The fuzzy or soft $k$-means objective is a popular generalization of the well-known $k$-means problem, extending the clustering capability of the $k$-means to datasets that are uncertain, vague and otherwise hard to cluster. In this paper, we propose a semi-supervised active clustering framework, where the learner is allowed to interact with an oracle (domain expert), asking for the similarity between a certain set of chosen items. We study the query and computational complexities of clustering in this framework. We prove that having a few of such similarity queries enables one to get a polynomial-time approximation algorithm to an otherwise conjecturally NP-hard problem. In particular, we provide algorithms for fuzzy clustering in this setting that ask $O(\mathsf{poly}(k)\log n)$ similarity queries and run with polynomial-time-complexity, where $n$ is the number of items. The fuzzy $k$-means objective is nonconvex, with $k$-means as a special case, and is equivalent to some other generic nonconvex problem such as non-negative matrix factorization. The ubiquitous Lloyd-type algorithms (or alternating-minimization algorithms) can get stuck at a local minima. Our results show that by making few similarity queries, the problem becomes easier to solve. Finally, we test our algorithms over real-world datasets, showing their effectiveness in real-world applications.

The fuzzy or soft k -means objective is a popular generalization of the well-known k -means problem, extending the clustering capability of the k -means to datasets that are uncertain, vague and otherwise hard to cluster. In this paper, we propose a semi-supervised active clustering framework, where the learner is allowed to interact with an oracle (domain expert), asking for the similarity between a certain set of chosen items. We study the query and computational complexities of clustering in this framework. We prove that having a few of such similarity queries enables one to get a polynomial-time approximation algorithm to an otherwise conjecturally NP-hard problem. In particular, we provide algorithms for fuzzy clustering in this setting that ask O(\mathsf{poly}(k)\log n) similarity queries and run with polynomial-time-complexity, where n is the number of items.

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 LLM-driven 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 the agentic systems on the retrieval of salient information for material design tasks. Moreover, alternative uses of predictive deep learning models, such as leveraging their latent representations to facilitate cross-modal retrieval augmented generation within agentic systems to enable task-specific materials design, has remained unexplored. Herein, we demonstrate that large, pre-trained chemistry foundation models can serve as a basis for enabling 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 image models such as OpenCLIP facilitate unprecedented queries and information retrieval across multiple characterization data domains. Finally, we demonstrate the integration of these systems within multi-agent systems to facilitate structure and topological-based natural language queries and information retrieval for complex research tasks.

The fuzzy or soft $k$-means objective is a popular generalization of the well-known $k$-means problem, extending the clustering capability of the $k$-means to datasets that are uncertain, vague, and otherwise hard to cluster. In this paper, we propose a semi-supervised active clustering framework, where the learner is allowed to interact with an oracle (domain expert), asking for the similarity between a certain set of chosen items. We study the query and computational complexities of clustering in this framework. We prove that having a few of such similarity queries enables one to get a polynomial-time approximation algorithm to an otherwise conjecturally NP-hard problem. In particular, we provide probabilistic algorithms for fuzzy clustering in this setting that asks $O(\mathsf{poly}(k)\log n)$ similarity queries and run with polynomial-time-complexity, where $n$ is the number of items. The fuzzy $k$-means objective is nonconvex, with $k$-means as a special case, and is equivalent to some other generic nonconvex problem such as non-negative matrix factorization. The ubiquitous Lloyd-type algorithms (or, expectation-maximization algorithm) can get stuck at a local minima. Our results show that by making few similarity queries, the problem becomes easier to solve. Finally, we test our algorithms over real-world datasets, showing their effectiveness in real-world applications.