The optimal assignment of Large Language Models (LLMs) to specialized roles in multi-agent systems is a significant challenge, defined by a vast combinatorial search space, expensive black-box evaluations, and an inherent trade-off between performance and cost. Current optimization methods focus on single-agent settings and lack a principled framework for this multi-agent, multi-objective problem. This thesis introduces MALBO (Multi-Agent LLM Bayesian Optimization), a systematic framework designed to automate the efficient composition of LLM-based agent teams. We formalize the assignment challenge as a multi-objective optimization problem, aiming to identify the Pareto front of configurations between task accuracy and inference cost. The methodology employs multi-objective Bayesian Optimization (MOBO) with independent Gaussian Process surrogate models. By searching over a continuous feature-space representation of the LLMs, this approach performs a sample-efficient exploration guided by the expected hypervolume improvement. The primary contribution is a principled and automated methodology that yields a Pareto front of optimal team configurations. Our results demonstrate that the Bayesian optimization phase, compared to an initial random search, maintained a comparable average performance while reducing the average configuration cost by over 45%. Furthermore, MALBO identified specialized, heterogeneous teams that achieve cost reductions of up to 65.8% compared to homogeneous baselines, all while maintaining maximum performance. The framework thus provides a data-driven tool for deploying cost-effective and highly specialized multi-agent AI systems.

Recent advances in text-to-image generation have produced strong single-shot models, yet no individual system reliably executes the long, compositional prompts typical of creative workflows. We introduce Image-POSER, a reflective reinforcement learning framework that (i) orchestrates a diverse registry of pretrained text-to-image and image-to-image experts, (ii) handles long-form prompts end-to-end through dynamic task decomposition, and (iii) supervises alignment at each step via structured feedback from a vision-language model critic. By casting image synthesis and editing as a Markov Decision Process, we learn non-trivial expert pipelines that adaptively combine strengths across models. Experiments show that Image-POSER outperforms baselines, including frontier models, across industry-standard and custom benchmarks in alignment, fidelity, and aesthetics, and is consistently preferred in human evaluations. These results highlight that reinforcement learning can endow AI systems with the capacity to autonomously decompose, reorder, and combine visual models, moving towards general-purpose visual assistants.

Benchmarks such as ARC, Raven-inspired tests, and the Blackbird Task are widely used to evaluate the intelligence of large language models (LLMs). Yet, the concept of intelligence remains elusive- lacking a stable definition and failing to predict performance on practical tasks such as question answering, summarization, or coding. Optimizing for such benchmarks risks misaligning evaluation with real-world utility. Our perspective is that evaluation should be grounded in generality rather than abstract notions of intelligence. We identify three assumptions that often underpin intelligence-focused evaluation: generality, stability, and realism. Through conceptual and formal analysis, we show that only generality withstands conceptual and empirical scrutiny. Intelligence is not what enables generality; generality is best understood as a multitask learning problem that directly links evaluation to measurable performance breadth and reliability. This perspective reframes how progress in AI should be assessed and proposes generality as a more stable foundation for evaluating capability across diverse and evolving tasks.

Generating complex, logically-sound SPARQL queries for multi-hop questions remains a critical bottleneck for Knowledge Graph Question Answering, as the brittle nature of one-shot generation by Large Language Models (LLMs) hinders reliable interaction with structured data. Current methods lack the adaptive policies needed to dynamically debug queries based on real-time execution feedback. This paper introduces a novel agentic framework where an LLM learns a resilient policy for the sequential process of iterative SPARQL construction. We show that a compact 3B-parameter model, trained exclusively via outcome-driven Reinforcement Learning (GRPO) without supervised fine-tuning, can learn effective policies for this task, discovering how to systematically recover from execution errors and refine its queries toward a correct answer. On a curated, executable single-answer subset of LC-QuAD 2.0, our agent achieves 49.7\% accuracy post-entity-linking, a significant 17.5 percentage point improvement over the strongest iterative zero-shot baseline. Further analysis reveals that while the agent's capability is driven by RL, its performance is enhanced by an explicit deliberative reasoning step that acts as a cognitive scaffold to improve policy precision. This work presents a generalizable blueprint for teaching agents to master formal, symbolic tools through interaction, bridging the gap between probabilistic LLMs and the structured world of Knowledge Graphs.

Molecular property prediction is fundamental to chemical engineering applications such as solvent screening. We present Socrates-Mol, a framework that transforms language models into empirical Bayesian reasoners through context engineering, addressing cold start problems without model fine-tuning. The system implements a reflective-prediction cycle where initial outputs serve as priors, retrieved molecular cases provide evidence, and refined predictions form posteriors, extracting reusable chemical rules from sparse data. We introduce ranking tasks aligned with industrial screening priorities and employ cross-model self-consistency across five language models to reduce variance. Experiments on amine solvent LogP prediction reveal task-dependent patterns: regression achieves 72% MAE reduction and 112% R-squared improvement through self-consistency, while ranking tasks show limited gains due to systematic multi-model biases. The framework reduces deployment costs by over 70% compared to full fine-tuning, providing a scalable solution for molecular property prediction while elucidating the task-adaptive nature of self-consistency mechanisms.

