Zhi Hong

Kevin Maik Jablonka, Qianxiang Ai, Alexander Al-Feghali et al. · cambridge

Large-language models (LLMs) such as GPT-4 caught the interest of many scientists. Recent studies suggested that these models could be useful in chemistry and materials science. To explore these possibilities, we organized a hackathon. This article chronicles the projects built as part of this hackathon. Participants employed LLMs for various applications, including predicting properties of molecules and materials, designing novel interfaces for tools, extracting knowledge from unstructured data, and developing new educational applications. The diverse topics and the fact that working prototypes could be generated in less than two days highlight that LLMs will profoundly impact the future of our fields. The rich collection of ideas and projects also indicates that the applications of LLMs are not limited to materials science and chemistry but offer potential benefits to a wide range of scientific disciplines.

Zhi Hong, Aswathy Ajith, Gregory Pauloski et al.

Transformer-based masked language models such as BERT, trained on general corpora, have shown impressive performance on downstream tasks. It has also been demonstrated that the downstream task performance of such models can be improved by pretraining larger models for longer on more data. In this work, we empirically evaluate the extent to which these results extend to tasks in science. We use 14 domain-specific transformer-based models (including ScholarBERT, a new 770M-parameter science-focused masked language model pretrained on up to 225B tokens) to evaluate the impact of training data, model size, pretraining and finetuning time on 12 downstream scientific tasks. Interestingly, we find that increasing model sizes, training data, or compute time does not always lead to significant improvements (i.e., >1% F1), if at all, in scientific information extraction tasks and offered possible explanations for the surprising performance differences.

Xiangyi Wang, Pingchen Lu, Jie Mao et al.

Contextual dueling bandits form a cornerstone of preference-based decision-making, with critical applications in recommender systems and large language model alignment. However, standard algorithms rely on the idealized assumption of immediate feedback, a condition frequently violated in real-world scenarios such as prompt optimization. This setting introduces a unique theoretical challenge: unlike linear bandits, dueling bandit estimators lack closed-form solutions, rendering naive adaptations of standard weighting techniques biased. To address this, we formalize the problem of Contextual Dueling Bandits with Stochastic Delayed Feedback and propose two novel algorithms: Linear (LDB-DF) and Neural (NDB-DF) Dueling Bandits with Delayed Feedback. Central to our approach is a novel estimator that integrates an Inverse Probability Weighting (IPW) mechanism directly into the loss function, ensuring unbiased correction for delayed or missing feedback. We provide comprehensive theoretical analysis, establishing an O(d*sqrt(T)) regret bound for the linear setting and sub-linear guarantees for the neural setting. Extensive experiments on both simulated and real-world datasets demonstrate the effectiveness of our propose.

Gheorghe Comanici, Eric Bieber, Mike Schaekermann et al. · amazon-science, baidu

In this report, we introduce the Gemini 2.X model family: Gemini 2.5 Pro and Gemini 2.5 Flash, as well as our earlier Gemini 2.0 Flash and Flash-Lite models. Gemini 2.5 Pro is our most capable model yet, achieving SoTA performance on frontier coding and reasoning benchmarks. In addition to its incredible coding and reasoning skills, Gemini 2.5 Pro is a thinking model that excels at multimodal understanding and it is now able to process up to 3 hours of video content. Its unique combination of long context, multimodal and reasoning capabilities can be combined to unlock new agentic workflows. Gemini 2.5 Flash provides excellent reasoning abilities at a fraction of the compute and latency requirements and Gemini 2.0 Flash and Flash-Lite provide high performance at low latency and cost. Taken together, the Gemini 2.X model generation spans the full Pareto frontier of model capability vs cost, allowing users to explore the boundaries of what is possible with complex agentic problem solving.

Zhi Hong, Qian Zhang, Jiahang Sun et al.

Large Language Models (LLMs) have achieved great success in many real-world applications, especially the one serving as the cognitive backbone of Multi-Agent Systems (MAS) to orchestrate complex workflows in practice. Since many deployment scenarios preclude MAS workflow modifications and its performance is highly sensitive to the input prompts, prompt optimization emerges as a more natural approach to improve its performance. However, real-world prompt optimization for MAS is impeded by three key challenges: (1) the need of sample efficiency due to prohibitive evaluation costs, (2) topology-induced coupling among prompts, and (3) the combinatorial explosion of the search space. To address these challenges, we introduce MASPOB (Multi-Agent System Prompt Optimization via Bandits), a novel sample-efficient framework based on bandits. By leveraging Upper Confidence Bound (UCB) to quantify uncertainty, the bandit framework balances exploration and exploitation, maximizing gains within a strictly limited budget. To handle topology-induced coupling, MASPOB integrates Graph Neural Networks (GNNs) to capture structural priors, learning topology-aware representations of prompt semantics. Furthermore, it employs coordinate ascent to decompose the optimization into univariate sub-problems, reducing search complexity from exponential to linear. Extensive experiments across diverse benchmarks demonstrate that MASPOB achieves state-of-the-art performance, consistently outperforming existing baselines.

