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Dec 29

SPOCKMIP: Segmentation of Vessels in MRAs with Enhanced Continuity using Maximum Intensity Projection as Loss

Identification of vessel structures of different sizes in biomedical images is crucial in the diagnosis of many neurodegenerative diseases. However, the sparsity of good-quality annotations of such images makes the task of vessel segmentation challenging. Deep learning offers an efficient way to segment vessels of different sizes by learning their high-level feature representations and the spatial continuity of such features across dimensions. Semi-supervised patch-based approaches have been effective in identifying small vessels of one to two voxels in diameter. This study focuses on improving the segmentation quality by considering the spatial correlation of the features using the Maximum Intensity Projection~(MIP) as an additional loss criterion. Two methods are proposed with the incorporation of MIPs of label segmentation on the single~(z-axis) and multiple perceivable axes of the 3D volume. The proposed MIP-based methods produce segmentations with improved vessel continuity, which is evident in visual examinations of ROIs. Patch-based training is improved by introducing an additional loss term, MIP loss, to penalise the predicted discontinuity of vessels. A training set of 14 volumes is selected from the StudyForrest dataset comprising of 18 7-Tesla 3D Time-of-Flight~(ToF) Magnetic Resonance Angiography (MRA) images. The generalisation performance of the method is evaluated using the other unseen volumes in the dataset. It is observed that the proposed method with multi-axes MIP loss produces better quality segmentations with a median Dice of 80.245 pm 0.129. Also, the method with single-axis MIP loss produces segmentations with a median Dice of 79.749 pm 0.109. Furthermore, a visual comparison of the ROIs in the predicted segmentation reveals a significant improvement in the continuity of the vessels when MIP loss is incorporated into training.

  • 8 authors
·
Jul 11, 2024

Value-Driven Mixed-Precision Quantization for Patch-Based Inference on Microcontrollers

Deploying neural networks on microcontroller units (MCUs) presents substantial challenges due to their constrained computation and memory resources. Previous researches have explored patch-based inference as a strategy to conserve memory without sacrificing model accuracy. However, this technique suffers from severe redundant computation overhead, leading to a substantial increase in execution latency. A feasible solution to address this issue is mixed-precision quantization, but it faces the challenges of accuracy degradation and a time-consuming search time. In this paper, we propose QuantMCU, a novel patch-based inference method that utilizes value-driven mixed-precision quantization to reduce redundant computation. We first utilize value-driven patch classification (VDPC) to maintain the model accuracy. VDPC classifies patches into two classes based on whether they contain outlier values. For patches containing outlier values, we apply 8-bit quantization to the feature maps on the dataflow branches that follow. In addition, for patches without outlier values, we utilize value-driven quantization search (VDQS) on the feature maps of their following dataflow branches to reduce search time. Specifically, VDQS introduces a novel quantization search metric that takes into account both computation and accuracy, and it employs entropy as an accuracy representation to avoid additional training. VDQS also adopts an iterative approach to determine the bitwidth of each feature map to further accelerate the search process. Experimental results on real-world MCU devices show that QuantMCU can reduce computation by 2.2x on average while maintaining comparable model accuracy compared to the state-of-the-art patch-based inference methods.

  • 8 authors
·
Jan 23, 2024

TriP-LLM: A Tri-Branch Patch-wise Large Language Model Framework for Time-Series Anomaly Detection

Time-series anomaly detection plays a central role across a wide range of application domains. With the increasing proliferation of the Internet of Things (IoT) and smart manufacturing, time-series data has dramatically increased in both scale and dimensionality. This growth has exposed the limitations of traditional statistical methods in handling the high heterogeneity and complexity of such data. Inspired by the recent success of large language models (LLMs) in multimodal tasks across language and vision domains, we propose a novel unsupervised anomaly detection framework: A Tri-Branch Patch-wise Large Language Model Framework for Time-Series Anomaly Detection (TriP-LLM). TriP-LLM integrates local and global temporal features through a tri-branch design-Patching, Selection, and Global-to encode the input time series into patch-wise tokens, which are then processed by a frozen, pretrained LLM. A lightweight patch-wise decoder reconstructs the input, from which anomaly scores are derived. We evaluate TriP-LLM on several public benchmark datasets using PATE, a recently proposed threshold-free evaluation metric, and conduct all comparisons within a unified open-source framework to ensure fairness. Experimental results show that TriP-LLM consistently outperforms recent state-of-the-art methods across all datasets, demonstrating strong detection capabilities. Furthermore, through extensive ablation studies, we verify the substantial contribution of the LLM to the overall architecture. Compared to LLM-based approaches using Channel Independence (CI) patch processing, TriP-LLM achieves significantly lower memory consumption, making it more suitable for GPU memory-constrained environments. All code and model checkpoints are publicly available on https://github.com/YYZStart/TriP-LLM.git

  • 3 authors
·
Jul 31

RAP-Gen: Retrieval-Augmented Patch Generation with CodeT5 for Automatic Program Repair

Automatic program repair (APR) is crucial to reduce manual debugging efforts for developers and improve software reliability. While conventional search-based techniques typically rely on heuristic rules or a redundancy assumption to mine fix patterns, recent years have witnessed the surge of deep learning (DL) based approaches to automate the program repair process in a data-driven manner. However, their performance is often limited by a fixed set of parameters to model the highly complex search space of APR. To ease such burden on the parametric models, in this work, we propose a novel Retrieval-Augmented Patch Generation framework (RAP-Gen) by explicitly leveraging relevant fix patterns retrieved from a codebase of previous bug-fix pairs. Specifically, we build a hybrid patch retriever to account for both lexical and semantic matching based on the raw source code in a language-agnostic manner, which does not rely on any code-specific features. In addition, we adapt a code-aware language model CodeT5 as our foundation model to facilitate both patch retrieval and generation tasks in a unified manner. We adopt a stage-wise approach where the patch retriever first retrieves a relevant external bug-fix pair to augment the buggy input for the CodeT5 patch generator, which synthesizes a ranked list of repair patch candidates. Notably, RAP-Gen is a generic APR framework that can flexibly integrate different patch retrievers and generators to repair various types of bugs. We thoroughly evaluate RAP-Gen on three benchmarks in two programming languages, including the TFix benchmark in JavaScript, and Code Refinement and Defects4J benchmarks in Java, where the bug localization information may or may not be provided. Experimental results show that RAP-Gen significantly outperforms previous state-of-the-art approaches on all benchmarks, e.g., repairing 15 more bugs on 818 Defects4J bugs.

  • 4 authors
·
Sep 12, 2023

Can LLM Generate Regression Tests for Software Commits?

