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Difficulties in replication and reproducibility of empirical evidences in machine learning research have become a prominent topic in recent years. Ensuring that machine learning research results are sound and reliable requires reproducibility, which verifies the reliability of research findings using the same code and data. This promotes open and accessible research, robust experimental workflows, and the rapid integration of new findings. Evaluating the degree to which research publications support these different aspects of reproducibility is one goal of the present work. For this we introduce an ontology of reproducibility in machine learning and apply it to methods for graph neural networks. Building on these efforts we turn towards another critical challenge in machine learning, namely the curse of dimensionality, which poses challenges in data collection, representation, and analysis, making it harder to find representative data and impeding the training and inference processes. Using the closely linked concept of geometric intrinsic dimension we investigate to which extend the used machine learning models are influenced by the intrinsic dimension of the data sets they are trained on.

Recent advancements in NLP have witnessed the groundbreaking impact of pretrained models, yielding impressive outcomes across various tasks. This study seeks to extend the power of pretraining methodologies to facilitating the prediction over tables in data science, a domain traditionally overlooked, yet inherently challenging due to the plethora of table schemas intrinsic to different tasks. The primary research questions underpinning this work revolve around the establishment of a universal pretraining protocol for tables with varied structures, the generalizability and transferability of learned knowledge across tasks, the adaptation to diverse downstream applications, and the incorporation of incremental columns over time. In response to these challenges, we introduce UniTabE, a straightforward yet effective method designed to process tables in a uniform manner, devoid of constraints imposed by specific table structures. UniTabE's core concept relies on representing each basic table element with a module, termed TabUnit. This is subsequently followed by a Transformer encoder to refine the representation. Moreover, our model is designed to facilitate pretraining and finetuning through the utilization of free-form prompts. In order to implement the pretraining phase, we curated an expansive tabular dataset comprising approximately 13B samples, meticulously gathered from the Kaggle platform. This research primarily centers on classification and regression tasks involving tabular data, and conducts rigorous experimental testing and analyses to validate the effectiveness of our methodology. The experimental results demonstrate UniTabE's superior performance against several baselines across massive benchmarks. This, therefore, underscores UniTabE's potential to significantly enhance the semantic representation of tabular data, thereby marking a significant stride for tabular data analysis.

Rapid advances in perception have enabled large pre-trained models to be used out of the box for processing high-dimensional, noisy, and partial observations of the world into rich geometric representations (e.g., occupancy predictions). However, safe integration of these models onto robots remains challenging due to a lack of reliable performance in unfamiliar environments. In this work, we present a framework for rigorously quantifying the uncertainty of pre-trained perception models for occupancy prediction in order to provide end-to-end statistical safety assurances for navigation. We build on techniques from conformal prediction for producing a calibrated perception system that lightly processes the outputs of a pre-trained model while ensuring generalization to novel environments and robustness to distribution shifts in states when perceptual outputs are used in conjunction with a planner. The calibrated system can be used in combination with any safe planner to provide an end-to-end statistical assurance on safety in a new environment with a user-specified threshold $1-\epsilon$. We evaluate the resulting approach - which we refer to as Perceive with Confidence (PwC) - with experiments in simulation and on hardware where a quadruped robot navigates through indoor environments containing objects unseen during training or calibration. These experiments validate the safety assurances provided by PwC and demonstrate significant improvements in empirical safety rates compared to baselines.

Recent advances in instruction-tuned Large Vision-Language Models (LVLMs) have imbued the models with the ability to generate high-level, image-grounded explanations with ease. While such capability is largely attributed to the rich world knowledge contained within the Large Language Models (LLMs), our work reveals their shortcomings in fine-grained visual categorization (FGVC) across six different benchmark settings. Most recent state-of-the-art LVLMs like LLaVa-1.5, InstructBLIP and GPT-4V not only severely deteriorate in terms of classification performance, e.g., average drop of 65.58 in EM for Stanford Dogs for LLaVA-1.5, but also struggle to generate an accurate explanation with detailed attributes based on the concept that appears within an input image despite their capability to generate holistic image-level descriptions. In-depth analyses show that instruction-tuned LVLMs exhibit modality gap, showing discrepancy when given textual and visual inputs that correspond to the same concept, preventing the image modality from leveraging the rich parametric knowledge within the LLMs. In an effort to further the community's endeavor in this direction, we propose a multiple granularity attribute-centric evaluation benchmark, Finer, which aims to establish a ground to evaluate LVLMs' fine-grained visual comprehension ability and provide significantly improved explainability.

