OpenRaiser/Intern-Atlas huggingface dataset:
Tokenizing 3D Molecule Structure with Quantized Spherical Coordinates
Venue: arXiv cs.LG 2024
Year: 2024

The application of language models (LMs) to molecular structure generation using line notations such as SMILES and SELFIES has been well-established in the field of cheminformatics. However, extending these models to generate 3D molecular structures presents significant challenges. Two primary obstacles emerge: (1) the difficulty in designing a 3D line notation that ensures SE(3)-invariant atomic coordinates, and (2) the non-trivial task of tokenizing continuous coordinates for use in LMs, which inherently require discrete inputs. To address these challenges, we propose Mol-StrucTok, a novel method for tokenizing 3D molecular structures. Our approach comprises two key innovations: (1) We design a line notation for 3D molecules by extracting local atomic coordinates in a spherical coordinate system. This notation builds upon existing 2D line notations and remains agnostic to their specific forms, ensuring compatibility with various molecular representation schemes. (2) We employ a Vector Quantized Variational Autoencoder (VQ-VAE) to tokenize these coordinates, treating them as generation descriptors. To further enhance the representation, we incorporate neighborhood bond lengths and bond angles as understanding descriptors. Leveraging this tokenization framework, we train a GPT-2 style model for 3D molecular generation tasks. Results demonstrate strong performance with significantly faster generation speeds and competitive chemical stability compared to previous methods. Further, by integrating our learned discrete representations into Graphormer model for property prediction on QM9 dataset, Mol-StrucTok reveals consistent improvements across various molecular properties, underscoring the versatility and robustness of our approach.
FairML: A Julia Package for Fair Classification
Venue: arXiv cs.LG 2024
Year: 2024

In this paper, we propose FairML.jl, a Julia package providing a framework for fair classification in machine learning. In this framework, the fair learning process is divided into three stages. Each stage aims to reduce unfairness, such as disparate impact and disparate mistreatment, in the final prediction. For the preprocessing stage, we present a resampling method that addresses unfairness coming from data imbalances. The in-processing phase consist of a classification method. This can be either one coming from the MLJ.jl package, or a user defined one. For this phase, we incorporate fair ML methods that can handle unfairness to a certain degree through their optimization process. In the post-processing, we discuss the choice of the cut-off value for fair prediction. With simulations, we show the performance of the single phases and their combinations.
NCDD: Nearest Centroid Distance Deficit for Out-Of-Distribution Detection in Gastrointestinal Vision
Venue: arXiv cs.CV 2024
Year: 2024

The integration of deep learning tools in gastrointestinal vision holds the potential for significant advancements in diagnosis, treatment, and overall patient care. A major challenge, however, is these tools' tendency to make overconfident predictions, even when encountering unseen or newly emerging disease patterns, undermining their reliability. We address this critical issue of reliability by framing it as an out-of-distribution (OOD) detection problem, where previously unseen and emerging diseases are identified as OOD examples. However, gastrointestinal images pose a unique challenge due to the overlapping feature representations between in- Distribution (ID) and OOD examples. Existing approaches often overlook this characteristic, as they are primarily developed for natural image datasets, where feature distinctions are more apparent. Despite the overlap, we hypothesize that the features of an in-distribution example will cluster closer to the centroids of their ground truth class, resulting in a shorter distance to the nearest centroid. In contrast, OOD examples maintain an equal distance from all class centroids. Based on this observation, we propose a novel nearest-centroid distance deficit (NCCD) score in the feature space for gastrointestinal OOD detection. Evaluations across multiple deep learning architectures and two publicly available benchmarks, Kvasir2 and Gastrovision, demonstrate the effectiveness of our approach compared to several state-of-the-art methods. The code and implementation details are publicly available at: https://github.com/bhattarailab/NCDD
FEVER-OOD: Free Energy Vulnerability Elimination for Robust Out-of-Distribution Detection
Venue: arXiv cs.CV 2024
Year: 2024

Modern machine learning models, that excel on computer vision tasks such as classification and object detection, are often overconfident in their predictions for Out-of-Distribution (OOD) examples, resulting in unpredictable behaviour for open-set environments. Recent works have demonstrated that the free energy score is an effective measure of uncertainty for OOD detection given its close relationship to the data distribution. However, despite free energy-based methods representing a significant empirical advance in OOD detection, our theoretical analysis reveals previously unexplored and inherent vulnerabilities within the free energy score formulation such that in-distribution and OOD instances can have distinct feature representations yet identical free energy scores. This phenomenon occurs when the vector direction representing the feature space difference between the in-distribution and OOD sample lies within the null space of the last layer of a neural-based classifier. To mitigate these issues, we explore lower-dimensional feature spaces to reduce the null space footprint and introduce novel regularisation to maximize the least singular value of the final linear layer, hence enhancing inter-sample free energy separation. We refer to these techniques as Free Energy Vulnerability Elimination for Robust Out-of-Distribution Detection (FEVER-OOD). Our experiments show that FEVER-OOD techniques achieve state of the art OOD detection in Imagenet-100, with average OOD false positive rate (at 95% true positive rate) of 35.83% when used with the baseline Dream-OOD model.
Review of Mathematical Optimization in Federated Learning
Venue: arXiv cs.LG 2024
Year: 2024

