We introduce a novel meta-analysis framework to combine dependent tests under a general setting, and utilize it to synthesize various microbiome association tests that are calculated from the same dataset. Our development builds upon the classical meta-analysis methods of aggregating $p$-values and also a more recent general method of combining confidence distributions, but makes generalizations to handle dependent tests. The proposed framework ensures rigorous statistical guarantees, and we provide a comprehensive study and compare it with various existing dependent combination methods. Notably, we demonstrate that the widely used Cauchy combination method for dependent tests, referred to as the vanilla Cauchy combination in this article, can be viewed as a special case within our framework. Moreover, the proposed framework provides a way to address the problem when the distributional assumptions underlying the vanilla Cauchy combination are violated. Our numerical results demonstrate that ignoring the dependence among the to-be-combined components may lead to a severe size distortion phenomenon. Compared to the existing $p$-value combination methods, including the vanilla Cauchy combination method, the proposed combination framework can handle the dependence accurately and utilizes the information efficiently to construct tests with accurate size and enhanced power. The development is applied to Microbiome Association Studies, where we aggregate information from multiple existing tests using the same dataset. The combined tests harness the strengths of each individual test across a wide range of alternative spaces, %resulting in a significant enhancement of testing power across a wide range of alternative spaces, enabling more efficient and meaningful discoveries of vital microbiome associations.
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Instructing the model to generate a sequence of intermediate steps, a.k.a., a chain of thought (CoT), is a highly effective method to improve the accuracy of large language models (LLMs) on arithmetics and symbolic reasoning tasks. However, the mechanism behind CoT remains unclear. This work provides a theoretical understanding of the power of CoT for decoder-only transformers through the lens of expressiveness. Conceptually, CoT empowers the model with the ability to perform inherently serial computation, which is otherwise lacking in transformers, especially when depth is low. Given input length $n$, previous works have shown that constant-depth transformers with finite precision $\mathsf{poly}(n)$ embedding size can only solve problems in $\mathsf{TC}^0$ without CoT. We first show an even tighter expressiveness upper bound for constant-depth transformers with constant-bit precision, which can only solve problems in $\mathsf{AC}^0$, a proper subset of $ \mathsf{TC}^0$. However, with $T$ steps of CoT, constant-depth transformers using constant-bit precision and $O(\log n)$ embedding size can solve any problem solvable by boolean circuits of size $T$. Empirically, enabling CoT dramatically improves the accuracy for tasks that are hard for parallel computation, including the composition of permutation groups, iterated squaring, and circuit value problems, especially for low-depth transformers.
In a context of a continuous digitalisation of processes, organisations must deal with the challenge of detecting anomalies that can reveal suspicious activities upon an increasing volume of data. To pursue this goal, audit engagements are carried out regularly, and internal auditors and purchase specialists are constantly looking for new methods to automate these processes. This work proposes a methodology to prioritise the investigation of the cases detected in two large purchase datasets from real data. The goal is to contribute to the effectiveness of the companies' control efforts and to increase the performance of carrying out such tasks. A comprehensive Exploratory Data Analysis is carried out before using unsupervised Machine Learning techniques addressed to detect anomalies. A univariate approach has been applied through the z-Score index and the DBSCAN algorithm, while a multivariate analysis is implemented with the k-Means and Isolation Forest algorithms, and the Silhouette index, resulting in each method having a transaction candidates' proposal to be reviewed. An ensemble prioritisation of the candidates is provided jointly with a proposal of explicability methods (LIME, Shapley, SHAP) to help the company specialists in their understanding.
Generative modeling over discrete data has recently seen numerous success stories, with applications spanning language modeling, biological sequence design, and graph-structured molecular data. The predominant generative modeling paradigm for discrete data is still autoregressive, with more recent alternatives based on diffusion or flow-matching falling short of their impressive performance in continuous data settings, such as image or video generation. In this work, we introduce Fisher-Flow, a novel flow-matching model for discrete data. Fisher-Flow takes a manifestly geometric perspective by considering categorical distributions over discrete data as points residing on a statistical manifold equipped with its natural Riemannian metric: the $\textit{Fisher-Rao metric}$. As a result, we demonstrate discrete data itself can be continuously reparameterised to points on the positive orthant of the $d$-hypersphere $\mathbb{S}^d_+$, which allows us to define flows that map any source distribution to target in a principled manner by transporting mass along (closed-form) geodesics of $\mathbb{S}^d_+$. Furthermore, the learned flows in Fisher-Flow can be further bootstrapped by leveraging Riemannian optimal transport leading to improved training dynamics. We prove that the gradient flow induced by Fisher-Flow is optimal in reducing the forward KL divergence. We evaluate Fisher-Flow on an array of synthetic and diverse real-world benchmarks, including designing DNA Promoter, and DNA Enhancer sequences. Empirically, we find that Fisher-Flow improves over prior diffusion and flow-matching models on these benchmarks.
