OpenRaiser/Intern-Atlas huggingface dataset:
Leveraging Chemistry Foundation Models to Facilitate Structure Focused Retrieval Augmented Generation in Multi-Agent Workflows for Catalyst and Materials Design
Venue: arXiv cs.AI 2024
Year: 2024

Molecular property prediction and generative design via deep learning models has been the subject of intense research given its potential to accelerate development of new, high-performance materials. More recently, these workflows have been significantly augmented with the advent of large language models (LLMs) and systems of autonomous agents capable of utilizing pre-trained models to make predictions in the context of more complex research tasks. While effective, there is still room for substantial improvement within agentic systems on the retrieval of salient information for material design tasks. Within this context, alternative uses of predictive deep learning models, such as leveraging their latent representations to facilitate cross-modal retrieval augmented generation within agentic systems for task-specific materials design, has remained unexplored. Herein, we demonstrate that large, pre-trained chemistry foundation models can serve as a basis for enabling structure-focused, semantic chemistry information retrieval for both small-molecules, complex polymeric materials, and reactions. Additionally, we show the use of chemistry foundation models in conjunction with multi-modal models such as OpenCLIP facilitate unprecedented queries and information retrieval across multiple characterization data domains. Finally, we demonstrate the integration of these models within multi-agent systems to facilitate structure and topological-based natural language queries and information retrieval for different research tasks.
Counting simplicial pairs in hypergraphs
Venue: arXiv cs.SI 2024
Year: 2024

We present two ways to measure the simplicial nature of a hypergraph: the simplicial ratio and the simplicial matrix. We show that the simplicial ratio captures the frequency, as well as the rarity, of simplicial interactions in a hypergraph while the simplicial matrix provides more fine-grained details. We then compute the simplicial ratio, as well as the simplicial matrix, for 10 real-world hypergraphs and, from the data collected, hypothesize that simplicial interactions are more and more deliberate as edge size increases. We then present a new Chung-Lu model that includes a parameter controlling (in expectation) the frequency of simplicial interactions. We use this new model, as well as the real-world hypergraphs, to show that multiple stochastic processes exhibit different behaviour when performed on simplicial hypergraphs vs. non-simplicial hypergraphs.
The Mechanics of Conceptual Interpretation in GPT Models: Interpretative Insights
Venue: arXiv cs.CL 2024
Year: 2024

Locating and editing knowledge in large language models (LLMs) is crucial for enhancing their accuracy, safety, and inference rationale. We introduce ``concept editing'', an innovative variation of knowledge editing that uncovers conceptualisation mechanisms within these models. Using the reverse dictionary task, inference tracing, and input abstraction, we analyse the Multi-Layer Perceptron (MLP), Multi-Head Attention (MHA), and hidden state components of transformer models. Our results reveal distinct patterns: MLP layers employ key-value retrieval mechanism and context-dependent processing, which are highly associated with relative input tokens. MHA layers demonstrate a distributed nature with significant higher-level activations, suggesting sophisticated semantic integration. Hidden states emphasise the importance of the last token and top layers in the inference process. We observe evidence of gradual information building and distributed representation. These observations elucidate how transformer models process semantic information, paving the way for targeted interventions and improved interpretability techniques. Our work highlights the complex, layered nature of semantic processing in LLMs and the challenges of isolating and modifying specific concepts within these models.
Web-based Visualization and Analytics of Petascale data: Equity as a Tide that Lifts All Boats
Venue: arXiv cs.HC 2024
Year: 2024

Scientists generate petabytes of data daily to help uncover environmental trends or behaviors that are hard to predict. For example, understanding climate simulations based on the long-term average of temperature, precipitation, and other environmental variables is essential to predicting and establishing root causes of future undesirable scenarios and assessing possible mitigation strategies. While supercomputer centers provide a powerful infrastructure for generating petabytes of simulation output, accessing and analyzing these datasets interactively remains challenging on multiple fronts. This paper presents an approach to managing, visualizing, and analyzing petabytes of data within a browser on equipment ranging from the top NASA supercomputer to commodity hardware like a laptop. Our novel data fabric abstraction layer allows user-friendly querying of scientific information while hiding the complexities of dealing with file systems or cloud services. We also optimize network utilization while streaming from petascale repositories through state-of-the-art progressive compression algorithms. Based on this abstraction, we provide customizable dashboards that can be accessed from any device with any internet connection, enabling interactive visual analysis of vast amounts of data to a wide range of users - from top scientists with access to leadership-class computing environments to undergraduate students of disadvantaged backgrounds from minority-serving institutions. We focus on NASA's use of petascale climate datasets as an example of particular societal impact and, therefore, a case where achieving equity in science participation is critical. We further validate our approach by deploying the dashboards and simplified training materials in the classroom at a minority-serving institution.
Unraveling Text Generation in LLMs: A Stochastic Differential Equation Approach
Venue: arXiv cs.LG 2024
Year: 2024