The fractal dimension of a surface allows its degree of roughness to be characterized quantitatively. However, limited effort is attempted to calculate the fractal dimension of surfaces computed from precisely known atomic coordinates from computational biomolecular and nanomaterial studies. This work proposes methods to estimate the fractal dimension of the surface of any 3D object composed of spheres, by representing the surface as either a voxelized point cloud or a mathematically exact surface, and computing its box-counting dimension. Sphractal is published as a Python package that provides these functionalities, and its utility is demonstrated on a set of simulated palladium nanoparticle data.

This paper presents hybrid numerical techniques for solving the Boltzmann transport equation formulated by means of low-order equations for angular moments of the angular flux. The moment equations are derived by the projection operator approach. The projected equations are closed exactly using a high-order transport solution. The low-order equations of the hybrid methods are approximated with a finite volume scheme of the second-order accuracy. Functionals defining the closures in the discretized low-order equations are calculated by Monte Carlo techniques. In this study, we analyze effects of statistical noise and discretization error on the accuracy of the hybrid transport solution.

In the big data era, the need to reevaluate traditional statistical methods is paramount due to the challenges posed by vast datasets. While larger samples theoretically enhance accuracy and hypothesis testing power without increasing false positives, practical concerns about inflated Type-I errors persist. The prevalent belief is that larger samples can uncover subtle effects, necessitating dual consideration of p-value and effect size. Yet, the reliability of p-values from large samples remains debated. This paper warns that larger samples can exacerbate minor issues into significant errors, leading to false conclusions. Through our simulation study, we demonstrate how growing sample sizes amplify issues arising from two commonly encountered violations of model assumptions in real-world data and lead to incorrect decisions. This underscores the need for vigilant analytical approaches in the era of big data. In response, we introduce a permutation-based test to counterbalance the effects of sample size and assumption discrepancies by neutralizing them between actual and permuted data. We demonstrate that this approach effectively stabilizes nominal Type I error rates across various sample sizes, thereby ensuring robust statistical inferences even amidst breached conventional assumptions in big data. For reproducibility, our R codes are publicly available at: \url{//github.com/ubcxzhang/bigDataIssue}.

Ensuring alignment, which refers to making models behave in accordance with human intentions [1,2], has become a critical task before deploying large language models (LLMs) in real-world applications. For instance, OpenAI devoted six months to iteratively aligning GPT-4 before its release [3]. However, a major challenge faced by practitioners is the lack of clear guidance on evaluating whether LLM outputs align with social norms, values, and regulations. This obstacle hinders systematic iteration and deployment of LLMs. To address this issue, this paper presents a comprehensive survey of key dimensions that are crucial to consider when assessing LLM trustworthiness. The survey covers seven major categories of LLM trustworthiness: reliability, safety, fairness, resistance to misuse, explainability and reasoning, adherence to social norms, and robustness. Each major category is further divided into several sub-categories, resulting in a total of 29 sub-categories. Additionally, a subset of 8 sub-categories is selected for further investigation, where corresponding measurement studies are designed and conducted on several widely-used LLMs. The measurement results indicate that, in general, more aligned models tend to perform better in terms of overall trustworthiness. However, the effectiveness of alignment varies across the different trustworthiness categories considered. This highlights the importance of conducting more fine-grained analyses, testing, and making continuous improvements on LLM alignment. By shedding light on these key dimensions of LLM trustworthiness, this paper aims to provide valuable insights and guidance to practitioners in the field. Understanding and addressing these concerns will be crucial in achieving reliable and ethically sound deployment of LLMs in various applications.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

With the advances of data-driven machine learning research, a wide variety of prediction problems have been tackled. It has become critical to explore how machine learning and specifically deep learning methods can be exploited to analyse healthcare data. A major limitation of existing methods has been the focus on grid-like data; however, the structure of physiological recordings are often irregular and unordered which makes it difficult to conceptualise them as a matrix. As such, graph neural networks have attracted significant attention by exploiting implicit information that resides in a biological system, with interactive nodes connected by edges whose weights can be either temporal associations or anatomical junctions. In this survey, we thoroughly review the different types of graph architectures and their applications in healthcare. We provide an overview of these methods in a systematic manner, organized by their domain of application including functional connectivity, anatomical structure and electrical-based analysis. We also outline the limitations of existing techniques and discuss potential directions for future research.