Large Language Models (LLMs) have shown tremendous promise in automated software engineering. In this paper, we investigate the opportunities of LLMs for automatic regression test generation for programs that take highly structured, human-readable inputs, such as XML parsers or JavaScript interpreters. Concretely, we explore the following regression test generation scenarios for such programs that have so far been difficult to test automatically in the absence of corresponding input grammars: bullet Bug finding. Given a code change (e.g., a commit or pull request), our LLM-based approach generates a test case with the objective of revealing any bugs that might be introduced if that change is applied. bullet Patch testing. Given a patch, our LLM-based approach generates a test case that fails before but passes after the patch. This test can be added to the regression test suite to catch similar bugs in the future. We implement Cleverest, a feedback-directed, zero-shot LLM-based regression test generation technique, and evaluate its effectiveness on 22 commits to three subject programs: Mujs, Libxml2, and Poppler. For programs using more human-readable file formats, like XML or JavaScript, we found Cleverest performed very well. It generated easy-to-understand bug-revealing or bug-reproduction test cases for the majority of commits in just under three minutes -- even when only the code diff or commit message (unless it was too vague) was given. For programs with more compact file formats, like PDF, as expected, it struggled to generate effective test cases. However, the LLM-supplied test cases are not very far from becoming effective (e.g., when used as a seed by a greybox fuzzer or as a starting point by the developer).

  • 4 authors
·
Jan 19

MMAR: Towards Lossless Multi-Modal Auto-Regressive Probabilistic Modeling

Recent advancements in multi-modal large language models have propelled the development of joint probabilistic models capable of both image understanding and generation. However, we have identified that recent methods inevitably suffer from loss of image information during understanding task, due to either image discretization or diffusion denoising steps. To address this issue, we propose a novel Multi-Modal Auto-Regressive (MMAR) probabilistic modeling framework. Unlike discretization line of method, MMAR takes in continuous-valued image tokens to avoid information loss. Differing from diffusion-based approaches, we disentangle the diffusion process from auto-regressive backbone model by employing a light-weight diffusion head on top each auto-regressed image patch embedding. In this way, when the model transits from image generation to understanding through text generation, the backbone model's hidden representation of the image is not limited to the last denoising step. To successfully train our method, we also propose a theoretically proven technique that addresses the numerical stability issue and a training strategy that balances the generation and understanding task goals. Through extensive evaluations on 18 image understanding benchmarks, MMAR demonstrates much more superior performance than other joint multi-modal models, matching the method that employs pretrained CLIP vision encoder, meanwhile being able to generate high quality images at the same time. We also showed that our method is scalable with larger data and model size.

  • 7 authors
·
Oct 14, 2024

Comparing Deep Learning Models for Rice Mapping in Bhutan Using High Resolution Satellite Imagery

The Bhutanese government is increasing its utilization of technological approaches such as including Remote Sensing-based knowledge in their decision-making process. This study focuses on crop type and crop extent in Paro, one of the top rice-yielding districts in Bhutan, and employs publicly available NICFI high-resolution satellite imagery from Planet. Two Deep Learning (DL) approaches, point-based (DNN) and patch-based (U-Net), models were used in conjunction with cloud-computing platforms. Three different models per DL approaches (DNN and U-Net) were trained: 1) RGBN channels from Planet; 2) RGBN and elevation data (RGBNE); 3) RGBN and Sentinel-1 (S1) data (RGBNS), and RGBN with E and S1 data (RGBNES). From this comprehensive analysis, the U-Net displayed higher performance metrics across both model training and model validation efforts. Among the U-Net model sets, the RGBN, RGBNE, RGBNS, and RGBNES models had an F1-score of 0.8546, 0.8563, 0.8467, and 0.8500 respectively. An independent model evaluation was performed and found a high level of performance variation across all the metrics. For this independent model evaluation, the U-Net RGBN, RGBNE, RGBNES, and RGBN models displayed the F1-scores of 0.5935, 0.6154, 0.5882, and 0.6582, suggesting U-Net RGBNES as the best model. The study shows that the DL approaches can predict rice. Also, DL methods can be used with the survey-based approaches currently utilized by the Bhutan Department of Agriculture. Further, this study demonstrated the usage of regional land cover products such as SERVIR's RLCMS as a weak label approach to capture different strata addressing the class imbalance problem and improving the sampling design for DL application. Finally, through preliminary model testing and comparisons outlined it was shown that using additional features such as NDVI, EVI, and NDWI did not drastically improve model performance.

  • 2 authors
·
Jun 11, 2024

Optimizing Breast Cancer Detection in Mammograms: A Comprehensive Study of Transfer Learning, Resolution Reduction, and Multi-View Classification

Mammography, an X-ray-based imaging technique, remains central to the early detection of breast cancer. Recent advances in artificial intelligence have enabled increasingly sophisticated computer-aided diagnostic methods, evolving from patch-based classifiers to whole-image approaches and then to multi-view architectures that jointly analyze complementary projections. Despite this progress, several critical questions remain unanswered. In this study, we systematically investigate these issues by addressing five key research questions: (1) the role of patch classifiers in performance, (2) the transferability of natural-image-trained backbones, (3) the advantages of learn-to-resize over conventional downscaling, (4) the contribution of multi-view integration, and (5) the robustness of findings across varying image quality. Beyond benchmarking, our experiments demonstrate clear performance gains over prior work. For the CBIS-DDSM dataset, we improved single-view AUC from 0.8153 to 0.8343, and multiple-view AUC from 0.8483 to 0.8658. Using a new comparative method, we also observed a 0.0217 AUC increase when extending from single to multiple-view analysis. On the complete VinDr-Mammo dataset, the multiple-view approach further improved results, achieving a 0.0492 AUC increase over single view and reaching 0.8511 AUC overall. These results establish new state-of-the-art benchmarks, providing clear evidence of the advantages of multi-view architectures for mammogram interpretation. Beyond performance, our analysis offers principled insights into model design and transfer learning strategies, contributing to the development of more accurate and reliable breast cancer screening tools. The inference code and trained models are publicly available at https://github.com/dpetrini/multiple-view.

