Pathology-genomic fusion via biologically informed cross-modality graph learning for survival analysis

The diagnosis and prognosis of cancer are typically based on multi-modal clinical data, including histology images and genomic data, due to the complex pathogenesis and high heterogeneity. Despite the advancements in digital pathology and high-throughput genome sequencing, establishing effective multi-modal fusion models for survival prediction and revealing the potential association between histopathology and transcriptomics remains challenging. In this paper, we propose Pathology-Genome Heterogeneous Graph (PGHG) that integrates whole slide images (WSI) and bulk RNA-Seq expression data with heterogeneous graph neural network for cancer survival analysis. The PGHG consists of biological knowledge-guided representation learning network and pathology-genome heterogeneous graph. The representation learning network utilizes the biological prior knowledge of intra-modal and inter-modal data associations to guide the feature extraction. The node features of each modality are updated through attention-based graph learning strategy. Unimodal features and bi-modal fused features are extracted via attention pooling module and then used for survival prediction. We evaluate the model on low-grade gliomas, glioblastoma, and kidney renal papillary cell carcinoma datasets from the Cancer Genome Atlas (TCGA) and the First Affiliated Hospital of Zhengzhou University (FAHZU). Extensive experimental results demonstrate that the proposed method outperforms both unimodal and other multi-modal fusion models. For demonstrating the model interpretability, we also visualize the attention heatmap of pathological images and utilize integrated gradient algorithm to identify important tissue structure, biological pathways and key genes.

Deepfake Generation and Detection: A Benchmark and Survey

In addition to the advancements in deepfake generation, corresponding detection technologies need to continuously evolve to regulate the potential misuse of deepfakes, such as for privacy invasion and phishing attacks. This survey comprehensively reviews the latest developments in deepfake generation and detection, summarizing and analyzing the current state of the art in this rapidly evolving field. We first unify task definitions, comprehensively introduce datasets and metrics, and discuss the development of generation and detection technology frameworks. Then, we discuss the development of several related sub-fields and focus on researching four mainstream deepfake fields: popular face swap, face reenactment, talking face generation, and facial attribute editing, as well as foreign detection. Subsequently, we comprehensively benchmark representative methods on popular datasets for each field, fully evaluating the latest and influential works published in top conferences/journals. Finally, we analyze the challenges and future research directions of the discussed fields. We closely follow the latest developments in https://github.com/flyingby/Awesome-Deepfake-Generation-and-Detection.

AddSR: Accelerating Diffusion-based Blind Super-Resolution with Adversarial Diffusion Distillation

Blind super-resolution methods based on stable diffusion showcase formidable generative capabilities in reconstructing clear high-resolution images with intricate details from low-resolution inputs. However, their practical applicability is often hampered by poor efficiency, stemming from the requirement of thousands or hundreds of sampling steps. Inspired by the efficient text-to-image approach adversarial diffusion distillation (ADD), we design AddSR to address this issue by incorporating the ideas of both distillation and ControlNet. Specifically, we first propose a prediction-based self-refinement strategy to provide high-frequency information in the student model output with marginal additional time cost. Furthermore, we refine the training process by employing HR images, rather than LR images, to regulate the teacher model, providing a more robust constraint for distillation. Second, we introduce a timestep-adapting loss to address the perception-distortion imbalance problem introduced by ADD. Extensive experiments demonstrate our AddSR generates better restoration results, while achieving faster speed than previous SD-based state-of-the-art models (e.g., 7x faster than SeeSR).

Invertible Diffusion Models for Compressed Sensing

While deep neural networks (NN) significantly advance image compressed sensing (CS) by improving reconstruction quality, the necessity of training current CS NNs from scratch constrains their effectiveness and hampers rapid deployment. Although recent methods utilize pre-trained diffusion models for image reconstruction, they struggle with slow inference and restricted adaptability to CS. To tackle these challenges, this paper proposes Invertible Diffusion Models (IDM), a novel efficient, end-to-end diffusion-based CS method. IDM repurposes a large-scale diffusion sampling process as a reconstruction model, and finetunes it end-to-end to recover original images directly from CS measurements, moving beyond the traditional paradigm of one-step noise estimation learning. To enable such memory-intensive end-to-end finetuning, we propose a novel two-level invertible design to transform both (1) the multi-step sampling process and (2) the noise estimation U-Net in each step into invertible networks. As a result, most intermediate features are cleared during training to reduce up to 93.8% GPU memory. In addition, we develop a set of lightweight modules to inject measurements into noise estimator to further facilitate reconstruction. Experiments demonstrate that IDM outperforms existing state-of-the-art CS networks by up to 2.64dB in PSNR. Compared to the recent diffusion model-based approach DDNM, our IDM achieves up to 10.09dB PSNR gain and 14.54 times faster inference.

