Reflections from the 2024 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry

Here, we present the outcomes from the second Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry, which engaged participants across global hybrid locations, resulting in 34 team submissions. The submissions spanned seven key application areas and demonstrated the diverse utility of LLMs for applications in (1) molecular and material property prediction; (2) molecular and material design; (3) automation and novel interfaces; (4) scientific communication and education; (5) research data management and automation; (6) hypothesis generation and evaluation; and (7) knowledge extraction and reasoning from scientific literature. Each team submission is presented in a summary table with links to the code and as brief papers in the appendix. Beyond team results, we discuss the hackathon event and its hybrid format, which included physical hubs in Toronto, Montreal, San Francisco, Berlin, Lausanne, and Tokyo, alongside a global online hub to enable local and virtual collaboration. Overall, the event highlighted significant improvements in LLM capabilities since the previous year's hackathon, suggesting continued expansion of LLMs for applications in materials science and chemistry research. These outcomes demonstrate the dual utility of LLMs as both multipurpose models for diverse machine learning tasks and platforms for rapid prototyping custom applications in scientific research.

LSHBloom: Memory-efficient, Extreme-scale Document Deduplication

Deduplication is a major focus for assembling and curating training datasets for large language models (LLM) -- detecting and eliminating additional instances of the same content -- in large collections of technical documents. Unrestrained, duplicates in the training dataset increase training costs and lead to undesirable properties such as memorization in trained models or cheating on evaluation. Contemporary approaches to document-level deduplication are often extremely expensive in both runtime and memory. We propose LSHBloom, an extension to MinhashLSH, which replaces the expensive LSHIndex with lightweight Bloom filters. LSHBloom demonstrates the same deduplication performance as MinhashLSH with only a marginal increase in false positives (as low as 1e-5 in our experiments); demonstrates competitive runtime (270\% faster than MinhashLSH on peS2o); and, crucially, uses just 0.6\% of the disk space required by MinhashLSH to deduplicate peS2o. We demonstrate that this space advantage scales with increased dataset size -- at the extreme scale of several billion documents, LSHBloom promises a 250\% speedup and a 54$\times$ space advantage over traditional MinHashLSH scaling deduplication of text datasets to many billions of documents.

SoK: On Finding Common Ground in Loss Landscapes Using Deep Model Merging Techniques

Understanding neural networks is crucial to creating reliable and trustworthy deep learning models. Most contemporary research in interpretability analyzes just one model at a time via causal intervention or activation analysis. Yet despite successes, these methods leave significant gaps in our understanding of the training behaviors of neural networks, how their inner representations emerge, and how we can predictably associate model components with task-specific behaviors. Seeking new insights from work in related fields, here we survey literature in the field of model merging, a field that aims to combine the abilities of various neural networks by merging their parameters and identifying task-specific model components in the process. We analyze the model merging literature through the lens of loss landscape geometry, an approach that enables us to connect observations from empirical studies on interpretability, security, model merging, and loss landscape analysis to phenomena that govern neural network training and the emergence of their inner representations. To systematize knowledge in this area, we present a novel taxonomy of model merging techniques organized by their core algorithmic principles. Additionally, we distill repeated empirical observations from the literature in these fields into characterizations of four major aspects of loss landscape geometry: mode convexity, determinism, directedness, and connectivity. We argue that by improving our understanding of the principles underlying model merging and loss landscape geometry, this work contributes to the goal of ensuring secure and trustworthy machine learning in practice.

Mitigating Memorization In Language Models

Language models (LMs) can "memorize" information, i.e., encode training data in their weights in such a way that inference-time queries can lead to verbatim regurgitation of that data. This ability to extract training data can be problematic, for example, when data are private or sensitive. In this work, we investigate methods to mitigate memorization: three regularizer-based, three finetuning-based, and eleven machine unlearning-based methods, with five of the latter being new methods that we introduce. We also introduce TinyMem, a suite of small, computationally-efficient LMs for the rapid development and evaluation of memorization-mitigation methods. We demonstrate that the mitigation methods that we develop using TinyMem can successfully be applied to production-grade LMs, and we determine via experiment that: regularizer-based mitigation methods are slow and ineffective at curbing memorization; fine-tuning-based methods are effective at curbing memorization, but overly expensive, especially for retaining higher accuracies; and unlearning-based methods are faster and more effective, allowing for the precise localization and removal of memorized information from LM weights prior to inference. We show, in particular, that our proposed unlearning method BalancedSubnet outperforms other mitigation methods at removing memorized information while preserving performance on target tasks.

Flight: A FaaS-Based Framework for Complex and Hierarchical Federated Learning

Federated Learning (FL) is a decentralized machine learning paradigm where models are trained on distributed devices and are aggregated at a central server. Existing FL frameworks assume simple two-tier network topologies where end devices are directly connected to the aggregation server. While this is a practical mental model, it does not exploit the inherent topology of real-world distributed systems like the Internet-of-Things. We present Flight, a novel FL framework that supports complex hierarchical multi-tier topologies, asynchronous aggregation, and decouples the control plane from the data plane. We compare the performance of Flight against Flower, a state-of-the-art FL framework. Our results show that Flight scales beyond Flower, supporting up to 2048 simultaneous devices, and reduces FL makespan across several models. Finally, we show that Flight's hierarchical FL model can reduce communication overheads by more than 60%.

