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Over the last five years, deep generative models have gradually been adopted for various tasks in biological research. Notably, image-to-image translation methods showed to be effective in revealing subtle phenotypic cell variations otherwise invisible to the human eye. Current methods to achieve this goal mainly rely on Generative Adversarial Networks (GANs). However, these models are known to suffer from some shortcomings such as training instability and mode collapse. Furthermore, the lack of robustness to invert a real image into the latent of a trained GAN prevents flexible editing of real images. In this work, we propose PhenDiff, an image-to-image translation method based on conditional diffusion models to identify subtle phenotypes in microscopy images. We evaluate this approach on biological datasets against previous work such as CycleGAN. We show that PhenDiff outperforms this baseline in terms of quality and diversity of the generated images. We then apply this method to display invisible phenotypic changes triggered by a rare neurodevelopmental disorder on microscopy images of organoids. Altogether, we demonstrate that PhenDiff is able to perform high quality biological image-to-image translation allowing to spot subtle phenotype variations on a real image.

Large Language Models (LLMs) are capable of reasoning over diverse input data modalities through pre-trained encoders. However, the growing diversity of input data modalities prevents incorporating all modalities into LLMs, especially when LLMs are deployed on resource-constrained edge devices for embodied AI applications. Instead, a better option is to adaptively involve only the useful modalities at runtime, depending on the current environmental contexts and task requirements. For such modality adaptation, existing work adopts fixed connections between encoders and the LLM's input layer, leading to high training cost at runtime and ineffective cross-modal interaction. In this paper, we address these limitations by presenting mPnP-LLM, a new technique that allows fully elastic, automated and prompt runtime modality adaptation, by connecting unimodal encoders to a flexible set of last LLM blocks and making such latent connections fully trainable at runtime. Experiments over the nuScenes-QA dataset show that mPnP-LLM can achieve up to 3.7x FLOPs reduction and 30% GPU memory usage reduction, while retaining on-par accuracy with the existing schemes. Under the same compute budget, mPnP-LLM improves the task accuracy by up to 4% compared to the best existing scheme.

Transformer-based models, such as BERT, have been widely applied in a wide range of natural language processing tasks. However, one inevitable side effect is that they require massive memory storage and inference cost when deployed in production. Quantization is one of the popularized ways to alleviate the cost. However, the previous 8-bit quantization strategy based on INT8 data format either suffers from the degradation of accuracy in a Post-Training Quantization (PTQ) fashion or requires an expensive Quantization-Aware Training (QAT) process. Recently, a new numeric format FP8 (i.e. floating-point of 8-bits) has been proposed and supported in commercial AI computing platforms such as H100. In this paper, we empirically validate the effectiveness of FP8 as a way to do Post-Training Quantization without significant loss of accuracy, with a simple calibration and format conversion process. We adopt the FP8 standard proposed by NVIDIA Corp. (2022) in our extensive experiments of BERT variants on GLUE and SQuAD v1.1 datasets, and show that PTQ with FP8 can significantly improve the accuracy upon that with INT8, to the extent of the full-precision model.

Many neural network architectures have been shown to be Turing Complete, and can thus implement arbitrary algorithms. However, Transformers are unique in that they can implement gradient-based learning algorithms \emph{under simple parameter configurations}. A line of recent work shows that linear Transformers naturally learn to implement gradient descent (GD) when trained on a linear regression in-context learning task. But the linearity assumption (either in the Transformer architecture or in the learning task) is far from realistic settings where non-linear activations crucially enable Transformers to learn complicated non-linear functions. In this paper, we provide theoretical and empirical evidence that non-linear Transformers can, and \emph{in fact do}, learn to implement learning algorithms to learn non-linear functions in context. Our results apply to a broad class of combinations of non-linear architectures, and non-linear in-context learning tasks. Interestingly, we show that the optimal choice of non-linear activation depends in a natural way on the non-linearity of the learning task.

Diffusion models trained on large datasets can synthesize photo-realistic images of remarkable quality and diversity. However, attributing these images back to the training data-that is, identifying specific training examples which caused an image to be generated-remains a challenge. In this paper, we propose a framework that: (i) provides a formal notion of data attribution in the context of diffusion models, and (ii) allows us to counterfactually validate such attributions. Then, we provide a method for computing these attributions efficiently. Finally, we apply our method to find (and evaluate) such attributions for denoising diffusion probabilistic models trained on CIFAR-10 and latent diffusion models trained on MS COCO. We provide code at //github.com/MadryLab/journey-TRAK .

