Visual as well as genetic biometrics are routinely employed to identify species and individuals in biological applications. However, no attempts have been made in this domain to computationally enhance visual classification of rare classes with little image data via genetics. In this paper, we thus propose aligned visual-genetic inference spaces with the aim to implicitly encode cross-domain associations for improved performance. We demonstrate for the first time that such alignment can be achieved via deep embedding models and that the approach is directly applicable to boosting long-tailed recognition (LTR) particularly for rare species. We experimentally demonstrate the efficacy of the concept via application to microscopic imagery of 30k+ planktic foraminifer shells across 32 species when used together with independent genetic data samples. Most importantly for practitioners, we show that visual-genetic alignment can significantly benefit visual-only recognition of the rarest species. Technically, we pre-train a visual ResNet50 deep learning model using triplet loss formulations to create an initial embedding space. We re-structure this space based on genetic anchors embedded via a Sequence Graph Transform (SGT) and linked to visual data by cross-domain cosine alignment. We show that an LTR approach improves the state-of-the-art across all benchmarks and that adding our visual-genetic alignment improves per-class and particularly rare tail class benchmarks significantly further. We conclude that visual-genetic alignment can be a highly effective tool for complementing visual biological data containing rare classes. The concept proposed may serve as an important future tool for integrating genetics and imageomics towards a more complete scientific representation of taxonomic spaces and life itself. Code, weights, and data splits are published for full reproducibility.
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While deep learning techniques have become extremely popular for solving a broad range of optimization problems, methods to enforce hard constraints during optimization, particularly on deep neural networks, remain underdeveloped. Inspired by the rich literature on meshless interpolation and its extension to spectral collocation methods in scientific computing, we develop a series of approaches for enforcing hard constraints on neural fields, which we refer to as Constrained Neural Fields (CNF). The constraints can be specified as a linear operator applied to the neural field and its derivatives. We also design specific model representations and training strategies for problems where standard models may encounter difficulties, such as conditioning of the system, memory consumption, and capacity of the network when being constrained. Our approaches are demonstrated in a wide range of real-world applications. Additionally, we develop a framework that enables highly efficient model and constraint specification, which can be readily applied to any downstream task where hard constraints need to be explicitly satisfied during optimization.
Navigating the landscape of particle accelerators has become increasingly challenging with recent surges in contributions. These intricate devices challenge comprehension, even within individual facilities. To address this, we introduce PACuna, a fine-tuned language model refined through publicly available accelerator resources like conferences, pre-prints, and books. We automated data collection and question generation to minimize expert involvement and make the data publicly available. PACuna demonstrates proficiency in addressing intricate accelerator questions, validated by experts. Our approach shows adapting language models to scientific domains by fine-tuning technical texts and auto-generated corpora capturing the latest developments can further produce pre-trained models to answer some intricate questions that commercially available assistants cannot and can serve as intelligent assistants for individual facilities.
Cluster-randomized trials often involve units that are irregularly distributed in space without well-separated communities. In these settings, cluster construction is a critical aspect of the design due to the potential for cross-cluster interference. The existing literature relies on partial interference models, which take clusters as given and assume no cross-cluster interference. We relax this assumption by allowing interference to decay with geographic distance between units. This induces a bias-variance trade-off: constructing fewer, larger clusters reduces bias due to interference but increases variance. We propose new estimators that exclude units most potentially impacted by cross-cluster interference and show that this substantially reduces asymptotic bias relative to conventional difference-in-means estimators. We then study the design of clusters to optimize the estimators' rates of convergence. We provide formal justification for a new design that chooses the number of clusters to balance the asymptotic bias and variance of our estimators and uses unsupervised learning to automate cluster construction.
We study the consistency of surrogate risks for robust binary classification. It is common to learn robust classifiers by adversarial training, which seeks to minimize the expected $0$-$1$ loss when each example can be maliciously corrupted within a small ball. We give a simple and complete characterization of the set of surrogate loss functions that are \emph{consistent}, i.e., that can replace the $0$-$1$ loss without affecting the minimizing sequences of the original adversarial risk, for any data distribution. We also prove a quantitative version of adversarial consistency for the $\rho$-margin loss. Our results reveal that the class of adversarially consistent surrogates is substantially smaller than in the standard setting, where many common surrogates are known to be consistent.
