspective on emerging trends and future research opportunities in educational analysis. The related papers and resources are available and regularly updated at the project page.

  • 7 authors
·
Aug 25, 2024

DCT-HistoTransformer: Efficient Lightweight Vision Transformer with DCT Integration for histopathological image analysis

In recent years, the integration of advanced imaging techniques and deep learning methods has significantly advanced computer-aided diagnosis (CAD) systems for breast cancer detection and classification. Transformers, which have shown great promise in computer vision, are now being applied to medical image analysis. However, their application to histopathological images presents challenges due to the need for extensive manual annotations of whole-slide images (WSIs), as these models require large amounts of data to work effectively, which is costly and time-consuming. Furthermore, the quadratic computational cost of Vision Transformers (ViTs) is particularly prohibitive for large, high-resolution histopathological images, especially on edge devices with limited computational resources. In this study, we introduce a novel lightweight breast cancer classification approach using transformers that operates effectively without large datasets. By incorporating parallel processing pathways for Discrete Cosine Transform (DCT) Attention and MobileConv, we convert image data from the spatial domain to the frequency domain to utilize the benefits such as filtering out high frequencies in the image, which reduces computational cost. This demonstrates the potential of our approach to improve breast cancer classification in histopathological images, offering a more efficient solution with reduced reliance on extensive annotated datasets. Our proposed model achieves an accuracy of 96.00% pm 0.48% for binary classification and 87.85% pm 0.93% for multiclass classification, which is comparable to state-of-the-art models while significantly reducing computational costs. This demonstrates the potential of our approach to improve breast cancer classification in histopathological images, offering a more efficient solution with reduced reliance on extensive annotated datasets.

  • 4 authors
·
Oct 24, 2024

Exploring the Impact of Table-to-Text Methods on Augmenting LLM-based Question Answering with Domain Hybrid Data

Augmenting Large Language Models (LLMs) for Question Answering (QA) with domain specific data has attracted wide attention. However, domain data often exists in a hybrid format, including text and semi-structured tables, posing challenges for the seamless integration of information. Table-to-Text Generation is a promising solution by facilitating the transformation of hybrid data into a uniformly text-formatted corpus. Although this technique has been widely studied by the NLP community, there is currently no comparative analysis on how corpora generated by different table-to-text methods affect the performance of QA systems. In this paper, we address this research gap in two steps. First, we innovatively integrate table-to-text generation into the framework of enhancing LLM-based QA systems with domain hybrid data. Then, we utilize this framework in real-world industrial data to conduct extensive experiments on two types of QA systems (DSFT and RAG frameworks) with four representative methods: Markdown format, Template serialization, TPLM-based method, and LLM-based method. Based on the experimental results, we draw some empirical findings and explore the underlying reasons behind the success of some methods. We hope the findings of this work will provide a valuable reference for the academic and industrial communities in developing robust QA systems.

  • 11 authors
·
Feb 20, 2024

Comparison of biomedical relationship extraction methods and models for knowledge graph creation

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

  • 2 authors
·
Jan 5, 2022

Interpretable graph-based models on multimodal biomedical data integration: A technical review and benchmarking

Integrating heterogeneous biomedical data including imaging, omics, and clinical records supports accurate diagnosis and personalised care. Graph-based models fuse such non-Euclidean data by capturing spatial and relational structure, yet clinical uptake requires regulator-ready interpretability. We present the first technical survey of interpretable graph based models for multimodal biomedical data, covering 26 studies published between Jan 2019 and Sep 2024. Most target disease classification, notably cancer and rely on static graphs from simple similarity measures, while graph-native explainers are rare; post-hoc methods adapted from non-graph domains such as gradient saliency, and SHAP predominate. We group existing approaches into four interpretability families, outline trends such as graph-in-graph hierarchies, knowledge-graph edges, and dynamic topology learning, and perform a practical benchmark. Using an Alzheimer disease cohort, we compare Sensitivity Analysis, Gradient Saliency, SHAP and Graph Masking. SHAP and Sensitivity Analysis recover the broadest set of known AD pathways and Gene-Ontology terms, whereas Gradient Saliency and Graph Masking surface complementary metabolic and transport signatures. Permutation tests show all four beat random gene sets, but with distinct trade-offs: SHAP and Graph Masking offer deeper biology at higher compute cost, while Gradient Saliency and Sensitivity Analysis are quicker though coarser. We also provide a step-by-step flowchart covering graph construction, explainer choice and resource budgeting to help researchers balance transparency and performance. This review synthesises the state of interpretable graph learning for multimodal medicine, benchmarks leading techniques, and charts future directions, from advanced XAI tools to under-studied diseases, serving as a concise reference for method developers and translational scientists.