Employing Artificial Intelligence to Steer Exascale Workflows with Colmena

Computational workflows are a common class of application on supercomputers, yet the loosely coupled and heterogeneous nature of workflows often fails to take full advantage of their capabilities. We created Colmena to leverage the massive parallelism of a supercomputer by using Artificial Intelligence (AI) to learn from and adapt a workflow as it executes. Colmena allows scientists to define how their application should respond to events (e.g., task completion) as a series of cooperative agents. In this paper, we describe the design of Colmena, the challenges we overcame while deploying applications on exascale systems, and the science workflows we have enhanced through interweaving AI. The scaling challenges we discuss include developing steering strategies that maximize node utilization, introducing data fabrics that reduce communication overhead of data-intensive tasks, and implementing workflow tasks that cache costly operations between invocations. These innovations coupled with a variety of application patterns accessible through our agent-based steering model have enabled science advances in chemistry, biophysics, and materials science using different types of AI. Our vision is that Colmena will spur creative solutions that harness AI across many domains of scientific computing.

A Perspective on Foundation Models for the Electric Power Grid

Foundation models (FMs) currently dominate news headlines. They employ advanced deep learning architectures to extract structural information autonomously from vast datasets through self-supervision. The resulting rich representations of complex systems and dynamics can be applied to many downstream applications. Therefore, FMs can find uses in electric power grids, challenged by the energy transition and climate change. In this paper, we call for the development of, and state why we believe in, the potential of FMs for electric grids. We highlight their strengths and weaknesses amidst the challenges of a changing grid. We argue that an FM learning from diverse grid data and topologies could unlock transformative capabilities, pioneering a new approach in leveraging AI to redefine how we manage complexity and uncertainty in the electric grid. Finally, we discuss a power grid FM concept, namely GridFM, based on graph neural networks and show how different downstream tasks benefit.

Causal Discovery over High-Dimensional Structured Hypothesis Spaces with Causal Graph Partitioning

The aim in many sciences is to understand the mechanisms that underlie the observed distribution of variables, starting from a set of initial hypotheses. Causal discovery allows us to infer mechanisms as sets of cause and effect relationships in a generalized way -- without necessarily tailoring to a specific domain. Causal discovery algorithms search over a structured hypothesis space, defined by the set of directed acyclic graphs, to find the graph that best explains the data. For high-dimensional problems, however, this search becomes intractable and scalable algorithms for causal discovery are needed to bridge the gap. In this paper, we define a novel causal graph partition that allows for divide-and-conquer causal discovery with theoretical guarantees. We leverage the idea of a superstructure -- a set of learned or existing candidate hypotheses -- to partition the search space. We prove under certain assumptions that learning with a causal graph partition always yields the Markov Equivalence Class of the true causal graph. We show our algorithm achieves comparable accuracy and a faster time to solution for biologically-tuned synthetic networks and networks up to ${10^4}$ variables. This makes our method applicable to gene regulatory network inference and other domains with high-dimensional structured hypothesis spaces.

Oil & Water? Diffusion of AI Within and Across Scientific Fields

This study empirically investigates claims of the increasing ubiquity of artificial intelligence (AI) within roughly 80 million research publications across 20 diverse scientific fields, by examining the change in scholarly engagement with AI from 1985 through 2022. We observe exponential growth, with AI-engaged publications increasing approximately thirteenfold (13x) across all fields, suggesting a dramatic shift from niche to mainstream. Moreover, we provide the first empirical examination of the distribution of AI-engaged publications across publication venues within individual fields, with results that reveal a broadening of AI engagement within disciplines. While this broadening engagement suggests a move toward greater disciplinary integration in every field, increased ubiquity is associated with a semantic tension between AI-engaged research and more traditional disciplinary research. Through an analysis of tens of millions of document embeddings, we observe a complex interplay between AI-engaged and non-AI-engaged research within and across fields, suggesting that increasing ubiquity is something of an oil-and-water phenomenon -- AI-engaged work is spreading out over fields, but not mixing well with non-AI-engaged work.

SciQAG: A Framework for Auto-Generated Scientific Question Answering Dataset with Fine-grained Evaluation

The use of question-answer (QA) pairs for training and evaluating large language models (LLMs) has attracted considerable attention. Yet few available QA datasets are based on knowledge from the scientific literature. Here we bridge this gap by presenting Automatic Generation of Scientific Question Answers (SciQAG), a framework for automatic generation and evaluation of scientific QA pairs sourced from published scientific literature. We fine-tune an open-source LLM to generate \num{960000} scientific QA pairs from full-text scientific papers and propose a five-dimensional metric to evaluate the quality of the generated QA pairs. We show via LLM-based evaluation that the generated QA pairs consistently achieve an average score of 2.5 out of 3 across five dimensions, indicating that our framework can distill key knowledge from papers into high-quality QA pairs at scale. We make the dataset, models, and evaluation codes publicly available.