Significant scientific discoveries have driven the progress of human civilisation. The explosion of scientific literature and data has created information barriers across disciplines that have slowed the pace of scientific discovery. Large Language Models (LLMs) hold a wealth of global and interdisciplinary knowledge that promises to break down these information barriers and foster a new wave of scientific discovery. However, the potential of LLMs for scientific discovery has not been formally explored. In this paper, we start from investigating whether LLMs can propose scientific hypotheses. To this end, we construct a dataset consist of background knowledge and hypothesis pairs from biomedical literature. The dataset is divided into training, seen, and unseen test sets based on the publication date to control visibility. We subsequently evaluate the hypothesis generation capabilities of various top-tier instructed models in zero-shot, few-shot, and fine-tuning settings, including both closed and open-source LLMs. Additionally, we introduce an LLM-based multi-agent cooperative framework with different role designs and external tools to enhance the capabilities related to generating hypotheses. We also design four metrics through a comprehensive review to evaluate the generated hypotheses for both ChatGPT-based and human evaluations. Through experiments and analyses, we arrive at the following findings: 1) LLMs surprisingly generate untrained yet validated hypotheses from testing literature. 2) Increasing uncertainty facilitates candidate generation, potentially enhancing zero-shot hypothesis generation capabilities. These findings strongly support the potential of LLMs as catalysts for new scientific discoveries and guide further exploration.
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Numerous statistical methods have been developed to explore genomic imprinting and maternal effects, which are causes of parent-of-origin patterns in complex human diseases. However, most of them either only model one of these two confounded epigenetic effects, or make strong yet unrealistic assumptions about the population to avoid over-parameterization. A recent partial likelihood method (LIME) can identify both epigenetic effects based on case-control family data without those assumptions. Theoretical and empirical studies have shown its validity and robustness. However, because LIME obtains parameter estimation by maximizing partial likelihood, it is interesting to compare its efficiency with full likelihood maximizer. To overcome the difficulty in over-parameterization when using full likelihood, in this study we propose a Monte Carlo Expectation Maximization (MCEM) method to detect imprinting and maternal effects jointly. Those unknown mating type probabilities, the nuisance parameters, can be considered as latent variables in EM algorithm. Monte Carlo samples are used to numerically approximate the expectation function that cannot be solved algebraically. Our simulation results show that though this MCEM algorithm takes longer computational time, and can give higher bias in some simulations compared to LIME, it can generally detect both epigenetic effects with higher power and smaller standard error which demonstrates that it can be a good complement of LIME method.
In many real-world problems, there is a limited set of training data, but an abundance of unlabeled data. We propose a new method, Generative Posterior Networks (GPNs), that uses unlabeled data to estimate epistemic uncertainty in high-dimensional problems. A GPN is a generative model that, given a prior distribution over functions, approximates the posterior distribution directly by regularizing the network towards samples from the prior. We prove theoretically that our method indeed approximates the Bayesian posterior and show empirically that it improves epistemic uncertainty estimation and scalability over competing methods.
2D-based Industrial Anomaly Detection has been widely discussed, however, multimodal industrial anomaly detection based on 3D point clouds and RGB images still has many untouched fields. Existing multimodal industrial anomaly detection methods directly concatenate the multimodal features, which leads to a strong disturbance between features and harms the detection performance. In this paper, we propose Multi-3D-Memory (M3DM), a novel multimodal anomaly detection method with hybrid fusion scheme: firstly, we design an unsupervised feature fusion with patch-wise contrastive learning to encourage the interaction of different modal features; secondly, we use a decision layer fusion with multiple memory banks to avoid loss of information and additional novelty classifiers to make the final decision. We further propose a point feature alignment operation to better align the point cloud and RGB features. Extensive experiments show that our multimodal industrial anomaly detection model outperforms the state-of-the-art (SOTA) methods on both detection and segmentation precision on MVTec-3D AD dataset. Code is available at //github.com/nomewang/M3DM.