  • 6 authors
·
May 3

Design, Integration, and Field Evaluation of a Robotic Blossom Thinning System for Tree Fruit Crops

The US apple industry relies heavily on semi-skilled manual labor force for essential field operations such as training, pruning, blossom and green fruit thinning, and harvesting. Blossom thinning is one of the crucial crop load management practices to achieve desired crop load, fruit quality, and return bloom. While several techniques such as chemical, and mechanical thinning are available for large-scale blossom thinning such approaches often yield unpredictable thinning results and may cause damage the canopy, spurs, and leaf tissue. Hence, growers still depend on laborious, labor intensive and expensive manual hand blossom thinning for desired thinning outcomes. This research presents a robotic solution for blossom thinning in apple orchards using a computer vision system with artificial intelligence, a six degrees of freedom robotic manipulator, and an electrically actuated miniature end-effector for robotic blossom thinning. The integrated robotic system was evaluated in a commercial apple orchard which showed promising results for targeted and selective blossom thinning. Two thinning approaches, center and boundary thinning, were investigated to evaluate the system ability to remove varying proportion of flowers from apple flower clusters. During boundary thinning the end effector was actuated around the cluster boundary while center thinning involved end-effector actuation only at the cluster centroid for a fixed duration of 2 seconds. The boundary thinning approach thinned 67.2% of flowers from the targeted clusters with a cycle time of 9.0 seconds per cluster, whereas center thinning approach thinned 59.4% of flowers with a cycle time of 7.2 seconds per cluster. When commercially adopted, the proposed system could help address problems faced by apple growers with current hand, chemical, and mechanical blossom thinning approaches.

  • 3 authors
·
Apr 10, 2023

Vision Language Models in Medicine

With the advent of Vision-Language Models (VLMs), medical artificial intelligence (AI) has experienced significant technological progress and paradigm shifts. This survey provides an extensive review of recent advancements in Medical Vision-Language Models (Med-VLMs), which integrate visual and textual data to enhance healthcare outcomes. We discuss the foundational technology behind Med-VLMs, illustrating how general models are adapted for complex medical tasks, and examine their applications in healthcare. The transformative impact of Med-VLMs on clinical practice, education, and patient care is highlighted, alongside challenges such as data scarcity, narrow task generalization, interpretability issues, and ethical concerns like fairness, accountability, and privacy. These limitations are exacerbated by uneven dataset distribution, computational demands, and regulatory hurdles. Rigorous evaluation methods and robust regulatory frameworks are essential for safe integration into healthcare workflows. Future directions include leveraging large-scale, diverse datasets, improving cross-modal generalization, and enhancing interpretability. Innovations like federated learning, lightweight architectures, and Electronic Health Record (EHR) integration are explored as pathways to democratize access and improve clinical relevance. This review aims to provide a comprehensive understanding of Med-VLMs' strengths and limitations, fostering their ethical and balanced adoption in healthcare.