Federated Learning (FL) has been becoming a popular interdisciplinary research area in both applied mathematics and information sciences. Mathematically, FL aims to collaboratively optimize aggregate objective functions over distributed datasets while satisfying a variety of privacy and system constraints.Different from conventional distributed optimization methods, FL needs to address several specific issues (e.g., non-i.i.d. data distributions and differential private noises), which pose a set of new challenges in the problem formulation, algorithm design, and convergence analysis. In this paper, we will systematically review existing FL optimization research including their assumptions, formulations, methods, and theoretical results. Potential future directions are also discussed.
Uncertainty-Aware Regularization for Image-to-Image Translation
Venue: arXiv cs.CV 2024
Year: 2024

The importance of quantifying uncertainty in deep networks has become paramount for reliable real-world applications. In this paper, we propose a method to improve uncertainty estimation in medical Image-to-Image (I2I) translation. Our model integrates aleatoric uncertainty and employs Uncertainty-Aware Regularization (UAR) inspired by simple priors to refine uncertainty estimates and enhance reconstruction quality. We show that by leveraging simple priors on parameters, our approach captures more robust uncertainty maps, effectively refining them to indicate precisely where the network encounters difficulties, while being less affected by noise. Our experiments demonstrate that UAR not only improves translation performance, but also provides better uncertainty estimations, particularly in the presence of noise and artifacts. We validate our approach using two medical imaging datasets, showcasing its effectiveness in maintaining high confidence in familiar regions while accurately identifying areas of uncertainty in novel/ambiguous scenarios.
Bisequent Calculi for Neutral Free Logic with Definite Descriptions
Venue: arXiv cs.LO 2024
Year: 2024

We present a bisequent calculus (BSC) for the minimal theory of definite descriptions (DD) in the setting of neutral free logic, where formulae with non-denoting terms have no truth value. The treatment of quantifiers, atomic formulae and simple terms is based on the approach developed by Pavlović and Gratzl. We extend their results to the version with identity and definite descriptions. In particular, the admissibility of cut is proven for this extended system.
Correspondence and Inverse Correspondence for Input/Output Logic and Region-Based Theories of Space
Venue: arXiv cs.LO 2024
Year: 2024

We further develop the algebraic approach to input/output logic initiated in \cite{wollic22}, where subordination algebras and a family of their generalizations were proposed as a semantic environment of various input/output logics. In particular: we extend the modal characterizations of a finite number of well known conditions on normative and permission systems, as well as on subordination, precontact, and dual precontact algebras developed in \cite{de2024obligations}, to those corresponding to the infinite class of {\em clopen-analytic inequalities} in a modal language consisting both of positive and of negative unary modal operators; we characterize the syntactic shape of first-order conditions on algebras endowed with subordination, precontact, and dual precontact relations which guarantees these conditions to be the first-order correspondents of axioms in the modal language above; we introduce algorithms for computing the first-order correspondents of modal axioms on algebras endowed with subordination, precontact, and dual precontact relations, and conversely, for computing the modal axioms of which the conditions satisfying the suitable syntactic shape are the first-order correspondents; finally, we extend Celani's dual characterization results between subordination lattices and subordination spaces to a wider environment which also encompasses precontact and dual precontact relations, and relative to an infinite class of first order conditions relating subordination, precontact and dual precontact relations on distributive lattices. The modal characterizations established in the present paper pave the way to establishing faithful embeddings for infinite classes of input/output logics, and hence to their implementation in LogiKEy, Isabelle/HOL, Lean, or other interactive systems.
Continuous-Time Human Motion Field from Events
Venue: arXiv cs.CV 2024
Year: 2024