Generative models can produce synthetic patient records for analytical tasks when real data is unavailable or limited. However, current methods struggle with adhering to domain-specific knowledge and removing invalid data. We present ConSequence, an effective approach to integrating domain knowledge into sequential generative neural network outputs. Our rule-based formulation includes temporal aggregation and antecedent evaluation modules, ensured by an efficient matrix multiplication formulation, to satisfy hard and soft logical constraints across time steps. Existing constraint methods often fail to guarantee constraint satisfaction, lack the ability to handle temporal constraints, and hinder the learning and computational efficiency of the model. In contrast, our approach efficiently handles all types of constraints with guaranteed logical coherence. We demonstrate ConSequence's effectiveness in generating electronic health records, outperforming competitors in achieving complete temporal and spatial constraint satisfaction without compromising runtime performance or generative quality. Specifically, ConSequence successfully prevents all rule violations while improving the model quality in reducing its test perplexity by 5% and incurring less than a 13% slowdown in generation speed compared to an unconstrained model.

Transformer is a promising neural network learner, and has achieved great success in various machine learning tasks. Thanks to the recent prevalence of multimodal applications and big data, Transformer-based multimodal learning has become a hot topic in AI research. This paper presents a comprehensive survey of Transformer techniques oriented at multimodal data. The main contents of this survey include: (1) a background of multimodal learning, Transformer ecosystem, and the multimodal big data era, (2) a theoretical review of Vanilla Transformer, Vision Transformer, and multimodal Transformers, from a geometrically topological perspective, (3) a review of multimodal Transformer applications, via two important paradigms, i.e., for multimodal pretraining and for specific multimodal tasks, (4) a summary of the common challenges and designs shared by the multimodal Transformer models and applications, and (5) a discussion of open problems and potential research directions for the community.

The content based image retrieval aims to find the similar images from a large scale dataset against a query image. Generally, the similarity between the representative features of the query image and dataset images is used to rank the images for retrieval. In early days, various hand designed feature descriptors have been investigated based on the visual cues such as color, texture, shape, etc. that represent the images. However, the deep learning has emerged as a dominating alternative of hand-designed feature engineering from a decade. It learns the features automatically from the data. This paper presents a comprehensive survey of deep learning based developments in the past decade for content based image retrieval. The categorization of existing state-of-the-art methods from different perspectives is also performed for greater understanding of the progress. The taxonomy used in this survey covers different supervision, different networks, different descriptor type and different retrieval type. A performance analysis is also performed using the state-of-the-art methods. The insights are also presented for the benefit of the researchers to observe the progress and to make the best choices. The survey presented in this paper will help in further research progress in image retrieval using deep learning.

Current state-of-the-art semantic role labeling (SRL) uses a deep neural network with no explicit linguistic features. However, prior work has shown that gold syntax trees can dramatically improve SRL decoding, suggesting the possibility of increased accuracy from explicit modeling of syntax. In this work, we present linguistically-informed self-attention (LISA): a neural network model that combines multi-head self-attention with multi-task learning across dependency parsing, part-of-speech tagging, predicate detection and SRL. Unlike previous models which require significant pre-processing to prepare linguistic features, LISA can incorporate syntax using merely raw tokens as input, encoding the sequence only once to simultaneously perform parsing, predicate detection and role labeling for all predicates. Syntax is incorporated by training one attention head to attend to syntactic parents for each token. Moreover, if a high-quality syntactic parse is already available, it can be beneficially injected at test time without re-training our SRL model. In experiments on CoNLL-2005 SRL, LISA achieves new state-of-the-art performance for a model using predicted predicates and standard word embeddings, attaining 2.5 F1 absolute higher than the previous state-of-the-art on newswire and more than 3.5 F1 on out-of-domain data, nearly 10% reduction in error. On ConLL-2012 English SRL we also show an improvement of more than 2.5 F1. LISA also out-performs the state-of-the-art with contextually-encoded (ELMo) word representations, by nearly 1.0 F1 on news and more than 2.0 F1 on out-of-domain text.

Inspired by recent development of artificial satellite, remote sensing images have attracted extensive attention. Recently, noticeable progress has been made in scene classification and target detection.However, it is still not clear how to describe the remote sensing image content with accurate and concise sentences. In this paper, we investigate to describe the remote sensing images with accurate and flexible sentences. First, some annotated instructions are presented to better describe the remote sensing images considering the special characteristics of remote sensing images. Second, in order to exhaustively exploit the contents of remote sensing images, a large-scale aerial image data set is constructed for remote sensing image caption. Finally, a comprehensive review is presented on the proposed data set to fully advance the task of remote sensing caption. Extensive experiments on the proposed data set demonstrate that the content of the remote sensing image can be completely described by generating language descriptions. The data set is available at //github.com/2051/RSICD_optimal