  • 3 authors
·
Feb 24

Inference Scaling vs Reasoning: An Empirical Analysis of Compute-Optimal LLM Problem-Solving

Recent advances in large language models (LLMs) have predominantly focused on maximizing accuracy and reasoning capabilities, often overlooking crucial computational efficiency considerations. While this approach has yielded impressive accuracy improvements, it has led to methods that may be impractical for real-world deployment due to computational overhead and latency constraints. This paper investigates the potential synergy between reasoning enhancement and computational efficiency by analyzing the integration of two contrasting approaches: Quiet-STaR (Self-Taught Reasoner) and REBASE (REward BAlanced SEarch). Through comprehensive empirical analysis using the Mistral-7B model on the GSM8K dataset, we demonstrate that while each method excels in its primary objective-Quiet-STaR achieving superior accuracy (32.03%) despite high computational cost (554.66s runtime, 12.73T FLOPs), and REBASE providing exceptional efficiency (8.47s runtime, 2.35T FLOPs) while maintaining baseline-comparable accuracy (10.94%)-their integration reveals fundamental challenges in reconciling reasoning depth with computational efficiency. The combined approach unexpectedly results in degraded performance (9.38% accuracy, 143.66s runtime), highlighting critical insights about the complex interplay between reasoning enhancement and efficiency optimization in LLMs. Our findings illuminate the need for novel architectures and algorithms specifically designed to bridge the gap between these competing objectives, while providing concrete directions for future research in compute-efficient reasoning methods.

  • 2 authors
·
Dec 20, 2024

UR$^2$: Unify RAG and Reasoning through Reinforcement Learning

Large Language Models (LLMs) have shown remarkable capabilities through two complementary paradigms: Retrieval-Augmented Generation (RAG), which enhances knowledge grounding, and Reinforcement Learning from Verifiable Rewards (RLVR), which optimizes complex reasoning abilities. However, these two capabilities are often developed in isolation, and existing efforts to unify them remain narrow in scope-typically limited to open-domain QA with fixed retrieval settings and task-specific assumptions. This lack of integration constrains generalization and limits the applicability of RAG-RL methods to broader domains. To bridge this gap, we propose UR2 (Unified RAG and Reasoning), a general framework that unifies retrieval and reasoning through reinforcement learning. UR2 introduces two key contributions: a difficulty-aware curriculum training that selectively invokes retrieval only for challenging problems, and a hybrid knowledge access strategy combining domain-specific offline corpora with LLM-generated summaries. These components are designed to enable dynamic coordination between retrieval and reasoning, improving adaptability across a diverse range of tasks. Experiments across open-domain QA, MMLU-Pro, medical, and mathematical reasoning tasks demonstrate that UR2 (built on Qwen2.5-3/7B and LLaMA-3.1-8B) significantly outperforms existing RAG and RL methods, achieving comparable performance to GPT-4o-mini and GPT-4.1-mini on several benchmarks. We have released all code, models, and data at https://github.com/Tsinghua-dhy/UR2.

  • 6 authors
·
Aug 8

BioGraphFusion: Graph Knowledge Embedding for Biological Completion and Reasoning

Motivation: Biomedical knowledge graphs (KGs) are crucial for drug discovery and disease understanding, yet their completion and reasoning are challenging. Knowledge Embedding (KE) methods capture global semantics but struggle with dynamic structural integration, while Graph Neural Networks (GNNs) excel locally but often lack semantic understanding. Even ensemble approaches, including those leveraging language models, often fail to achieve a deep, adaptive, and synergistic co-evolution between semantic comprehension and structural learning. Addressing this critical gap in fostering continuous, reciprocal refinement between these two aspects in complex biomedical KGs is paramount. Results: We introduce BioGraphFusion, a novel framework for deeply synergistic semantic and structural learning. BioGraphFusion establishes a global semantic foundation via tensor decomposition, guiding an LSTM-driven mechanism to dynamically refine relation embeddings during graph propagation. This fosters adaptive interplay between semantic understanding and structural learning, further enhanced by query-guided subgraph construction and a hybrid scoring mechanism. Experiments across three key biomedical tasks demonstrate BioGraphFusion's superior performance over state-of-the-art KE, GNN, and ensemble models. A case study on Cutaneous Malignant Melanoma 1 (CMM1) highlights its ability to unveil biologically meaningful pathways. Availability and Implementation: Source code and all training data are freely available for download at https://github.com/Y-TARL/BioGraphFusion. Supplementary information: Supplementary data are available at Bioinformatics online.