Tri-Perspective View Decomposition for Geometry-Aware Depth Completion

Depth completion is a vital task for autonomous driving, as it involves reconstructing the precise 3D geometry of a scene from sparse and noisy depth measurements. However, most existing methods either rely only on 2D depth representations or directly incorporate raw 3D point clouds for compensation, which are still insufficient to capture the fine-grained 3D geometry of the scene. To address this challenge, we introduce Tri-Perspective view Decomposition (TPVD), a novel framework that can explicitly model 3D geometry. In particular, (1) TPVD ingeniously decomposes the original point cloud into three 2D views, one of which corresponds to the sparse depth input. (2) We design TPV Fusion to update the 2D TPV features through recurrent 2D-3D-2D aggregation, where a Distance-Aware Spherical Convolution (DASC) is applied. (3) By adaptively choosing TPV affinitive neighbors, the newly proposed Geometric Spatial Propagation Network (GSPN) further improves the geometric consistency. As a result, our TPVD outperforms existing methods on KITTI, NYUv2, and SUN RGBD. Furthermore, we build a novel depth completion dataset named TOFDC, which is acquired by the time-of-flight (TOF) sensor and the color camera on smartphones. Project page: https://yanzq95.github.io/projectpage/TOFDC/index.html

GaLore: Memory-Efficient LLM Training by Gradient Low-Rank Projection

Training Large Language Models (LLMs) presents significant memory challenges, predominantly due to the growing size of weights and optimizer states. Common memory-reduction approaches, such as low-rank adaptation (LoRA), add a trainable low-rank matrix to the frozen pre-trained weight in each layer, reducing trainable parameters and optimizer states. However, such approaches typically underperform training with full-rank weights in both pre-training and fine-tuning stages since they limit the parameter search to a low-rank subspace and alter the training dynamics, and further, may require full-rank warm start. In this work, we propose Gradient Low-Rank Projection (GaLore), a training strategy that allows full-parameter learning but is more memory-efficient than common low-rank adaptation methods such as LoRA. Our approach reduces memory usage by up to 65.5% in optimizer states while maintaining both efficiency and performance for pre-training on LLaMA 1B and 7B architectures with C4 dataset with up to 19.7B tokens, and on fine-tuning RoBERTa on GLUE tasks. Our 8-bit GaLore further reduces optimizer memory by up to 82.5% and total training memory by 63.3%, compared to a BF16 baseline. Notably, we demonstrate, for the first time, the feasibility of pre-training a 7B model on consumer GPUs with 24GB memory (e.g., NVIDIA RTX 4090) without model parallel, checkpointing, or offloading strategies.

Found in the Middle: How Language Models Use Long Contexts Better via Plug-and-Play Positional Encoding

This paper aims to overcome the "lost-in-the-middle" challenge of large language models (LLMs). While recent advancements have successfully enabled LLMs to perform stable language modeling with up to 4 million tokens, the persistent difficulty faced by most LLMs in identifying relevant information situated in the middle of the context has not been adequately tackled. To address this problem, this paper introduces Multi-scale Positional Encoding (Ms-PoE) which is a simple yet effective plug-and-play approach to enhance the capacity of LLMs to handle the relevant information located in the middle of the context, without fine-tuning or introducing any additional overhead. Ms-PoE leverages the position indice rescaling to relieve the long-term decay effect introduced by RoPE, while meticulously assigning distinct scaling ratios to different attention heads to preserve essential knowledge learned during the pre-training step, forming a multi-scale context fusion from short to long distance. Extensive experiments with a wide range of LLMs demonstrate the efficacy of our approach. Notably, Ms-PoE achieves an average accuracy gain of up to 3.8 on the Zero-SCROLLS benchmark over the original LLMs. Code are available at https://github.com/VITA-Group/Ms-PoE.

Pushing Auto-regressive Models for 3D Shape Generation at Capacity and Scalability

Auto-regressive models have achieved impressive results in 2D image generation by modeling joint distributions in grid space. In this paper, we extend auto-regressive models to 3D domains, and seek a stronger ability of 3D shape generation by improving auto-regressive models at capacity and scalability simultaneously. Firstly, we leverage an ensemble of publicly available 3D datasets to facilitate the training of large-scale models. It consists of a comprehensive collection of approximately 900,000 objects, with multiple properties of meshes, points, voxels, rendered images, and text captions. This diverse labeled dataset, termed Objaverse-Mix, empowers our model to learn from a wide range of object variations. However, directly applying 3D auto-regression encounters critical challenges of high computational demands on volumetric grids and ambiguous auto-regressive order along grid dimensions, resulting in inferior quality of 3D shapes. To this end, we then present a novel framework Argus3D in terms of capacity. Concretely, our approach introduces discrete representation learning based on a latent vector instead of volumetric grids, which not only reduces computational costs but also preserves essential geometric details by learning the joint distributions in a more tractable order. The capacity of conditional generation can thus be realized by simply concatenating various conditioning inputs to the latent vector, such as point clouds, categories, images, and texts. In addition, thanks to the simplicity of our model architecture, we naturally scale up our approach to a larger model with an impressive 3.6 billion parameters, further enhancing the quality of versatile 3D generation. Extensive experiments on four generation tasks demonstrate that Argus3D can synthesize diverse and faithful shapes across multiple categories, achieving remarkable performance.

Get More with LESS: Synthesizing Recurrence with KV Cache Compression for Efficient LLM Inference

Many computational factors limit broader deployment of large language models. In this paper, we focus on a memory bottleneck imposed by the key-value (KV) cache, a computational shortcut that requires storing previous KV pairs during decoding. While existing KV cache methods approach this problem by pruning or evicting large swaths of relatively less important KV pairs to dramatically reduce the memory footprint of the cache, they can have limited success in tasks that require recollecting a majority of previous tokens. To alleviate this issue, we propose LESS, a simple integration of a (nearly free) constant sized cache with eviction-based cache methods, such that all tokens can be queried at later decoding steps. Its ability to retain information throughout time shows merit on a variety of tasks where we demonstrate LESS can help reduce the performance gap from caching everything, sometimes even matching it, all while being efficient.