  • 2 authors
·
Mar 25

BUS:Efficient and Effective Vision-language Pre-training with Bottom-Up Patch Summarization

Vision Transformer (ViT) based Vision-Language Pre-training (VLP) models have demonstrated impressive performance in various tasks. However, the lengthy visual token sequences fed into ViT can lead to training inefficiency and ineffectiveness. Existing efforts address the challenge by either bottom-level patch extraction in the ViT backbone or top-level patch abstraction outside, not balancing training efficiency and effectiveness well. Inspired by text summarization in natural language processing, we propose a Bottom-Up Patch Summarization approach named BUS, coordinating bottom-level extraction and top-level abstraction to learn a concise summary of lengthy visual token sequences efficiently. Specifically, We incorporate a Text-Semantics-Aware Patch Selector (TSPS) into the ViT backbone to perform a coarse-grained visual token extraction and then attach a flexible Transformer-based Patch Abstraction Decoder (PAD) upon the backbone for top-level visual abstraction. This bottom-up collaboration enables our BUS to yield high training efficiency while maintaining or even improving effectiveness. We evaluate our approach on various visual-language understanding and generation tasks and show competitive downstream task performance while boosting the training efficiency by 50\%. Additionally, our model achieves state-of-the-art performance on many downstream tasks by increasing input image resolution without increasing computational costs over baselines.

  • 10 authors
·
Jul 17, 2023

MultiMend: Multilingual Program Repair with Context Augmentation and Multi-Hunk Patch Generation

Context: Bugs in code are inevitable and can lead to severe consequences, ranging from security vulnerabilities to operational failures. Debugging software remains challenging despite advances in testing and verification, often requiring extensive manual effort. Learning-based automated program repair (APR) has shown promise in reducing the time, effort, and cost of manually fixing bugs. However, existing techniques face several challenges, including language-dependent strategies, limited bug context utilization, and difficulties in handling bugs that span multiple locations in the code. Objective: This paper introduces MultiMend, a learning-based APR approach designed to improve repair performance on multiple programming languages with language-independent context augmentation and multi-hunk patch generation. Method: MultiMend fine-tunes a pre-trained encoder-decoder transformer model (CodeT5) to generate bug-fixing patches. It embeds source code lines and applies retrieval-augmented generation to augment the buggy context with relevant lines during patch generation. The approach systematically constructs patches for multi-hunk bugs to reduce the needed patch validations. We evaluate MultiMend on four benchmarks with four programming languages and compare it with state-of-the-art methods. Results: Experimental results show that MultiMend achieves competitive effectiveness and efficiency against compared tools. Across all benchmarks, MultiMend fixes 2,077 bugs, of which 1,455 are identical to the developer's patch, and 106 are for multi-hunk bugs. Both context augmentation and multi-hunk patch generation positively contribute to the results. Conclusion: MultiMend shows promising performance across benchmarks. The findings highlight its applicability to real-world software maintenance and its potential to reduce manual debugging efforts.

  • 3 authors
·
Jan 27

Latent-OFER: Detect, Mask, and Reconstruct with Latent Vectors for Occluded Facial Expression Recognition

Most research on facial expression recognition (FER) is conducted in highly controlled environments, but its performance is often unacceptable when applied to real-world situations. This is because when unexpected objects occlude the face, the FER network faces difficulties extracting facial features and accurately predicting facial expressions. Therefore, occluded FER (OFER) is a challenging problem. Previous studies on occlusion-aware FER have typically required fully annotated facial images for training. However, collecting facial images with various occlusions and expression annotations is time-consuming and expensive. Latent-OFER, the proposed method, can detect occlusions, restore occluded parts of the face as if they were unoccluded, and recognize them, improving FER accuracy. This approach involves three steps: First, the vision transformer (ViT)-based occlusion patch detector masks the occluded position by training only latent vectors from the unoccluded patches using the support vector data description algorithm. Second, the hybrid reconstruction network generates the masking position as a complete image using the ViT and convolutional neural network (CNN). Last, the expression-relevant latent vector extractor retrieves and uses expression-related information from all latent vectors by applying a CNN-based class activation map. This mechanism has a significant advantage in preventing performance degradation from occlusion by unseen objects. The experimental results on several databases demonstrate the superiority of the proposed method over state-of-the-art methods.

  • 3 authors
·
Jul 21, 2023

Navigating Gigapixel Pathology Images with Large Multimodal Models

Despite being widely used to support clinical care, general-purpose large multimodal models (LMMs) have generally shown poor or inconclusive performance in medical image interpretation, particularly in pathology, where gigapixel images are used. However, prior studies have used either low-resolution thumbnails or random patches, which likely underestimated model performance. Here, we ask whether LMMs can be adapted to reason coherently and accurately in the evaluation of such images. In this study, we introduce Gigapixel Image Agent for Navigating Tissue (GIANT), the first framework that allows LMMs to iteratively navigate whole-slide images (WSIs) like a pathologist. Accompanying GIANT, we release MultiPathQA, a new benchmark, which comprises 934 WSI-level questions, encompassing five clinically-relevant tasks ranging from cancer diagnosis to open-ended reasoning. MultiPathQA also includes 128 questions, authored by two professional pathologists, requiring direct slide interpretation. Using MultiPathQA, we show that our simple agentic system substantially outperforms conventional patch- and thumbnail-based baselines, approaching or surpassing the performance of specialized models trained on millions of images. For example, on pathologist-authored questions, GPT-5 with GIANT achieves 62.5% accuracy, outperforming specialist pathology models such as TITAN (43.8%) and SlideChat (37.5%). Our findings reveal the strengths and limitations of current foundation models and ground future development of LMMs for expert reasoning in pathology.

  • 6 authors
·
Nov 24

Revisiting Multimodal Representation in Contrastive Learning: From Patch and Token Embeddings to Finite Discrete Tokens

Contrastive learning-based vision-language pre-training approaches, such as CLIP, have demonstrated great success in many vision-language tasks. These methods achieve cross-modal alignment by encoding a matched image-text pair with similar feature embeddings, which are generated by aggregating information from visual patches and language tokens. However, direct aligning cross-modal information using such representations is challenging, as visual patches and text tokens differ in semantic levels and granularities. To alleviate this issue, we propose a Finite Discrete Tokens (FDT) based multimodal representation. FDT is a set of learnable tokens representing certain visual-semantic concepts. Both images and texts are embedded using shared FDT by first grounding multimodal inputs to FDT space and then aggregating the activated FDT representations. The matched visual and semantic concepts are enforced to be represented by the same set of discrete tokens by a sparse activation constraint. As a result, the granularity gap between the two modalities is reduced. Through both quantitative and qualitative analyses, we demonstrate that using FDT representations in CLIP-style models improves cross-modal alignment and performance in visual recognition and vision-language downstream tasks. Furthermore, we show that our method can learn more comprehensive representations, and the learned FDT capture meaningful cross-modal correspondence, ranging from objects to actions and attributes.