  • 6 authors
·
Jul 19

FlamePINN-1D: Physics-informed neural networks to solve forward and inverse problems of 1D laminar flames

Given the existence of various forward and inverse problems in combustion studies and applications that necessitate distinct methods for resolution, a framework to solve them in a unified way is critically needed. A promising approach is the integration of machine learning methods with governing equations of combustion systems, which exhibits superior generality and few-shot learning ability compared to purely data-driven methods. In this work, the FlamePINN-1D framework is proposed to solve the forward and inverse problems of 1D laminar flames based on physics-informed neural networks. Three cases with increasing complexity have been tested: Case 1 are freely-propagating premixed (FPP) flames with simplified physical models, while Case 2 and Case 3 are FPP and counterflow premixed (CFP) flames with detailed models, respectively. For forward problems, FlamePINN-1D aims to solve the flame fields and infer the unknown eigenvalues (such as laminar flame speeds) under the constraints of governing equations and boundary conditions. For inverse problems, FlamePINN-1D aims to reconstruct the continuous fields and infer the unknown parameters (such as transport and chemical kinetics parameters) from noisy sparse observations of the flame. Our results strongly validate these capabilities of FlamePINN-1D across various flames and working conditions. Compared to traditional methods, FlamePINN-1D is differentiable and mesh-free, exhibits no discretization errors, and is easier to implement for inverse problems. The inverse problem results also indicate the possibility of optimizing chemical mechanisms from measurements of laboratory 1D flames. Furthermore, some proposed strategies, such as hard constraints and thin-layer normalization, are proven to be essential for the robust learning of FlamePINN-1D. The code for this paper is partially available at https://github.com/CAME-THU/FlamePINN-1D.

  • 6 authors
·
Jun 7, 2024

MemOS: An Operating System for Memory-Augmented Generation (MAG) in Large Language Models

Large Language Models (LLMs) have emerged as foundational infrastructure in the pursuit of Artificial General Intelligence (AGI). Despite their remarkable capabilities in language perception and generation, current LLMs fundamentally lack a unified and structured architecture for handling memory. They primarily rely on parametric memory (knowledge encoded in model weights) and ephemeral activation memory (context-limited runtime states). While emerging methods like Retrieval-Augmented Generation (RAG) incorporate plaintext memory, they lack lifecycle management and multi-modal integration, limiting their capacity for long-term knowledge evolution. To address this, we introduce MemOS, a memory operating system designed for LLMs that, for the first time, elevates memory to a first-class operational resource. It builds unified mechanisms for representation, organization, and governance across three core memory types: parametric, activation, and plaintext. At its core is the MemCube, a standardized memory abstraction that enables tracking, fusion, and migration of heterogeneous memory, while offering structured, traceable access across tasks and contexts. MemOS establishes a memory-centric execution framework with strong controllability, adaptability, and evolvability. It fills a critical gap in current LLM infrastructure and lays the groundwork for continual adaptation, personalized intelligence, and cross-platform coordination in next-generation intelligent systems.