This paper explores the application of Stochastic Differential Equations (SDE) to interpret the text generation process of Large Language Models (LLMs) such as GPT-4. Text generation in LLMs is modeled as a stochastic process where each step depends on previously generated content and model parameters, sampling the next word from a vocabulary distribution. We represent this generation process using SDE to capture both deterministic trends and stochastic perturbations. The drift term describes the deterministic trends in the generation process, while the diffusion term captures the stochastic variations. We fit these functions using neural networks and validate the model on real-world text corpora. Through numerical simulations and comprehensive analyses, including drift and diffusion analysis, stochastic process property evaluation, and phase space exploration, we provide deep insights into the dynamics of text generation. This approach not only enhances the understanding of the inner workings of LLMs but also offers a novel mathematical perspective on language generation, which is crucial for diagnosing, optimizing, and controlling the quality of generated text.
Crossing New Frontiers: Knowledge-Augmented Large Language Model Prompting for Zero-Shot Text-Based De Novo Molecule Design
Venue: arXiv cs.CL 2024
Year: 2024

Molecule design is a multifaceted approach that leverages computational methods and experiments to optimize molecular properties, fast-tracking new drug discoveries, innovative material development, and more efficient chemical processes. Recently, text-based molecule design has emerged, inspired by next-generation AI tasks analogous to foundational vision-language models. Our study explores the use of knowledge-augmented prompting of large language models (LLMs) for the zero-shot text-conditional de novo molecular generation task. Our approach uses task-specific instructions and a few demonstrations to address distributional shift challenges when constructing augmented prompts for querying LLMs to generate molecules consistent with technical descriptions. Our framework proves effective, outperforming state-of-the-art (SOTA) baseline models on benchmark datasets.
Hierarchical Retrieval-Augmented Generation Model with Rethink for Multi-hop Question Answering
Venue: arXiv cs.CL 2024
Year: 2024

Multi-hop Question Answering (QA) necessitates complex reasoning by integrating multiple pieces of information to resolve intricate questions. However, existing QA systems encounter challenges such as outdated information, context window length limitations, and an accuracy-quantity trade-off. To address these issues, we propose a novel framework, the Hierarchical Retrieval-Augmented Generation Model with Rethink (HiRAG), comprising Decomposer, Definer, Retriever, Filter, and Summarizer five key modules. We introduce a new hierarchical retrieval strategy that incorporates both sparse retrieval at the document level and dense retrieval at the chunk level, effectively integrating their strengths. Additionally, we propose a single-candidate retrieval method to mitigate the limitations of multi-candidate retrieval. We also construct two new corpora, Indexed Wikicorpus and Profile Wikicorpus, to address the issues of outdated and insufficient knowledge. Our experimental results on four datasets demonstrate that HiRAG outperforms state-of-the-art models across most metrics, and our Indexed Wikicorpus is effective. The code for HiRAG is available at https://github.com/2282588541a/HiRAG
Invariants for One-Counter Automata with Disequality Tests
Venue: arXiv cs.FL 2024
Year: 2024

We study the reachability problem for one-counter automata in which transitions can carry disequality tests. A disequality test is a guard that prohibits a specified counter value. This reachability problem has been known to be NP-hard and in PSPACE, and characterising its computational complexity has been left as a challenging open question by Almagor, Cohen, Pérez, Shirmohammadi, and Worrell (2020). We reduce the complexity gap, placing the problem into the second level of the polynomial hierarchy, namely into the class $\mathsf{coNP}^{\mathsf{NP}}$. In the presence of both equality and disequality tests, our upper bound is at the third level, $\mathsf{P}^{\mathsf{NP}^{\mathsf{NP}}}$. To prove this result, we show that non-reachability can be witnessed by a pair of invariants (forward and backward). These invariants are almost inductive. They aim to over-approximate only a "core" of the reachability set instead of the entire set. The invariants are also leaky: it is possible to escape the set. We complement this with separate checks as the leaks can only occur in a controlled way.
Neural Symbolic Logical Rule Learner for Interpretable Learning
Venue: arXiv cs.LG 2024
Year: 2024