  • 8 authors
·
Mar 26, 2023

Improved Robustness for Deep Learning-based Segmentation of Multi-Center Myocardial Perfusion MRI Datasets Using Data Adaptive Uncertainty-guided Space-time Analysis

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

  • 11 authors
·
Aug 8, 2024

Hierarchical Patch Compression for ColPali: Efficient Multi-Vector Document Retrieval with Dynamic Pruning and Quantization

Multi-vector document retrieval systems, such as ColPali, excel in fine-grained matching for complex queries but incur significant storage and computational costs due to their reliance on high-dimensional patch embeddings and late-interaction scoring. To address these challenges, we propose HPC-ColPali, a Hierarchical Patch Compression framework that enhances the efficiency of ColPali while preserving its retrieval accuracy. Our approach integrates three innovative techniques: (1) K-Means quantization, which compresses patch embeddings into 1-byte centroid indices, achieving up to 32times storage reduction; (2) attention-guided dynamic pruning, utilizing Vision-Language Model attention weights to retain only the top-p% most salient patches, reducing late-interaction computation by up to 60\% with less than 2\% nDCG@10 loss; and (3) optional binary encoding of centroid indices into b-bit strings (b=lceillog_2 Krceil), enabling rapid Hamming distance-based similarity search for resource-constrained environments. Evaluated on the ViDoRe and SEC-Filings datasets, HPC-ColPali achieves 30--50\% lower query latency under HNSW indexing while maintaining high retrieval precision. When integrated into a Retrieval-Augmented Generation pipeline for legal summarization, it reduces hallucination rates by 30\% and halves end-to-end latency. These advancements establish HPC-ColPali as a scalable and efficient solution for multi-vector document retrieval across diverse applications. Code is available at https://github.com/DngBack/HPC-ColPali.

  • 1 authors
·
Jun 19

PatchFusion: An End-to-End Tile-Based Framework for High-Resolution Monocular Metric Depth Estimation

Single image depth estimation is a foundational task in computer vision and generative modeling. However, prevailing depth estimation models grapple with accommodating the increasing resolutions commonplace in today's consumer cameras and devices. Existing high-resolution strategies show promise, but they often face limitations, ranging from error propagation to the loss of high-frequency details. We present PatchFusion, a novel tile-based framework with three key components to improve the current state of the art: (1) A patch-wise fusion network that fuses a globally-consistent coarse prediction with finer, inconsistent tiled predictions via high-level feature guidance, (2) A Global-to-Local (G2L) module that adds vital context to the fusion network, discarding the need for patch selection heuristics, and (3) A Consistency-Aware Training (CAT) and Inference (CAI) approach, emphasizing patch overlap consistency and thereby eradicating the necessity for post-processing. Experiments on UnrealStereo4K, MVS-Synth, and Middleburry 2014 demonstrate that our framework can generate high-resolution depth maps with intricate details. PatchFusion is independent of the base model for depth estimation. Notably, our framework built on top of SOTA ZoeDepth brings improvements for a total of 17.3% and 29.4% in terms of the root mean squared error (RMSE) on UnrealStereo4K and MVS-Synth, respectively.

  • 3 authors
·
Dec 4, 2023 1

Pseudo-Q: Generating Pseudo Language Queries for Visual Grounding

Visual grounding, i.e., localizing objects in images according to natural language queries, is an important topic in visual language understanding. The most effective approaches for this task are based on deep learning, which generally require expensive manually labeled image-query or patch-query pairs. To eliminate the heavy dependence on human annotations, we present a novel method, named Pseudo-Q, to automatically generate pseudo language queries for supervised training. Our method leverages an off-the-shelf object detector to identify visual objects from unlabeled images, and then language queries for these objects are obtained in an unsupervised fashion with a pseudo-query generation module. Then, we design a task-related query prompt module to specifically tailor generated pseudo language queries for visual grounding tasks. Further, in order to fully capture the contextual relationships between images and language queries, we develop a visual-language model equipped with multi-level cross-modality attention mechanism. Extensive experimental results demonstrate that our method has two notable benefits: (1) it can reduce human annotation costs significantly, e.g., 31% on RefCOCO without degrading original model's performance under the fully supervised setting, and (2) without bells and whistles, it achieves superior or comparable performance compared to state-of-the-art weakly-supervised visual grounding methods on all the five datasets we have experimented. Code is available at https://github.com/LeapLabTHU/Pseudo-Q.

  • 5 authors
·
Mar 16, 2022

Token-level Correlation-guided Compression for Efficient Multimodal Document Understanding

Cropping high-resolution document images into multiple sub-images is the most widely used approach for current Multimodal Large Language Models (MLLMs) to do document understanding. Most of current document understanding methods preserve all tokens within sub-images and treat them equally. This neglects their different informativeness and leads to a significant increase in the number of image tokens. To perform a more adaptive and efficient document understanding, we propose Token-level Correlation-guided Compression, a parameter-free and plug-and-play methodology to optimize token processing. Firstly, we propose an innovative approach for assessing the pattern repetitiveness based on the correlation between each patch tokens. This method identifies redundant tokens, allowing for the determination of the sub-image's information density. Secondly, we present a token-level sampling method that efficiently captures the most informative tokens by delving into the correlation between the [CLS] token and patch tokens. By integrating these strategies, we develop a plug-and-play adaptive compressor module that can be seamlessly incorporated into MLLMs utilizing cropping techniques. This module not only enhances the processing speed during training and inference but also maintains comparable performance. We conduct experiments with the SOTA document understanding model mPLUG-DocOwl1.5 and the effectiveness is demonstrated through extensive comparisons with other compression methods.

  • 6 authors
·
Jul 19, 2024

Perturbation Ontology based Graph Attention Networks

In recent years, graph representation learning has undergone a paradigm shift, driven by the emergence and proliferation of graph neural networks (GNNs) and their heterogeneous counterparts. Heterogeneous GNNs have shown remarkable success in extracting low-dimensional embeddings from complex graphs that encompass diverse entity types and relationships. While meta-path-based techniques have long been recognized for their ability to capture semantic affinities among nodes, their dependence on manual specification poses a significant limitation. In contrast, matrix-focused methods accelerate processing by utilizing structural cues but often overlook contextual richness. In this paper, we challenge the current paradigm by introducing ontology as a fundamental semantic primitive within complex graphs. Our goal is to integrate the strengths of both matrix-centric and meta-path-based approaches into a unified framework. We propose perturbation Ontology-based Graph Attention Networks (POGAT), a novel methodology that combines ontology subgraphs with an advanced self-supervised learning paradigm to achieve a deep contextual understanding. The core innovation of POGAT lies in our enhanced homogeneous perturbing scheme designed to generate rigorous negative samples, encouraging the model to explore minimal contextual features more thoroughly. Through extensive empirical evaluations, we demonstrate that POGAT significantly outperforms state-of-the-art baselines, achieving a groundbreaking improvement of up to 10.78\% in F1-score for the critical task of link prediction and 12.01\% in Micro-F1 for the critical task of node classification.