  • 22 authors
·
May 28

KMTalk: Speech-Driven 3D Facial Animation with Key Motion Embedding

We present a novel approach for synthesizing 3D facial motions from audio sequences using key motion embeddings. Despite recent advancements in data-driven techniques, accurately mapping between audio signals and 3D facial meshes remains challenging. Direct regression of the entire sequence often leads to over-smoothed results due to the ill-posed nature of the problem. To this end, we propose a progressive learning mechanism that generates 3D facial animations by introducing key motion capture to decrease cross-modal mapping uncertainty and learning complexity. Concretely, our method integrates linguistic and data-driven priors through two modules: the linguistic-based key motion acquisition and the cross-modal motion completion. The former identifies key motions and learns the associated 3D facial expressions, ensuring accurate lip-speech synchronization. The latter extends key motions into a full sequence of 3D talking faces guided by audio features, improving temporal coherence and audio-visual consistency. Extensive experimental comparisons against existing state-of-the-art methods demonstrate the superiority of our approach in generating more vivid and consistent talking face animations. Consistent enhancements in results through the integration of our proposed learning scheme with existing methods underscore the efficacy of our approach. Our code and weights will be at the project website: https://github.com/ffxzh/KMTalk.

  • 7 authors
·
Sep 2, 2024

From Density to Geometry: YOLOv8 Instance Segmentation for Reverse Engineering of Optimized Structures

This paper introduces YOLOv8-TO, a novel approach for reverse engineering of topology-optimized structures into interpretable geometric parameters using the YOLOv8 instance segmentation model. Density-based topology optimization methods require post-processing to convert the optimal density distribution into a parametric representation for design exploration and integration with CAD tools. Traditional methods such as skeletonization struggle with complex geometries and require manual intervention. YOLOv8-TO addresses these challenges by training a custom YOLOv8 model to automatically detect and reconstruct structural components from binary density distributions. The model is trained on a diverse dataset of both optimized and random structures generated using the Moving Morphable Components method. A custom reconstruction loss function based on the dice coefficient of the predicted geometry is used to train the new regression head of the model via self-supervised learning. The method is evaluated on test sets generated from different topology optimization methods, including out-of-distribution samples, and compared against a skeletonization approach. Results show that YOLOv8-TO significantly outperforms skeletonization in reconstructing visually and structurally similar designs. The method showcases an average improvement of 13.84% in the Dice coefficient, with peak enhancements reaching 20.78%. The method demonstrates good generalization to complex geometries and fast inference times, making it suitable for integration into design workflows using regular workstations. Limitations include the sensitivity to non-max suppression thresholds. YOLOv8-TO represents a significant advancement in topology optimization post-processing, enabling efficient and accurate reverse engineering of optimized structures for design exploration and manufacturing.

  • 4 authors
·
Apr 29, 2024

CM$^3$: Calibrating Multimodal Recommendation

Alignment and uniformity are fundamental principles within the domain of contrastive learning. In recommender systems, prior work has established that optimizing the Bayesian Personalized Ranking (BPR) loss contributes to the objectives of alignment and uniformity. Specifically, alignment aims to draw together the representations of interacting users and items, while uniformity mandates a uniform distribution of user and item embeddings across a unit hypersphere. This study revisits the alignment and uniformity properties within the context of multimodal recommender systems, revealing a proclivity among extant models to prioritize uniformity to the detriment of alignment. Our hypothesis challenges the conventional assumption of equitable item treatment through a uniformity loss, proposing a more nuanced approach wherein items with similar multimodal attributes converge toward proximal representations within the hyperspheric manifold. Specifically, we leverage the inherent similarity between items' multimodal data to calibrate their uniformity distribution, thereby inducing a more pronounced repulsive force between dissimilar entities within the embedding space. A theoretical analysis elucidates the relationship between this calibrated uniformity loss and the conventional uniformity function. Moreover, to enhance the fusion of multimodal features, we introduce a Spherical B\'ezier method designed to integrate an arbitrary number of modalities while ensuring that the resulting fused features are constrained to the same hyperspherical manifold. Empirical evaluations conducted on five real-world datasets substantiate the superiority of our approach over competing baselines. We also shown that the proposed methods can achieve up to a 5.4% increase in NDCG@20 performance via the integration of MLLM-extracted features. Source code is available at: https://github.com/enoche/CM3.