Rule-based neural networks stand out for enabling interpretable classification by learning logical rules for both prediction and interpretation. However, existing models often lack flexibility due to the fixed model structure. Addressing this, we introduce the Normal Form Rule Learner (NFRL) algorithm, leveraging a selective discrete neural network, that treat weight parameters as hard selectors, to learn rules in both Conjunctive Normal Form (CNF) and Disjunctive Normal Form (DNF) for enhanced accuracy and interpretability. Instead of adopting a deep, complex structure, the NFRL incorporates two specialized Normal Form Layers (NFLs) with adaptable AND/OR neurons, a Negation Layer for input negations, and a Normal Form Constraint (NFC) to streamline neuron connections. We also show the novel network architecture can be optimized using adaptive gradient update together with Straight-Through Estimator to overcome the gradient vanishing challenge. Through extensive experiments on 11 datasets, NFRL demonstrates superior classification performance, quality of learned rules, efficiency and interpretability compared to 12 state-of-the-art alternatives. Code and data are available at \url{https://anonymous.4open.science/r/NFRL-27B4/}.
PAL: A Variability-Aware Policy for Scheduling ML Workloads in GPU Clusters
Venue: arXiv cs.DC 2024
Year: 2024

Large-scale computing systems are increasingly using accelerators such as GPUs to enable peta- and exa-scale levels of compute to meet the needs of Machine Learning (ML) and scientific computing applications. Given the widespread and growing use of ML, including in some scientific applications, optimizing these clusters for ML workloads is particularly important. However, recent work has demonstrated that accelerators in these clusters can suffer from performance variability and this variability can lead to resource under-utilization and load imbalance. In this work we focus on how clusters schedulers, which are used to share accelerator-rich clusters across many concurrent ML jobs, can embrace performance variability to mitigate its effects. Our key insight to address this challenge is to characterize which applications are more likely to suffer from performance variability and take that into account while placing jobs on the cluster. We design a novel cluster scheduler, PAL, which uses performance variability measurements and application-specific profiles to improve job performance and resource utilization. PAL also balances performance variability with locality to ensure jobs are spread across as few nodes as possible. Overall, PAL significantly improves GPU-rich cluster scheduling: across traces for six ML workload applications spanning image, language, and vision models with a variety of variability profiles, PAL improves geomean job completion time by 42%, cluster utilization by 28%, and makespan by 47% over existing state-of-the-art schedulers.
Matmul or No Matmul in the Era of 1-bit LLMs
Venue: arXiv cs.AI 2024
Year: 2024

The advent of 1-bit large language models (LLMs) has attracted considerable attention and opened up new research opportunities. However, 1-bit LLMs only improve a fraction of models by applying extreme quantization to the projection layers while leaving attention heads unchanged. Therefore, to avoid fundamentally wrong choices of goals in future research, it is crucial to understand the actual improvements in computation and memory usage that 1-bit LLMs can deliver. In this work, we present an adaptation of Amdahl's Law tailored for the 1-bit LLM context, which illustrates how partial improvements in 1-bit LLMs impact overall model performance. Through extensive experiments, we uncover key nuances across different model architectures and hardware configurations, offering a roadmap for future research in the era of 1-bit LLMs.
Advances in Preference-based Reinforcement Learning: A Review
Venue: arXiv cs.AI 2024
Year: 2024

Reinforcement Learning (RL) algorithms suffer from the dependency on accurately engineered reward functions to properly guide the learning agents to do the required tasks. Preference-based reinforcement learning (PbRL) addresses that by utilizing human preferences as feedback from the experts instead of numeric rewards. Due to its promising advantage over traditional RL, PbRL has gained more focus in recent years with many significant advances. In this survey, we present a unified PbRL framework to include the newly emerging approaches that improve the scalability and efficiency of PbRL. In addition, we give a detailed overview of the theoretical guarantees and benchmarking work done in the field, while presenting its recent applications in complex real-world tasks. Lastly, we go over the limitations of the current approaches and the proposed future research directions.
Visual Localization in 3D Maps: Comparing Point Cloud, Mesh, and NeRF Representations
Venue: arXiv cs.CV 2024
Year: 2024

Recent advances in mapping techniques have enabled the creation of highly accurate dense 3D maps during robotic missions, such as point clouds, meshes, or NeRF-based representations. These developments present new opportunities for reusing these maps for localization. However, there remains a lack of a unified approach that can operate seamlessly across different map representations. This paper presents and evaluates a global visual localization system capable of localizing a single camera image across various 3D map representations built using both visual and lidar sensing. Our system generates a database by synthesizing novel views of the scene, creating RGB and depth image pairs. Leveraging the precise 3D geometric map, our method automatically defines rendering poses, reducing the number of database images while preserving retrieval performance. To bridge the domain gap between real query camera images and synthetic database images, our approach utilizes learning-based descriptors and feature detectors. We evaluate the system's performance through extensive real-world experiments conducted in both indoor and outdoor settings, assessing the effectiveness of each map representation and demonstrating its advantages over traditional structure-from-motion (SfM) localization approaches. The results show that all three map representations can achieve consistent localization success rates of 55% and higher across various environments. NeRF synthesized images show superior performance, localizing query images at an average success rate of 72%. Furthermore, we demonstrate an advantage over SfM-based approaches that our synthesized database enables localization in the reverse travel direction which is unseen during the mapping process. Our system, operating in real-time on a mobile laptop equipped with a GPU, achieves a processing rate of 1Hz.
Floating-Point Multiply-Add with Approximate Normalization for Low-Cost Matrix Engines
Venue: arXiv cs.AR 2024
Year: 2024

