Minh Hoang

Gabrielle Cohn, Rohan Gumaste, Minh Hoang et al.

Protein homology search underlies function annotation, structure prediction, and evolutionary analysis, but remains challenging in the "twilight zone," where global sequence similarity is weak and classical alignment methods lose sensitivity. Protein language models provide context-aware representations that could improve alignment sensitivity in this regime. However, prior protein embedding-based retrieval pipelines often pool these representations into a single vector, potentially obscuring local motifs, domains, or conserved residues that reveal remote homology. We introduce ProtoCol, a model which represents proteins as sets of residue embeddings and uses ColBERT-style late interaction to test whether residue-level comparison improves homolog retrieval. ProtoCol encodes proteins independently, keeps candidate representations pre-computable, and scores candidates with MaxSim over residue embeddings. On SCOPe superfamily and Pfam clan benchmarks, ProtoCol outperforms sequence-composition, alignment-based, pooled PLM, and trained single-vector baselines, supporting late interaction as an effective retrieval layer for remote homology search.

Hang Thi-Thuy Le, Long Minh Bui, Minh Hoang et al.

Continual fine-tuning aims to adapt a pre-trained backbone to new tasks sequentially while preserving performance on earlier tasks whose data are no longer available. Existing approaches fall into two categories which include input- and parameter-adaptation. Input-adaptation methods rely on retrieving the most relevant prompts at test time, but require continuously learning a retrieval function that is prone to forgetting. Parameter-adaptation methods instead use a fixed input embedding function to enable retrieval-free prediction and avoid forgetting, but sacrifice representation adaptability. To combine their best strengths, we propose a new parameter-adaptation method that enables adaptive use of input embeddings during test time with parameter-free retrieval. We derive task-retrieval error bounds for a clustering-based, parameter-free paradigm, providing theoretical guarantees that link low retrieval error to structural properties of task-specific representation clusters, revealing a fresh insight into how well-organized clustering structure will enable reliable retrieval. Motivated by this insight, our method is designed with two key components: (i) an adaptive module composition strategy that learns informative task-specific updates to preserve and complement prior knowledge, and (ii) a clustering-based retrieval mechanism that captures distinct representation signatures for each task, enabling adaptive representation use at test time. Extensive experiments show that these components work synergistically to improve retrieval and predictive performance under large shifts in task semantics.

Pei-Yau Weng, Minh Hoang, Lam M. Nguyen et al.

Fine-tuning pre-trained models is a popular approach in machine learning for solving complex tasks with moderate data. However, fine-tuning the entire pre-trained model is ineffective in federated data scenarios where local data distributions are diversely skewed. To address this, we explore integrating federated learning with a more effective prompt-tuning method, optimizing for a small set of input prefixes to reprogram the pre-trained model's behavior. Our approach transforms federated learning into a distributed set modeling task, aggregating diverse sets of prompts to globally fine-tune the pre-trained model. We benchmark various baselines based on direct adaptations of existing federated model aggregation techniques and introduce a new probabilistic prompt aggregation method that substantially outperforms these baselines. Our reported results on a variety of computer vision datasets confirm that the proposed method is most effective to combat extreme data heterogeneity in federated learning.

Minh Hoang, Azza Fadhel, Aryan Deshwal et al.

Offline design optimization problem arises in numerous science and engineering applications including material and chemical design, where expensive online experimentation necessitates the use of in silico surrogate functions to predict and maximize the target objective over candidate designs. Although these surrogates can be learned from offline data, their predictions are often inaccurate outside the offline data regime. This challenge raises a fundamental question about the impact of imperfect surrogate model on the performance gap between its optima and the true optima, and to what extent the performance loss can be mitigated. Although prior work developed methods to improve the robustness of surrogate models and their associated optimization processes, a provably quantifiable relationship between an imperfect surrogate and the corresponding performance gap, as well as whether prior methods directly address it, remain elusive. To shed light on this important question, we present a theoretical framework to understand offline black-box optimization, by explicitly bounding the optimization quality based on how well the surrogate matches the latent gradient field that underlines the offline data. Inspired by our theoretical analysis, we propose a principled black-box gradient matching algorithm to create effective surrogate models for offline optimization, improving over prior approaches on various real-world benchmarks.

Sahil Verma, Varich Boonsanong, Minh Hoang et al.

Machine learning plays a role in many deployed decision systems, often in ways that are difficult or impossible to understand by human stakeholders. Explaining, in a human-understandable way, the relationship between the input and output of machine learning models is essential to the development of trustworthy machine learning based systems. A burgeoning body of research seeks to define the goals and methods of explainability in machine learning. In this paper, we seek to review and categorize research on counterfactual explanations, a specific class of explanation that provides a link between what could have happened had input to a model been changed in a particular way. Modern approaches to counterfactual explainability in machine learning draw connections to the established legal doctrine in many countries, making them appealing to fielded systems in high-impact areas such as finance and healthcare. Thus, we design a rubric with desirable properties of counterfactual explanation algorithms and comprehensively evaluate all currently proposed algorithms against that rubric. Our rubric provides easy comparison and comprehension of the advantages and disadvantages of different approaches and serves as an introduction to major research themes in this field. We also identify gaps and discuss promising research directions in the space of counterfactual explainability.