  • 6 authors
·
Nov 27, 2024

neural concatenative singing voice conversion: rethinking concatenation-based approach for one-shot singing voice conversion

Any-to-any singing voice conversion is confronted with a significant challenge of ``timbre leakage'' issue caused by inadequate disentanglement between the content and the speaker timbre. To address this issue, this study introduces a novel neural concatenative singing voice conversion (NeuCoSVC) framework. The NeuCoSVC framework comprises a self-supervised learning (SSL) representation extractor, a neural harmonic signal generator, and a waveform synthesizer. Specifically, the SSL extractor condenses the audio into a sequence of fixed-dimensional SSL features. The harmonic signal generator produces both raw and filtered harmonic signals as the pitch information by leveraging a linear time-varying (LTV) filter. Finally, the audio generator reconstructs the audio waveform based on the SSL features, as well as the harmonic signals and the loudness information. During inference, the system performs voice conversion by substituting source SSL features with their nearest counterparts from a matching pool, which comprises SSL representations extracted from the target audio, while the raw harmonic signals and the loudness are extracted from the source audio and are kept unchanged. Since the utilized SSL features in the conversion stage are directly from the target audio, the proposed framework has great potential to address the ``timbre leakage'' issue caused by previous disentanglement-based approaches. Experimental results confirm that the proposed system delivers much better performance than the speaker embedding approach (disentanglement-based) in the context of one-shot SVC across intra-language, cross-language, and cross-domain evaluations.

  • 5 authors
·
Dec 8, 2023

Deceptive Path Planning via Reinforcement Learning with Graph Neural Networks

Deceptive path planning (DPP) is the problem of designing a path that hides its true goal from an outside observer. Existing methods for DPP rely on unrealistic assumptions, such as global state observability and perfect model knowledge, and are typically problem-specific, meaning that even minor changes to a previously solved problem can force expensive computation of an entirely new solution. Given these drawbacks, such methods do not generalize to unseen problem instances, lack scalability to realistic problem sizes, and preclude both on-the-fly tunability of deception levels and real-time adaptivity to changing environments. In this paper, we propose a reinforcement learning (RL)-based scheme for training policies to perform DPP over arbitrary weighted graphs that overcomes these issues. The core of our approach is the introduction of a local perception model for the agent, a new state space representation distilling the key components of the DPP problem, the use of graph neural network-based policies to facilitate generalization and scaling, and the introduction of new deception bonuses that translate the deception objectives of classical methods to the RL setting. Through extensive experimentation we show that, without additional fine-tuning, at test time the resulting policies successfully generalize, scale, enjoy tunable levels of deception, and adapt in real-time to changes in the environment.

  • 3 authors
·
Feb 9, 2024

Data-driven Tracking of the Bounce-back Path after Disasters: Critical Milestones of Population Activity Recovery and Their Spatial Inequality

The ability to measure and track the speed and trajectory of a community's post-disaster recovery is essential to inform resource allocation and prioritization. The current survey-based approaches to examining community recovery, however, have significant lags and put the burden of data collection on affected people. Also, the existing literature lacks quantitative measures for important milestones to inform the assessment of recovery trajectory. Recognizing these gaps, this study uses location-based data related to visitation patterns and credit card transactions to specify critical recovery milestones related to population activity recovery. Using data from 2017 Hurricane Harvey in Harris County (Texas), the study specifies four critical post-disaster recovery milestones and calculates quantitative measurements of the length of time between the end of a hazard event and when the spatial areas (census tracts) reached these milestones based on fluctuations in visits to essential and non-essential facilities, and essential and non-essential credit card transactions. Accordingly, an integrated recovery metric is created for an overall measurement of each spatial area's recovery progression. Exploratory statistical analyses were conducted to examine whether variations in community recovery progression in achieving the critical milestones is correlated to its flood status, socioeconomic characteristics, and demographic composition. Finally, the extent of spatial inequality is examined. The results show the presence of moderate spatial inequality in population activity recovery in Hurricane Harvey, based upon which the inequality of recovery is measured. Results of this study can benefit post-disaster recovery resource allocation as well as improve community resilience towards future natural hazards.

  • 6 authors
·
Nov 20, 2022

CARFT: Boosting LLM Reasoning via Contrastive Learning with Annotated Chain-of-Thought-based Reinforced Fine-Tuning

Reasoning capability plays a significantly critical role in the the broad applications of Large Language Models (LLMs). To enhance the reasoning performance of LLMs, diverse Reinforcement Learning (RL)-based fine-tuning approaches have been proposed to address the limited generalization capability of LLMs trained solely via Supervised Fine-Tuning (SFT). Despite their effectiveness, two major limitations hinder the advancement of LLMs. First, vanilla RL-based approaches ignore annotated Chain-of-Thought (CoT) and incorporate unstable reasoning path sampling, which typically results in model collapse, unstable training process, and suboptimal performance. Second, existing SFT approaches generally overemphasize the annotated CoT, potentially leading to performance degradation due to insufficient exploitation of potential CoT. In this paper, we propose a Contrastive learning with annotated CoT-based Reinforced Fine-Tuning approach, i.e., , to enhance the reasoning performance of LLMs while addressing the aforementioned limitations. Specifically, we propose learning a representation for each CoT. Based on this representation, we design novel contrastive signals to guide the fine-tuning process. Our approach not only fully exploits the available annotated CoT but also stabilizes the fine-tuning procedure by incorporating an additional unsupervised learning signal. We conduct comprehensive experiments and in-depth analysis with three baseline approaches, two foundation models, and two datasets to demonstrate significant advantages of in terms of robustness, performance (up to 10.15\%), and efficiency (up to 30.62\%). Code is available at https://github.com/WNQzhu/CARFT.

  • 5 authors
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Aug 20 3

GID: Graph-based Intrusion Detection on Massive Process Traces for Enterprise Security Systems

Intrusion detection system (IDS) is an important part of enterprise security system architecture. In particular, anomaly-based IDS has been widely applied to detect abnormal process behaviors that deviate from the majority. However, such abnormal behavior usually consists of a series of low-level heterogeneous events. The gap between the low-level events and the high-level abnormal behaviors makes it hard to infer which single events are related to the real abnormal activities, especially considering that there are massive "noisy" low-level events happening in between. Hence, the existing work that focus on detecting single entities/events can hardly achieve high detection accuracy. Different from previous work, we design and implement GID, an efficient graph-based intrusion detection technique that can identify abnormal event sequences from a massive heterogeneous process traces with high accuracy. GID first builds a compact graph structure to capture the interactions between different system entities. The suspiciousness or anomaly score of process paths is then measured by leveraging random walk technique to the constructed acyclic directed graph. To eliminate the score bias from the path length, the Box-Cox power transformation based approach is introduced to normalize the anomaly scores so that the scores of paths of different lengths have the same distribution. The efficiency of suspicious path discovery is further improved by the proposed optimization scheme. We fully implement our GID algorithm and deploy it into a real enterprise security system, and it greatly helps detect the advanced threats, and optimize the incident response. Executing GID on system monitoring datasets showing that GID is efficient (about 2 million records per minute) and accurate (higher than 80% in terms of detection rate).