The widespread adoption of machine learning algorithms necessitates hardware acceleration to ensure efficient performance. This acceleration relies on custom matrix engines that operate on full or reduced-precision floating-point arithmetic. However, conventional floating-point implementations can be power hungry. This paper proposes a method to improve the energy efficiency of the matrix engines used in machine learning algorithm acceleration. Our approach leverages approximate normalization within the floating-point multiply-add units as a means to reduce their hardware complexity, without sacrificing overall machine-learning model accuracy. Hardware synthesis results show that this technique reduces area and power consumption roughly by 16% and 13% on average for Bfloat16 format. Also, the error introduced in transformer model accuracy is 1% on average, for the most efficient configuration of the proposed approach.
Does It Look Sequential? An Analysis of Datasets for Evaluation of Sequential Recommendations
Venue: arXiv cs.IR 2024
Year: 2024

Sequential recommender systems are an important and demanded area of research. Such systems aim to use the order of interactions in a user's history to predict future interactions. The premise is that the order of interactions and sequential patterns play an essential role. Therefore, it is crucial to use datasets that exhibit a sequential structure to evaluate sequential recommenders properly. We apply several methods based on the random shuffling of the user's sequence of interactions to assess the strength of sequential structure across 15 datasets, frequently used for sequential recommender systems evaluation in recent research papers presented at top-tier conferences. As shuffling explicitly breaks sequential dependencies inherent in datasets, we estimate the strength of sequential patterns by comparing metrics for shuffled and original versions of the dataset. Our findings show that several popular datasets have a rather weak sequential structure.
Exploring Large Language Models for Feature Selection: A Data-centric Perspective
Venue: arXiv cs.AI 2024
Year: 2024

The rapid advancement of Large Language Models (LLMs) has significantly influenced various domains, leveraging their exceptional few-shot and zero-shot learning capabilities. In this work, we aim to explore and understand the LLMs-based feature selection methods from a data-centric perspective. We begin by categorizing existing feature selection methods with LLMs into two groups: data-driven feature selection which requires numerical values of samples to do statistical inference and text-based feature selection which utilizes prior knowledge of LLMs to do semantical associations using descriptive context. We conduct experiments in both classification and regression tasks with LLMs in various sizes (e.g., GPT-4, ChatGPT and LLaMA-2). Our findings emphasize the effectiveness and robustness of text-based feature selection methods and showcase their potentials using a real-world medical application. We also discuss the challenges and future opportunities in employing LLMs for feature selection, offering insights for further research and development in this emerging field.
Golden Eye: The Theory of Havana Syndrome
Venue: arXiv cs.CY 2024
Year: 2024

Beginning around 2016, US Diplomats reported unusual injuries while serving abroad. Personnel suffered from symptoms such as nausea, vertigo, and disorientation. The collective set of ailments was subbed "Havana Syndrome". This whitepaper delves into an analysis of competing hypotheses with respect to potential origins of these symptoms. Whitepaper cleared for release on 18 JUN 2024. The views expressed by this whitepaper are those of the author and do not reflect the official policy or position of Dakota State University, the N.H. Army National Guard, the U.S. Army, the Department of Defense, or the U.S. Government.
Hell Divers: The Dark Future of Next-Gen Asymmetric Warfighting
Venue: arXiv cs.CY 2024
Year: 2024

This whitepaper was written in response to the open-to-public writing prompt hosted by the US Army Training & Doctrine Command (TRADOC) Mad Scientist Initiative. The 2024 Mad Scientist Writing Prompt called for a predictive discussion or fictional narrative regarding what the next-generation of asymmetric warfighting may look like. This follows lessons learned from historical context, current events or crises, and global uncertainty. The views expressed by this whitepaper are those of the author and do not reflect the official policy or position of Dakota State University, the N.H. Army National Guard, the U.S. Army, the Department of Defense, or the U.S. Government. The appearance of hyperlinks for academic, government, or military websites does not constitute any form of endorsement of the same. Whitepaper cleared for public release on 30 APR 2024.