This paper addresses the challenges of estimating a continuous-time human motion field from a stream of events. Existing Human Mesh Recovery (HMR) methods rely predominantly on frame-based approaches, which are prone to aliasing and inaccuracies due to limited temporal resolution and motion blur. In this work, we predict a continuous-time human motion field directly from events by leveraging a recurrent feed-forward neural network to predict human motion in the latent space of possible human motions. Prior state-of-the-art event-based methods rely on computationally intensive optimization across a fixed number of poses at high frame rates, which becomes prohibitively expensive as we increase the temporal resolution. In comparison, we present the first work that replaces traditional discrete-time predictions with a continuous human motion field represented as a time-implicit function, enabling parallel pose queries at arbitrary temporal resolutions. Despite the promises of event cameras, few benchmarks have tested the limit of high-speed human motion estimation. We introduce Beam-splitter Event Agile Human Motion Dataset-a hardware-synchronized high-speed human dataset to fill this gap. On this new data, our method improves joint errors by 23.8% compared to previous event human methods while reducing the computational time by 69%.
Dynamics of Resource Allocation in O-RANs: An In-depth Exploration of On-Policy and Off-Policy Deep Reinforcement Learning for Real-Time Applications
Venue: arXiv cs.NI 2024
Year: 2024

Deep Reinforcement Learning (DRL) is a powerful tool used for addressing complex challenges in mobile networks. This paper investigates the application of two DRL models, on-policy and off-policy, in the field of resource allocation for Open Radio Access Networks (O-RAN). The on-policy model is the Proximal Policy Optimization (PPO), and the off-policy model is the Sample Efficient Actor-Critic with Experience Replay (ACER), which focuses on resolving the challenges of resource allocation associated with a Quality of Service (QoS) application that has strict requirements. Motivated by the original work of Nessrine Hammami and Kim Khoa Nguyen, this study is a replication to validate and prove the findings. Both PPO and ACER are used within the same experimental setup to assess their performance in a scenario of latency-sensitive and latency-tolerant users and compare them. The aim is to verify the efficacy of on-policy and off-policy DRL models in the context of O-RAN resource allocation. Results from this replication contribute to the ongoing scientific research and offer insights into the reproducibility and generalizability of the original research. This analysis reaffirms that both on-policy and off-policy DRL models have better performance than greedy algorithms in O-RAN settings. In addition, it confirms the original observations that the on-policy model (PPO) gives a favorable balance between energy consumption and user latency, while the off-policy model (ACER) shows a faster convergence. These findings give good insights to optimize resource allocation strategies in O-RANs. Index Terms: 5G, O-RAN, resource allocation, ML, DRL, PPO, ACER.
Communication efficient application of sequences of planar rotations to a matrix
Venue: arXiv cs.PF 2024
Year: 2024

We present an efficient algorithm for the application of sequences of planar rotations to a matrix. Applying such sequences efficiently is important in many numerical linear algebra algorithms for eigenvalues. Our algorithm is novel in three main ways. First, we introduce a new kernel that is optimized for register reuse in a novel way. Second, we introduce a blocking and packing scheme that improves the cache efficiency of the algorithm. Finally, we thoroughly analyze the memory operations of the algorithm which leads to important theoretical insights and makes it easier to select good parameters. Numerical experiments show that our algorithm outperforms the state-of-the-art and achieves a flop rate close to the theoretical peak on modern hardware.
Recurrent Neural Network on PICTURE Model
Venue: arXiv cs.AI 2024
Year: 2024

Intensive Care Units (ICUs) provide critical care and life support for most severely ill and injured patients in the hospital. With the need for ICUs growing rapidly and unprecedentedly, especially during COVID-19, accurately identifying the most critical patients helps hospitals to allocate resources more efficiently and save more lives. The Predicting Intensive Care Transfers and Other Unforeseen Events (PICTURE) model predicts patient deterioration by separating those at high risk for imminent intensive care unit transfer, respiratory failure, or death from those at lower risk. This study aims to implement a deep learning model to benchmark the performance from the XGBoost model, an existing model which has competitive results on prediction.
A Shared Standard for Valid Measurement of Generative AI Systems' Capabilities, Risks, and Impacts
Venue: arXiv cs.CY 2024
Year: 2024

The valid measurement of generative AI (GenAI) systems' capabilities, risks, and impacts forms the bedrock of our ability to evaluate these systems. We introduce a shared standard for valid measurement that helps place many of the disparate-seeming evaluation practices in use today on a common footing. Our framework, grounded in measurement theory from the social sciences, extends the work of Adcock & Collier (2001) in which the authors formalized valid measurement of concepts in political science via three processes: systematizing background concepts, operationalizing systematized concepts via annotation procedures, and applying those procedures to instances. We argue that valid measurement of GenAI systems' capabilities, risks, and impacts, further requires systematizing, operationalizing, and applying not only the entailed concepts, but also the contexts of interest and the metrics used. This involves both descriptive reasoning about particular instances and inferential reasoning about underlying populations, which is the purview of statistics. By placing many disparate-seeming GenAI evaluation practices on a common footing, our framework enables individual evaluations to be better understood, interrogated for reliability and validity, and meaningfully compared. This is an important step in advancing GenAI evaluation practices toward more formalized and theoretically grounded processes -- i.e., toward a science of GenAI evaluations.
Geometry-aware PINNs for Turbulent Flow Prediction
Venue: arXiv cs.LG 2024
Year: 2024