  • 8 authors
·
Aug 8, 2016

Select2Plan: Training-Free ICL-Based Planning through VQA and Memory Retrieval

This study explores the potential of off-the-shelf Vision-Language Models (VLMs) for high-level robot planning in the context of autonomous navigation. Indeed, while most of existing learning-based approaches for path planning require extensive task-specific training/fine-tuning, we demonstrate how such training can be avoided for most practical cases. To do this, we introduce Select2Plan (S2P), a novel training-free framework for high-level robot planning which completely eliminates the need for fine-tuning or specialised training. By leveraging structured Visual Question-Answering (VQA) and In-Context Learning (ICL), our approach drastically reduces the need for data collection, requiring a fraction of the task-specific data typically used by trained models, or even relying only on online data. Our method facilitates the effective use of a generally trained VLM in a flexible and cost-efficient way, and does not require additional sensing except for a simple monocular camera. We demonstrate its adaptability across various scene types, context sources, and sensing setups. We evaluate our approach in two distinct scenarios: traditional First-Person View (FPV) and infrastructure-driven Third-Person View (TPV) navigation, demonstrating the flexibility and simplicity of our method. Our technique significantly enhances the navigational capabilities of a baseline VLM of approximately 50% in TPV scenario, and is comparable to trained models in the FPV one, with as few as 20 demonstrations.

  • 6 authors
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Nov 6, 2024

FreeControl: Efficient, Training-Free Structural Control via One-Step Attention Extraction

Controlling the spatial and semantic structure of diffusion-generated images remains a challenge. Existing methods like ControlNet rely on handcrafted condition maps and retraining, limiting flexibility and generalization. Inversion-based approaches offer stronger alignment but incur high inference cost due to dual-path denoising. We present FreeControl, a training-free framework for semantic structural control in diffusion models. Unlike prior methods that extract attention across multiple timesteps, FreeControl performs one-step attention extraction from a single, optimally chosen key timestep and reuses it throughout denoising. This enables efficient structural guidance without inversion or retraining. To further improve quality and stability, we introduce Latent-Condition Decoupling (LCD): a principled separation of the key timestep and the noised latent used in attention extraction. LCD provides finer control over attention quality and eliminates structural artifacts. FreeControl also supports compositional control via reference images assembled from multiple sources - enabling intuitive scene layout design and stronger prompt alignment. FreeControl introduces a new paradigm for test-time control, enabling structurally and semantically aligned, visually coherent generation directly from raw images, with the flexibility for intuitive compositional design and compatibility with modern diffusion models at approximately 5 percent additional cost.

  • 10 authors
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Nov 7

ExpertFlow: Optimized Expert Activation and Token Allocation for Efficient Mixture-of-Experts Inference

Sparse Mixture of Experts (MoE) models, while outperforming dense Large Language Models (LLMs) in terms of performance, face significant deployment challenges during inference due to their high memory demands. Existing offloading techniques, which involve swapping activated and idle experts between the GPU and CPU, often suffer from rigid expert caching mechanisms. These mechanisms fail to adapt to dynamic routing, leading to inefficient cache utilization, or incur prohibitive costs for prediction training. To tackle these inference-specific challenges, we introduce ExpertFlow, a comprehensive system specifically designed to enhance inference efficiency by accommodating flexible routing and enabling efficient expert scheduling between CPU and GPU. This reduces overhead and boosts system performance. Central to our approach is a predictive routing path-based offloading mechanism that utilizes a lightweight predictor to accurately forecast routing paths before computation begins. This proactive strategy allows for real-time error correction in expert caching, significantly increasing cache hit ratios and reducing the frequency of expert transfers, thereby minimizing I/O overhead. Additionally, we implement a dynamic token scheduling strategy that optimizes MoE inference by rearranging input tokens across different batches. This method not only reduces the number of activated experts per batch but also improves computational efficiency. Our extensive experiments demonstrate that ExpertFlow achieves up to 93.72\% GPU memory savings and enhances inference speed by 2 to 10 times compared to baseline methods, highlighting its effectiveness and utility as a robust solution for resource-constrained inference scenarios.

  • 10 authors
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Oct 23, 2024

Evaluating the Impact of Source Code Parsers on ML4SE Models

As researchers and practitioners apply Machine Learning to increasingly more software engineering problems, the approaches they use become more sophisticated. A lot of modern approaches utilize internal code structure in the form of an abstract syntax tree (AST) or its extensions: path-based representation, complex graph combining AST with additional edges. Even though the process of extracting ASTs from code can be done with different parsers, the impact of choosing a parser on the final model quality remains unstudied. Moreover, researchers often omit the exact details of extracting particular code representations. In this work, we evaluate two models, namely Code2Seq and TreeLSTM, in the method name prediction task backed by eight different parsers for the Java language. To unify the process of data preparation with different parsers, we develop SuperParser, a multi-language parser-agnostic library based on PathMiner. SuperParser facilitates the end-to-end creation of datasets suitable for training and evaluation of ML models that work with structural information from source code. Our results demonstrate that trees built by different parsers vary in their structure and content. We then analyze how this diversity affects the models' quality and show that the quality gap between the most and least suitable parsers for both models turns out to be significant. Finally, we discuss other features of the parsers that researchers and practitioners should take into account when selecting a parser along with the impact on the models' quality. The code of SuperParser is publicly available at https://doi.org/10.5281/zenodo.6366591. We also publish Java-norm, the dataset we use to evaluate the models: https://doi.org/10.5281/zenodo.6366599.