NLP models have progressed drastically in recent years, according to numerous datasets proposed to evaluate performance. Questions remain, however, about how particular dataset design choices may impact the conclusions we draw about model capabilities. In this work, we investigate this question in the domain of compositional generalization. We examine the performance of six modeling approaches across 4 datasets, split according to 8 compositional splitting strategies, ranking models by 18 compositional generalization splits in total. Our results show that: i) the datasets, although all designed to evaluate compositional generalization, rank modeling approaches differently; ii) datasets generated by humans align better with each other than they with synthetic datasets, or than synthetic datasets among themselves; iii) generally, whether datasets are sampled from the same source is more predictive of the resulting model ranking than whether they maintain the same interpretation of compositionality; and iv) which lexical items are used in the data can strongly impact conclusions. Overall, our results demonstrate that much work remains to be done when it comes to assessing whether popular evaluation datasets measure what they intend to measure, and suggest that elucidating more rigorous standards for establishing the validity of evaluation sets could benefit the field.
Self-training is a well-known approach for semi-supervised learning. It consists of iteratively assigning pseudo-labels to unlabeled data for which the model is confident and treating them as labeled examples. For neural networks, softmax prediction probabilities are often used as a confidence measure, despite the fact that they are known to be overconfident, even for wrong predictions. This phenomenon is particularly intensified in the presence of sample selection bias, i.e., when data labeling is subject to some constraint. To address this issue, we propose a novel confidence measure, called $\mathcal{T}$-similarity, built upon the prediction diversity of an ensemble of linear classifiers. We provide the theoretical analysis of our approach by studying stationary points and describing the relationship between the diversity of the individual members and their performance. We empirically demonstrate the benefit of our confidence measure for three different pseudo-labeling policies on classification datasets of various data modalities.
Graph neural networks are prominent models for representation learning over graph-structured data. While the capabilities and limitations of these models are well-understood for simple graphs, our understanding remains incomplete in the context of knowledge graphs. Our goal is to provide a systematic understanding of the landscape of graph neural networks for knowledge graphs pertaining to the prominent task of link prediction. Our analysis entails a unifying perspective on seemingly unrelated models and unlocks a series of other models. The expressive power of various models is characterized via a corresponding relational Weisfeiler-Leman algorithm. This analysis is extended to provide a precise logical characterization of the class of functions captured by a class of graph neural networks. The theoretical findings presented in this paper explain the benefits of some widely employed practical design choices, which are validated empirically.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
Human-in-the-loop aims to train an accurate prediction model with minimum cost by integrating human knowledge and experience. Humans can provide training data for machine learning applications and directly accomplish some tasks that are hard for computers in the pipeline with the help of machine-based approaches. In this paper, we survey existing works on human-in-the-loop from a data perspective and classify them into three categories with a progressive relationship: (1) the work of improving model performance from data processing, (2) the work of improving model performance through interventional model training, and (3) the design of the system independent human-in-the-loop. Using the above categorization, we summarize major approaches in the field, along with their technical strengths/ weaknesses, we have simple classification and discussion in natural language processing, computer vision, and others. Besides, we provide some open challenges and opportunities. This survey intends to provide a high-level summarization for human-in-the-loop and motivates interested readers to consider approaches for designing effective human-in-the-loop solutions.
Attention Model has now become an important concept in neural networks that has been researched within diverse application domains. This survey provides a structured and comprehensive overview of the developments in modeling attention. In particular, we propose a taxonomy which groups existing techniques into coherent categories. We review the different neural architectures in which attention has been incorporated, and also show how attention improves interpretability of neural models. Finally, we discuss some applications in which modeling attention has a significant impact. We hope this survey will provide a succinct introduction to attention models and guide practitioners while developing approaches for their applications.
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