Recent contrastive representation learning methods rely on estimating mutual information (MI) between multiple views of an underlying context. E.g., we can derive multiple views of a given image by applying data augmentation, or we can split a sequence into views comprising the past and future of some step in the sequence. Contrastive lower bounds on MI are easy to optimize, but have a strong underestimation bias when estimating large amounts of MI. We propose decomposing the full MI estimation problem into a sum of smaller estimation problems by splitting one of the views into progressively more informed subviews and by applying the chain rule on MI between the decomposed views. This expression contains a sum of unconditional and conditional MI terms, each measuring modest chunks of the total MI, which facilitates approximation via contrastive bounds. To maximize the sum, we formulate a contrastive lower bound on the conditional MI which can be approximated efficiently. We refer to our general approach as Decomposed Estimation of Mutual Information (DEMI). We show that DEMI can capture a larger amount of MI than standard non-decomposed contrastive bounds in a synthetic setting, and learns better representations in a vision domain and for dialogue generation.
Recently, a considerable literature has grown up around the theme of Graph Convolutional Network (GCN). How to effectively leverage the rich structural information in complex graphs, such as knowledge graphs with heterogeneous types of entities and relations, is a primary open challenge in the field. Most GCN methods are either restricted to graphs with a homogeneous type of edges (e.g., citation links only), or focusing on representation learning for nodes only instead of jointly propagating and updating the embeddings of both nodes and edges for target-driven objectives. This paper addresses these limitations by proposing a novel framework, namely the Knowledge Embedding based Graph Convolutional Network (KE-GCN), which combines the power of GCNs in graph-based belief propagation and the strengths of advanced knowledge embedding (a.k.a. knowledge graph embedding) methods, and goes beyond. Our theoretical analysis shows that KE-GCN offers an elegant unification of several well-known GCN methods as specific cases, with a new perspective of graph convolution. Experimental results on benchmark datasets show the advantageous performance of KE-GCN over strong baseline methods in the tasks of knowledge graph alignment and entity classification.
Humans have a natural instinct to identify unknown object instances in their environments. The intrinsic curiosity about these unknown instances aids in learning about them, when the corresponding knowledge is eventually available. This motivates us to propose a novel computer vision problem called: `Open World Object Detection', where a model is tasked to: 1) identify objects that have not been introduced to it as `unknown', without explicit supervision to do so, and 2) incrementally learn these identified unknown categories without forgetting previously learned classes, when the corresponding labels are progressively received. We formulate the problem, introduce a strong evaluation protocol and provide a novel solution, which we call ORE: Open World Object Detector, based on contrastive clustering and energy based unknown identification. Our experimental evaluation and ablation studies analyze the efficacy of ORE in achieving Open World objectives. As an interesting by-product, we find that identifying and characterizing unknown instances helps to reduce confusion in an incremental object detection setting, where we achieve state-of-the-art performance, with no extra methodological effort. We hope that our work will attract further research into this newly identified, yet crucial research direction.
Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.
Graph Convolutional Networks (GCNs) and their variants have experienced significant attention and have become the de facto methods for learning graph representations. GCNs derive inspiration primarily from recent deep learning approaches, and as a result, may inherit unnecessary complexity and redundant computation. In this paper, we reduce this excess complexity through successively removing nonlinearities and collapsing weight matrices between consecutive layers. We theoretically analyze the resulting linear model and show that it corresponds to a fixed low-pass filter followed by a linear classifier. Notably, our experimental evaluation demonstrates that these simplifications do not negatively impact accuracy in many downstream applications. Moreover, the resulting model scales to larger datasets, is naturally interpretable, and yields up to two orders of magnitude speedup over FastGCN.
This paper is an attempt to explain all the matrix calculus you need in order to understand the training of deep neural networks. We assume no math knowledge beyond what you learned in calculus 1, and provide links to help you refresh the necessary math where needed. Note that you do not need to understand this material before you start learning to train and use deep learning in practice; rather, this material is for those who are already familiar with the basics of neural networks, and wish to deepen their understanding of the underlying math. Don't worry if you get stuck at some point along the way---just go back and reread the previous section, and try writing down and working through some examples. And if you're still stuck, we're happy to answer your questions in the Theory category at forums.fast.ai. Note: There is a reference section at the end of the paper summarizing all the key matrix calculus rules and terminology discussed here. See related articles at //explained.ai
We study the problem of textual relation embedding with distant supervision. To combat the wrong labeling problem of distant supervision, we propose to embed textual relations with global statistics of relations, i.e., the co-occurrence statistics of textual and knowledge base relations collected from the entire corpus. This approach turns out to be more robust to the training noise introduced by distant supervision. On a popular relation extraction dataset, we show that the learned textual relation embedding can be used to augment existing relation extraction models and significantly improve their performance. Most remarkably, for the top 1,000 relational facts discovered by the best existing model, the precision can be improved from 83.9% to 89.3%.
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