We transitioned our post-CS1 course that introduces various subfields of computer science so that it integrates Large Language Models (LLMs) in a structured, critical, and practical manner. It aims to help students develop the skills needed to engage meaningfully and responsibly with AI. The course now includes explicit instruction on how LLMs work, exposure to current tools, ethical issues, and activities that encourage student reflection on personal use of LLMs as well as the larger evolving landscape of AI-assisted programming. In class, we demonstrate the use and verification of LLM outputs, guide students in the use of LLMs as an ingredient in a larger problem-solving loop, and require students to disclose and acknowledge the nature and extent of LLM assistance. Throughout the course, we discuss risks and benefits of LLMs across CS subfields. In our first iteration of the course, we collected and analyzed data from students pre and post surveys. Student understanding of how LLMs work became more technical, and their verification and use of LLMs shifted to be more discerning and collaborative. These strategies can be used in other courses to prepare students for the AI-integrated future.

We present an end-to-end demonstration of how attackers can exploit AI safety failures to harm vulnerable populations: from jailbreaking LLMs to generate phishing content, to deploying those messages against real targets, to successfully compromising elderly victims. We systematically evaluated safety guardrails across six frontier LLMs spanning four attack categories, revealing critical failures where several models exhibited near-complete susceptibility to certain attack vectors. In a human validation study with 108 senior volunteers, AI-generated phishing emails successfully compromised 11\% of participants. Our work uniquely demonstrates the complete attack pipeline targeting elderly populations, highlighting that current AI safety measures fail to protect those most vulnerable to fraud. Beyond generating phishing content, LLMs enable attackers to overcome language barriers and conduct multi-turn trust-building conversations at scale, fundamentally transforming fraud economics. While some providers report voluntary counter-abuse efforts, we argue these remain insufficient.

Protein structure is central to biological function, and enabling multimodal protein models requires joint reasoning over sequence, structure, and function. A key barrier is the lack of principled protein structure tokenizers (PSTs): existing approaches fix token size or rely on continuous vector codebooks, limiting interpretability, multi-scale control, and transfer across architectures. We introduce GeoBPE, a geometry-grounded PST that transforms continuous, noisy, multi-scale backbone conformations into discrete ``sentences'' of geometry while enforcing global constraints. Analogous to byte-pair encoding, GeoBPE generates a hierarchical vocabulary of geometric primitives by iteratively (i) clustering Geo-Pair occurrences with k-medoids to yield a resolution-controllable vocabulary; (ii) quantizing each Geo-Pair to its closest medoid prototype; and (iii) reducing drift through differentiable inverse kinematics that optimizes boundary glue angles under an $\mathrm{SE}(3)$ end-frame loss. GeoBPE offers compression ($>$10x reduction in bits-per-residue at similar distortion rate), data efficiency ($>$10x less training data), and generalization (maintains test/train distortion ratio of $1.0-1.1$). It is architecture-agnostic: (a) its hierarchical vocabulary provides a strong inductive bias for coarsening residue-level embeddings from large PLMs into motif- and protein-level representations, consistently outperforming leading PSTs across $12$ tasks and $24$ test splits; (b) paired with a transformer, GeoBPE supports unconditional backbone generation via language modeling; and (c) tokens align with CATH functional families and support expert-interpretable case studies, offering functional meaning absent in prior PSTs. Code is available at https://github.com/shiningsunnyday/PT-BPE/.

Research on how the popularization of generative Artificial Intelligence (AI) tools impacts learning environments has led to hesitancy among educators to teach these tools in classrooms, creating two observed disconnects. Generative AI competency is increasingly valued in industry but not in higher education, and students are experimenting with generative AI without formal guidance. The authors argue students across fields must be taught to responsibly and expertly harness the potential of AI tools to ensure job market readiness and positive outcomes. Computer Science trajectories are particularly impacted, and while consistently top ranked U.S. Computer Science departments teach the mechanisms and frameworks underlying AI, few appear to offer courses on applications for existing generative AI tools. A course was developed at a private research university to teach undergraduate and graduate Computer Science students applications for generative AI tools in software development. Two mixed method surveys indicated students overwhelmingly found the course valuable and effective. Co-authored by the instructor and one of the graduate students, this paper explores the context, implementation, and impact of the course through data analysis and reflections from both perspectives. It additionally offers recommendations for replication in and beyond Computer Science departments. This is the extended version of this paper to include technical appendices.

Systematic logistics, conveyance amenities and facilities as well as warehousing information play a key role in fostering profitable development in a supply chain. The aim of transformation in industries is the improvement of the resiliency regarding the supply chain. The resiliency policies are required for companies to affect the collaboration with logistics service providers positively. The decrement of air pollutant emissions is a persistent advantage of the efficient management of logistics and transportation in supply chain. The management of shipment type is a significant factor in analyzing the sustainability of logistics and supply chain. An automatic approach to predict the shipment type, logistics delay and traffic status are required to improve the efficiency of the supply chain management. A hybrid graphsage network (H-GSN) is proposed in this paper for multi-task purpose of logistics management in a supply chain. The shipment type, shipment status, traffic status, logistics ID and logistics delay are the objectives in this article regarding three different databases including DataCo, Shipping and Smart Logistcis available on Kaggle as supply chain logistics databases. The average accuracy of 97.8% and 100% are acquired for 10 kinds of logistics ID and 3 types of traffic status prediction in Smart Logistics dataset. The average accuracy of 98.7% and 99.4% are obtained for shipment type prediction in DataCo and logistics delay in Shipping database, respectively. The evaluation metrics for different logistics scenarios confirm the efficiency of the proposed method to improve the resilience and sustainability of the supply chain.