  • 4 authors
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Jun 17, 2022

Learning Efficient and Generalizable Graph Retriever for Knowledge-Graph Question Answering

Large Language Models (LLMs) have shown strong inductive reasoning ability across various domains, but their reliability is hindered by the outdated knowledge and hallucinations. Retrieval-Augmented Generation mitigates these issues by grounding LLMs with external knowledge; however, most existing RAG pipelines rely on unstructured text, limiting interpretability and structured reasoning. Knowledge graphs, which represent facts as relational triples, offer a more structured and compact alternative. Recent studies have explored integrating knowledge graphs with LLMs for knowledge graph question answering (KGQA), with a significant proportion adopting the retrieve-then-reasoning paradigm. In this framework, graph-based retrievers have demonstrated strong empirical performance, yet they still face challenges in generalization ability. In this work, we propose RAPL, a novel framework for efficient and effective graph retrieval in KGQA. RAPL addresses these limitations through three aspects: (1) a two-stage labeling strategy that combines heuristic signals with parametric models to provide causally grounded supervision; (2) a model-agnostic graph transformation approach to capture both intra- and inter-triple interactions, thereby enhancing representational capacity; and (3) a path-based reasoning strategy that facilitates learning from the injected rational knowledge, and supports downstream reasoner through structured inputs. Empirically, RAPL outperforms state-of-the-art methods by 2.66%-20.34%, and significantly reduces the performance gap between smaller and more powerful LLM-based reasoners, as well as the gap under cross-dataset settings, highlighting its superior retrieval capability and generalizability. Codes are available at: https://github.com/tianyao-aka/RAPL.

  • 6 authors
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Jun 11

Polyline Path Masked Attention for Vision Transformer

Global dependency modeling and spatial position modeling are two core issues of the foundational architecture design in current deep learning frameworks. Recently, Vision Transformers (ViTs) have achieved remarkable success in computer vision, leveraging the powerful global dependency modeling capability of the self-attention mechanism. Furthermore, Mamba2 has demonstrated its significant potential in natural language processing tasks by explicitly modeling the spatial adjacency prior through the structured mask. In this paper, we propose Polyline Path Masked Attention (PPMA) that integrates the self-attention mechanism of ViTs with an enhanced structured mask of Mamba2, harnessing the complementary strengths of both architectures. Specifically, we first ameliorate the traditional structured mask of Mamba2 by introducing a 2D polyline path scanning strategy and derive its corresponding structured mask, polyline path mask, which better preserves the adjacency relationships among image tokens. Notably, we conduct a thorough theoretical analysis on the structural characteristics of the proposed polyline path mask and design an efficient algorithm for the computation of the polyline path mask. Next, we embed the polyline path mask into the self-attention mechanism of ViTs, enabling explicit modeling of spatial adjacency prior. Extensive experiments on standard benchmarks, including image classification, object detection, and segmentation, demonstrate that our model outperforms previous state-of-the-art approaches based on both state-space models and Transformers. For example, our proposed PPMA-T/S/B models achieve 48.7%/51.1%/52.3% mIoU on the ADE20K semantic segmentation task, surpassing RMT-T/S/B by 0.7%/1.3%/0.3%, respectively. Code is available at https://github.com/zhongchenzhao/PPMA.

  • 6 authors
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Jun 18

Synthesizing Diverse Human Motions in 3D Indoor Scenes

We present a novel method for populating 3D indoor scenes with virtual humans that can navigate in the environment and interact with objects in a realistic manner. Existing approaches rely on training sequences that contain captured human motions and the 3D scenes they interact with. However, such interaction data are costly, difficult to capture, and can hardly cover all plausible human-scene interactions in complex environments. To address these challenges, we propose a reinforcement learning-based approach that enables virtual humans to navigate in 3D scenes and interact with objects realistically and autonomously, driven by learned motion control policies. The motion control policies employ latent motion action spaces, which correspond to realistic motion primitives and are learned from large-scale motion capture data using a powerful generative motion model. For navigation in a 3D environment, we propose a scene-aware policy with novel state and reward designs for collision avoidance. Combined with navigation mesh-based path-finding algorithms to generate intermediate waypoints, our approach enables the synthesis of diverse human motions navigating in 3D indoor scenes and avoiding obstacles. To generate fine-grained human-object interactions, we carefully curate interaction goal guidance using a marker-based body representation and leverage features based on the signed distance field (SDF) to encode human-scene proximity relations. Our method can synthesize realistic and diverse human-object interactions (e.g.,~sitting on a chair and then getting up) even for out-of-distribution test scenarios with different object shapes, orientations, starting body positions, and poses. Experimental results demonstrate that our approach outperforms state-of-the-art methods in terms of both motion naturalness and diversity. Code and video results are available at: https://zkf1997.github.io/DIMOS.

  • 5 authors
·
May 21, 2023

Panacea: A foundation model for clinical trial search, summarization, design, and recruitment

Clinical trials are fundamental in developing new drugs, medical devices, and treatments. However, they are often time-consuming and have low success rates. Although there have been initial attempts to create large language models (LLMs) for clinical trial design and patient-trial matching, these models remain task-specific and not adaptable to diverse clinical trial tasks. To address this challenge, we propose a clinical trial foundation model named Panacea, designed to handle multiple tasks, including trial search, trial summarization, trial design, and patient-trial matching. We also assemble a large-scale dataset, named TrialAlign, of 793,279 trial documents and 1,113,207 trial-related scientific papers, to infuse clinical knowledge into the model by pre-training. We further curate TrialInstruct, which has 200,866 of instruction data for fine-tuning. These resources enable Panacea to be widely applicable for a range of clinical trial tasks based on user requirements. We evaluated Panacea on a new benchmark, named TrialPanorama, which covers eight clinical trial tasks. Our method performed the best on seven of the eight tasks compared to six cutting-edge generic or medicine-specific LLMs. Specifically, Panacea showed great potential to collaborate with human experts in crafting the design of eligibility criteria, study arms, and outcome measures, in multi-round conversations. In addition, Panacea achieved 14.42% improvement in patient-trial matching, 41.78% to 52.02% improvement in trial search, and consistently ranked at the top for five aspects of trial summarization. Our approach demonstrates the effectiveness of Panacea in clinical trials and establishes a comprehensive resource, including training data, model, and benchmark, for developing clinical trial foundation models, paving the path for AI-based clinical trial development.

  • 5 authors
·
Jun 25, 2024

HOPE: A Reinforcement Learning-based Hybrid Policy Path Planner for Diverse Parking Scenarios

Automated parking stands as a highly anticipated application of autonomous driving technology. However, existing path planning methodologies fall short of addressing this need due to their incapability to handle the diverse and complex parking scenarios in reality. While non-learning methods provide reliable planning results, they are vulnerable to intricate occasions, whereas learning-based ones are good at exploration but unstable in converging to feasible solutions. To leverage the strengths of both approaches, we introduce Hybrid pOlicy Path plannEr (HOPE). This novel solution integrates a reinforcement learning agent with Reeds-Shepp curves, enabling effective planning across diverse scenarios. HOPE guides the exploration of the reinforcement learning agent by applying an action mask mechanism and employs a transformer to integrate the perceived environmental information with the mask. To facilitate the training and evaluation of the proposed planner, we propose a criterion for categorizing the difficulty level of parking scenarios based on space and obstacle distribution. Experimental results demonstrate that our approach outperforms typical rule-based algorithms and traditional reinforcement learning methods, showing higher planning success rates and generalization across various scenarios. We also conduct real-world experiments to verify the practicability of HOPE. The code for our solution is openly available on https://github.com/jiamiya/HOPE.