  • 3 authors
·
Aug 2 2

Weight-Entanglement Meets Gradient-Based Neural Architecture Search

Weight sharing is a fundamental concept in neural architecture search (NAS), enabling gradient-based methods to explore cell-based architecture spaces significantly faster than traditional blackbox approaches. In parallel, weight entanglement has emerged as a technique for intricate parameter sharing among architectures within macro-level search spaces. %However, the macro structure of such spaces poses compatibility challenges for gradient-based NAS methods. %As a result, blackbox optimization methods have been commonly employed, particularly in conjunction with supernet training, to maintain search efficiency. %Due to the inherent differences in the structure of these search spaces, these Since weight-entanglement poses compatibility challenges for gradient-based NAS methods, these two paradigms have largely developed independently in parallel sub-communities. This paper aims to bridge the gap between these sub-communities by proposing a novel scheme to adapt gradient-based methods for weight-entangled spaces. This enables us to conduct an in-depth comparative assessment and analysis of the performance of gradient-based NAS in weight-entangled search spaces. Our findings reveal that this integration of weight-entanglement and gradient-based NAS brings forth the various benefits of gradient-based methods (enhanced performance, improved supernet training properties and superior any-time performance), while preserving the memory efficiency of weight-entangled spaces. The code for our work is openly accessible https://anonymous.4open.science/r/TangleNAS-527C{here}

  • 4 authors
·
Dec 16, 2023

SAR Strikes Back: A New Hope for RSVQA

Remote sensing visual question answering (RSVQA) is a task that automatically extracts information from satellite images and processes a question to predict the answer from the images in textual form, helping with the interpretation of the image. While different methods have been proposed to extract information from optical images with different spectral bands and resolutions, no method has been proposed to answer questions from Synthetic Aperture Radar (SAR) images. SAR images capture electromagnetic information from the scene, and are less affected by atmospheric conditions, such as clouds. In this work, our objective is to introduce SAR in the RSVQA task, finding the best way to use this modality. In our research, we carry out a study on different pipelines for the task of RSVQA taking into account information from both SAR and optical data. To this purpose, we also present a dataset that allows for the introduction of SAR images in the RSVQA framework. We propose two different models to include the SAR modality. The first one is an end-to-end method in which we add an additional encoder for the SAR modality. In the second approach, we build on a two-stage framework. First, relevant information is extracted from SAR and, optionally, optical data. This information is then translated into natural language to be used in the second step which only relies on a language model to provide the answer. We find that the second pipeline allows us to obtain good results with SAR images alone. We then try various types of fusion methods to use SAR and optical images together, finding that a fusion at the decision level achieves the best results on the proposed dataset. We show that SAR data offers additional information when fused with the optical modality, particularly for questions related to specific land cover classes, such as water areas.

  • 4 authors
·
Jan 14

FaceXFormer: A Unified Transformer for Facial Analysis

In this work, we introduce FaceXformer, an end-to-end unified transformer model for a comprehensive range of facial analysis tasks such as face parsing, landmark detection, head pose estimation, attributes recognition, and estimation of age, gender, race, and landmarks visibility. Conventional methods in face analysis have often relied on task-specific designs and preprocessing techniques, which limit their approach to a unified architecture. Unlike these conventional methods, our FaceXformer leverages a transformer-based encoder-decoder architecture where each task is treated as a learnable token, enabling the integration of multiple tasks within a single framework. Moreover, we propose a parameter-efficient decoder, FaceX, which jointly processes face and task tokens, thereby learning generalized and robust face representations across different tasks. To the best of our knowledge, this is the first work to propose a single model capable of handling all these facial analysis tasks using transformers. We conducted a comprehensive analysis of effective backbones for unified face task processing and evaluated different task queries and the synergy between them. We conduct experiments against state-of-the-art specialized models and previous multi-task models in both intra-dataset and cross-dataset evaluations across multiple benchmarks. Additionally, our model effectively handles images "in-the-wild," demonstrating its robustness and generalizability across eight different tasks, all while maintaining the real-time performance of 37 FPS.

  • 4 authors
·
Mar 19, 2024