Design exploration or optimization using computational fluid dynamics (CFD) is commonly used in the industry. Geometric variation is a key component of such design problems, especially in turbulent flow scenarios, which involves running costly simulations at every design iteration. While parametric RANS-PINN type approaches have been proven to make effective turbulent surrogates, as a means of predicting unknown Reynolds number flows for a given geometry at near real-time, geometry aware physics informed surrogates with the ability to predict varying geometries are a relatively less studied topic. A novel geometry aware parametric PINN surrogate model has been created, which can predict flow fields for NACA 4 digit airfoils in turbulent conditions, for unseen shapes as well as inlet flow conditions. A local+global approach for embedding has been proposed, where known global design parameters for an airfoil as well as local SDF values can be used as inputs to the model along with velocity inlet/Reynolds number ($\mathcal{R}_e$) to predict the flow fields. A RANS formulation of the Navier-Stokes equations with a 2-equation k-epsilon turbulence model has been used for the PDE losses, in addition to limited CFD data from 8 different NACA airfoils for training. The models have then been validated with unknown NACA airfoils at unseen Reynolds numbers.
BN-AuthProf: Benchmarking Machine Learning for Bangla Author Profiling on Social Media Texts
Venue: arXiv cs.CL 2024
Year: 2024

Author profiling, the analysis of texts to uncover attributes such as gender and age of the author, has become essential with the widespread use of social media platforms. This paper focuses on author profiling in the Bangla language, aiming to extract valuable insights about anonymous authors based on their writing style on social media. The primary objective is to introduce and benchmark the performance of machine learning approaches on a newly created Bangla Author Profiling dataset, BN-AuthProf. The dataset comprises 30,131 social media posts from 300 authors, labeled by their age and gender. Authors' identities and sensitive information were anonymized to ensure privacy. Various classical machine learning and deep learning techniques were employed to evaluate the dataset. For gender classification, the best accuracy achieved was 80% using Support Vector Machine (SVM), while a Multinomial Naive Bayes (MNB) classifier achieved the best F1 score of 0.756. For age classification, MNB attained a maximum accuracy score of 91% with an F1 score of 0.905. This research highlights the effectiveness of machine learning in gender and age classification for Bangla author profiling, with practical implications spanning marketing, security, forensic linguistics, education, and criminal investigations, considering privacy and biases.
Comparative Analysis of Black-Box and White-Box Machine Learning Model in Phishing Detection
Venue: arXiv cs.CR 2024
Year: 2024

Background: Explainability in phishing detection model can support a further solution of phishing attack mitigation by increasing trust and understanding how phishing can be detected. Objective: The aims of this study to determine and best recommendation to apply an approach which has several components with abilities to fulfil the critical needs Methods: A methodology starting with analyzing both black-box and white-box models to get the pros and cons specifically in phishing detection. The conclusion of the analysis will be validated by experiment using a set of well-known algorithms and public phishing datasets. Experimental metrics covers 3 measurements such as predictive accuracy and explainability metrics. Conclusion: Both models are comparable in terms of interpretability and consistency, with room for improvement in diverse datasets. EBM as an example of white-box model is generally better suited for applications requiring explainability and actionable insights. Finally, each model, white-box and black-box model has positive and negative aspects both for performance metric and for explainable metric. It is important to consider the objective of model usage.
Leveraging Large Language Models for Comparative Literature Summarization with Reflective Incremental Mechanisms
Venue: arXiv cs.CL 2024
Year: 2024

In this paper, we introduce ChatCite, a novel method leveraging large language models (LLMs) for generating comparative literature summaries. The ability to summarize research papers with a focus on key comparisons between studies is an essential task in academic research. Existing summarization models, while effective at generating concise summaries, fail to provide deep comparative insights. ChatCite addresses this limitation by incorporating a multi-step reasoning mechanism that extracts critical elements from papers, incrementally builds a comparative summary, and refines the output through a reflective memory process. We evaluate ChatCite on a custom dataset, CompLit-LongContext, consisting of 1000 research papers with annotated comparative summaries. Experimental results show that ChatCite outperforms several baseline methods, including GPT-4, BART, T5, and CoT, across various automatic evaluation metrics such as ROUGE and the newly proposed G-Score. Human evaluation further confirms that ChatCite generates more coherent, insightful, and fluent summaries compared to these baseline models. Our method provides a significant advancement in automatic literature review generation, offering researchers a powerful tool for efficiently comparing and synthesizing scientific research.