  • 6 authors
·
May 30, 2024

Reducing Domain Gap with Diffusion-Based Domain Adaptation for Cell Counting

Generating realistic synthetic microscopy images is critical for training deep learning models in label-scarce environments, such as cell counting with many cells per image. However, traditional domain adaptation methods often struggle to bridge the domain gap when synthetic images lack the complex textures and visual patterns of real samples. In this work, we adapt the Inversion-Based Style Transfer (InST) framework originally designed for artistic style transfer to biomedical microscopy images. Our method combines latent-space Adaptive Instance Normalization with stochastic inversion in a diffusion model to transfer the style from real fluorescence microscopy images to synthetic ones, while weakly preserving content structure. We evaluate the effectiveness of our InST-based synthetic dataset for downstream cell counting by pre-training and fine-tuning EfficientNet-B0 models on various data sources, including real data, hard-coded synthetic data, and the public Cell200-s dataset. Models trained with our InST-synthesized images achieve up to 37\% lower Mean Absolute Error (MAE) compared to models trained on hard-coded synthetic data, and a 52\% reduction in MAE compared to models trained on Cell200-s (from 53.70 to 25.95 MAE). Notably, our approach also outperforms models trained on real data alone (25.95 vs. 27.74 MAE). Further improvements are achieved when combining InST-synthesized data with lightweight domain adaptation techniques such as DACS with CutMix. These findings demonstrate that InST-based style transfer most effectively reduces the domain gap between synthetic and real microscopy data. Our approach offers a scalable path for enhancing cell counting performance while minimizing manual labeling effort. The source code and resources are publicly available at: https://github.com/MohammadDehghan/InST-Microscopy.

  • 2 authors
·
Dec 12

Cognitively Inspired Energy-Based World Models

One of the predominant methods for training world models is autoregressive prediction in the output space of the next element of a sequence. In Natural Language Processing (NLP), this takes the form of Large Language Models (LLMs) predicting the next token; in Computer Vision (CV), this takes the form of autoregressive models predicting the next frame/token/pixel. However, this approach differs from human cognition in several respects. First, human predictions about the future actively influence internal cognitive processes. Second, humans naturally evaluate the plausibility of predictions regarding future states. Based on this capability, and third, by assessing when predictions are sufficient, humans allocate a dynamic amount of time to make a prediction. This adaptive process is analogous to System 2 thinking in psychology. All these capabilities are fundamental to the success of humans at high-level reasoning and planning. Therefore, to address the limitations of traditional autoregressive models lacking these human-like capabilities, we introduce Energy-Based World Models (EBWM). EBWM involves training an Energy-Based Model (EBM) to predict the compatibility of a given context and a predicted future state. In doing so, EBWM enables models to achieve all three facets of human cognition described. Moreover, we developed a variant of the traditional autoregressive transformer tailored for Energy-Based models, termed the Energy-Based Transformer (EBT). Our results demonstrate that EBWM scales better with data and GPU Hours than traditional autoregressive transformers in CV, and that EBWM offers promising early scaling in NLP. Consequently, this approach offers an exciting path toward training future models capable of System 2 thinking and intelligently searching across state spaces.

  • 6 authors
·
Jun 13, 2024 7

Time-R1: Towards Comprehensive Temporal Reasoning in LLMs

Large Language Models (LLMs) demonstrate impressive capabilities but lack robust temporal intelligence, struggling to integrate reasoning about the past with predictions and plausible generations of the future. Meanwhile, existing methods typically target isolated temporal skills, such as question answering about past events or basic forecasting, and exhibit poor generalization, particularly when dealing with events beyond their knowledge cutoff or requiring creative foresight. To address these limitations, we introduce Time-R1, the first framework to endow a moderate-sized (3B-parameter) LLM with comprehensive temporal abilities: understanding, prediction, and creative generation. Our approach features a novel three-stage development path; the first two constitute a reinforcement learning (RL) curriculum driven by a meticulously designed dynamic rule-based reward system. This framework progressively builds (1) foundational temporal understanding and logical event-time mappings from historical data, (2) future event prediction skills for events beyond its knowledge cutoff, and finally (3) enables remarkable generalization to creative future scenario generation without any fine-tuning. Strikingly, experiments demonstrate that Time-R1 outperforms models over 200 times larger, including the state-of-the-art 671B DeepSeek-R1, on highly challenging future event prediction and creative scenario generation benchmarks. This work provides strong evidence that thoughtfully engineered, progressive RL fine-tuning allows smaller, efficient models to achieve superior temporal performance, offering a practical and scalable path towards truly time-aware AI. To foster further research, we also release Time-Bench, a large-scale multi-task temporal reasoning dataset derived from 10 years of news data, and our series of Time-R1 checkpoints.

  • 5 authors
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May 16 3

Learning Geometrically Disentangled Representations of Protein Folding Simulations

Massive molecular simulations of drug-target proteins have been used as a tool to understand disease mechanism and develop therapeutics. This work focuses on learning a generative neural network on a structural ensemble of a drug-target protein, e.g. SARS-CoV-2 Spike protein, obtained from computationally expensive molecular simulations. Model tasks involve characterizing the distinct structural fluctuations of the protein bound to various drug molecules, as well as efficient generation of protein conformations that can serve as an complement of a molecular simulation engine. Specifically, we present a geometric autoencoder framework to learn separate latent space encodings of the intrinsic and extrinsic geometries of the protein structure. For this purpose, the proposed Protein Geometric AutoEncoder (ProGAE) model is trained on the protein contact map and the orientation of the backbone bonds of the protein. Using ProGAE latent embeddings, we reconstruct and generate the conformational ensemble of a protein at or near the experimental resolution, while gaining better interpretability and controllability in term of protein structure generation from the learned latent space. Additionally, ProGAE models are transferable to a different state of the same protein or to a new protein of different size, where only the dense layer decoding from the latent representation needs to be retrained. Results show that our geometric learning-based method enjoys both accuracy and efficiency for generating complex structural variations, charting the path toward scalable and improved approaches for analyzing and enhancing high-cost simulations of drug-target proteins.

  • 5 authors
·
May 20, 2022