Zhi Hong, Kyle Chard, Ian Foster

Relation extraction is an efficient way of mining the extraordinary wealth of human knowledge on the Web. Existing methods rely on domain-specific training data or produce noisy outputs. We focus here on extracting targeted relations from semi-structured web pages given only a short description of the relation. We present GraphScholarBERT, an open-domain information extraction method based on a joint graph and language model structure. GraphScholarBERT can generalize to previously unseen domains without additional data or training and produces only clean extraction results matched to the search keyword. Experiments show that GraphScholarBERT can improve extraction F1 scores by as much as 34.8\% compared to previous work in a zero-shot domain and zero-shot website setting.

Mingze Kong, Zikun Qu, Zhongquan Zhou et al.

The rapid evolution of agentic workflows has demonstrated strong performance of LLM-based agents in addressing complex reasoning tasks. However, existing workflow optimization methods typically formulate workflow synthesis as a static, one-shot code-centric generation problem. This paradigm imposes excessive constraints on the model's coding capabilities and restricts the flexibility required for dynamic problem-solving. In this paper, we present Workflow-R1, a framework that reformulates workflow construction as a multi-turn, natural language-based sequential decision-making process. To resolve the optimization granularity mismatch inherent in such multi-turn interactions, we introduce Group Sub-sequence Policy Optimization (GSsPO). While explicitly tailored to align with the interleaved Think-Action dynamics of agentic reasoning, GSsPO fundamentally functions as a structure-aware RL algorithm generalizable to a broad class of multi-turn agentic sequential decision-making tasks. By recalibrating the optimization unit to the composite sub-sequence, specifically the atomic Think-Action cycle, it aligns gradient updates with the semantic boundaries of these interactions, ensuring robust learning in complex multi-turn reasoning tasks. Through extensive experiments on multiple QA benchmarks, Workflow-R1 outperforms competitive baselines, validating GSsPO as a generalized solution for sequential reasoning and establishing Workflow-R1 as a promising new paradigm for automated workflow optimization.

Pingchen Lu, Zhi Hong, Zhiwei Shang et al.

The performance of large language models (LLMs) is highly sensitive to the input prompt, making prompt optimization a critical task. However, real-world application is hindered by three major challenges: (1) the black-box nature of powerful proprietary LLMs, (2) the need for high sample efficiency due to query costs, and (3) the desire for privacy-preserving collaboration among multiple users. To address these challenges simultaneously, we introduce a novel framework for sample-efficient federated prompt optimization based on multi-armed bandits (MABs). The MAB framework is uniquely suited for this problem as it is (1) inherently a black-box optimization method, (2) practically sample-efficient, and (3) enables collaborative learning with theoretically guaranteed benefit from more participating agents. We first propose the Federated Prompt Optimization via Bandits (FedPOB) algorithm, a federated variant of the Linear UCB algorithm, where agents collaborate by sharing model parameters instead of raw data. We then extend our approach to the practical setting of comparative user feedback by introducing FedPOB with Preference Feedback (FedPOB-Pref), an efficient algorithm based on federated dueling bandits. Extensive experiments demonstrate that both FedPOB and FedPOB-Pref significantly outperform existing baselines and that their performance consistently improves as more agents participate in the collaboration, validating the effectiveness of our federated approach.

Zhi Hong, J. Gregory Pauloski, Logan Ward et al.

Researchers worldwide are seeking to repurpose existing drugs or discover new drugs to counter the disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A promising source of candidates for such studies is molecules that have been reported in the scientific literature to be drug-like in the context of coronavirus research. We report here on a project that leverages both human and artificial intelligence to detect references to drug-like molecules in free text. We engage non-expert humans to create a corpus of labeled text, use this labeled corpus to train a named entity recognition model, and employ the trained model to extract 10912 drug-like molecules from the COVID-19 Open Research Dataset Challenge (CORD-19) corpus of 198875 papers. Performance analyses show that our automated extraction model can achieve performance on par with that of non-expert humans.

Yadu Babuji, Ben Blaiszik, Tom Brettin et al.

Researchers across the globe are seeking to rapidly repurpose existing drugs or discover new drugs to counter the the novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). One promising approach is to train machine learning (ML) and artificial intelligence (AI) tools to screen large numbers of small molecules. As a contribution to that effort, we are aggregating numerous small molecules from a variety of sources, using high-performance computing (HPC) to computer diverse properties of those molecules, using the computed properties to train ML/AI models, and then using the resulting models for screening. In this first data release, we make available 23 datasets collected from community sources representing over 4.2 B molecules enriched with pre-computed: 1) molecular fingerprints to aid similarity searches, 2) 2D images of molecules to enable exploration and application of image-based deep learning methods, and 3) 2D and 3D molecular descriptors to speed development of machine learning models. This data release encompasses structural information on the 4.2 B molecules and 60 TB of pre-computed data. Future releases will expand the data to include more detailed molecular simulations, computed models, and other products.