In knowledge graph construction, a challenging issue is how to extract complex (e.g., overlapping) entities and relationships from a small amount of unstructured historical data. The traditional pipeline methods are to divide the extraction into two separate subtasks, which misses the potential interaction between the two subtasks and may lead to error propagation. In this work, we propose an effective cascade dual-decoder method to extract overlapping relational triples, which includes a text-specific relation decoder and a relation-corresponded entity decoder. Our approach is straightforward and it includes a text-specific relation decoder and a relation-corresponded entity decoder. The text-specific relation decoder detects relations from a sentence at the text level. That is, it does this according to the semantic information of the whole sentence. For each extracted relation, which is with trainable embedding, the relation-corresponded entity decoder detects the corresponding head and tail entities using a span-based tagging scheme. In this way, the overlapping triple problem can be tackled naturally. We conducted experiments on a real-world open-pit mine dataset and two public datasets to verify the method's generalizability. The experimental results demonstrate the effectiveness and competitiveness of our proposed method and achieve better F1 scores under strict evaluation metrics. Our implementation is available at //github.com/prastunlp/DualDec.
We present a novel framework to explore neural control and design of complex fluidic systems with dynamic solid boundaries. Our system features a fast differentiable Navier-Stokes solver with solid-fluid interface handling, a low-dimensional differentiable parametric geometry representation, a control-shape co-design algorithm, and gym-like simulation environments to facilitate various fluidic control design applications. Additionally, we present a benchmark of design, control, and learning tasks on high-fidelity, high-resolution dynamic fluid environments that pose challenges for existing differentiable fluid simulators. These tasks include designing the control of artificial hearts, identifying robotic end-effector shapes, and controlling a fluid gate. By seamlessly incorporating our differentiable fluid simulator into a learning framework, we demonstrate successful design, control, and learning results that surpass gradient-free solutions in these benchmark tasks.
This paper studies a variant of the rate-distortion problem motivated by task-oriented semantic communication and distributed learning problems, where $M$ correlated sources are independently encoded for a central decoder. The decoder has access to a correlated side information in addition to the messages received from the encoders, and aims to recover a latent random variable correlated with the sources observed by the encoders within a given distortion constraint rather than recovering the sources themselves. We provide bounds on the rate-distortion region for this scenario in general, and characterize the rate-distortion function exactly when the sources are conditionally independent given the side information.
Reinforcement learning (RL) provides a compelling framework for enabling autonomous vehicles to continue to learn and improve diverse driving behaviors on their own. However, training real-world autonomous vehicles with current RL algorithms presents several challenges. One critical challenge, often overlooked in these algorithms, is the need to reset a driving environment between every episode. While resetting an environment after each episode is trivial in simulated settings, it demands significant human intervention in the real world. In this paper, we introduce a novel autonomous algorithm that allows off-the-shelf RL algorithms to train an autonomous vehicle with minimal human intervention. Our algorithm takes into account the learning progress of the autonomous vehicle to determine when to abort episodes before it enters unsafe states and where to reset it for subsequent episodes in order to gather informative transitions. The learning progress is estimated based on the novelty of both current and future states. We also take advantage of rule-based autonomous driving algorithms to safely reset an autonomous vehicle to an initial state. We evaluate our algorithm against baselines on diverse urban driving tasks. The experimental results show that our algorithm is task-agnostic and achieves better driving performance with fewer manual resets than baselines.
We introduce a multi-task setup of identifying and classifying entities, relations, and coreference clusters in scientific articles. We create SciERC, a dataset that includes annotations for all three tasks and develop a unified framework called Scientific Information Extractor (SciIE) for with shared span representations. The multi-task setup reduces cascading errors between tasks and leverages cross-sentence relations through coreference links. Experiments show that our multi-task model outperforms previous models in scientific information extraction without using any domain-specific features. We further show that the framework supports construction of a scientific knowledge graph, which we use to analyze information in scientific literature.
We propose a new method for event extraction (EE) task based on an imitation learning framework, specifically, inverse reinforcement learning (IRL) via generative adversarial network (GAN). The GAN estimates proper rewards according to the difference between the actions committed by the expert (or ground truth) and the agent among complicated states in the environment. EE task benefits from these dynamic rewards because instances and labels yield to various extents of difficulty and the gains are expected to be diverse -- e.g., an ambiguous but correctly detected trigger or argument should receive high gains -- while the traditional RL models usually neglect such differences and pay equal attention on all instances. Moreover, our experiments also demonstrate that the proposed framework outperforms state-of-the-art methods, without explicit feature engineering.
We introduce a generic framework that reduces the computational cost of object detection while retaining accuracy for scenarios where objects with varied sizes appear in high resolution images. Detection progresses in a coarse-to-fine manner, first on a down-sampled version of the image and then on a sequence of higher resolution regions identified as likely to improve the detection accuracy. Built upon reinforcement learning, our approach consists of a model (R-net) that uses coarse detection results to predict the potential accuracy gain for analyzing a region at a higher resolution and another model (Q-net) that sequentially selects regions to zoom in. Experiments on the Caltech Pedestrians dataset show that our approach reduces the number of processed pixels by over 50% without a drop in detection accuracy. The merits of our approach become more significant on a high resolution test set collected from YFCC100M dataset, where our approach maintains high detection performance while reducing the number of processed pixels by about 70% and the detection time by over 50%.
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