An Invariant Compiler for Neural ODEs in AI-Accelerated Scientific Simulation

Neural ODEs are increasingly used as continuous-time models for scientific and sensor data, but unconstrained neural ODEs can drift and violate domain invariants (e.g., conservation laws), yielding physically implausible solutions. In turn, this can compound error in long-horizon prediction and surrogate simulation. Existing solutions typically aim to enforce invariance by soft penalties or other forms of regularization, which can reduce overall error but do not guarantee that trajectories will not leave the constraint manifold. We introduce the invariant compiler, a framework that enforces invariants by construction: it treats invariants as first-class types and uses an LLM-driven compilation workflow to translate a generic neural ODE specification into a structure-preserving architecture whose trajectories remain on the admissible manifold in continuous time (and up to numerical integration error in practice). This compiler view cleanly separates what must be preserved (scientific structure) from what is learned from data (dynamics within that structure). It provides a systematic design pattern for invariant-respecting neural surrogates across scientific domains.

Modeling Epidemiological Dynamics Under Adversarial Data and User Deception

Epidemiological models increasingly rely on self-reported behavioral data such as vaccination status, mask usage, and social distancing adherence to forecast disease transmission and assess the impact of non-pharmaceutical interventions (NPIs). While such data provide valuable real-time insights, they are often subject to strategic misreporting, driven by individual incentives to avoid penalties, access benefits, or express distrust in public health authorities. To account for such human behavior, in this paper, we introduce a game-theoretic framework that models the interaction between the population and a public health authority as a signaling game. Individuals (senders) choose how to report their behaviors, while the public health authority (receiver) updates their epidemiological model(s) based on potentially distorted signals. Focusing on deception around masking and vaccination, we characterize analytically game equilibrium outcomes and evaluate the degree to which deception can be tolerated while maintaining epidemic control through policy interventions. Our results show that separating equilibria-with minimal deception-drive infections to near zero over time. Remarkably, even under pervasive dishonesty in pooling equilibria, well-designed sender and receiver strategies can still maintain effective epidemic control. This work advances the understanding of adversarial data in epidemiology and offers tools for designing more robust public health models in the presence of strategic user behavior.

How (Not) to Hybridize Neural and Mechanistic Models for Epidemiological Forecasting

Epidemiological forecasting from surveillance data is a hard problem and hybridizing mechanistic compartmental models with neural models is a natural direction. The mechanistic structure helps keep trajectories epidemiologically plausible, while neural components can capture non-stationary, data-adaptive effects. In practice, however, many seemingly straightforward couplings fail under partial observability and continually shifting transmission dynamics driven by behavior, waning immunity, seasonality, and interventions. We catalog these failure modes and show that robust performance requires making non-stationarity explicit: we extract multi-scale structure from the observed infection series and use it as an interpretable control signal for a controlled neural ODE coupled to an epidemiological model. Concretely, we decompose infections into trend, seasonal, and residual components and use these signals to drive continuous-time latent dynamics while jointly forecasting and inferring time-varying transmission, recovery, and immunity-loss rates. Across seasonal and non-seasonal settings, including early outbreaks and multi-wave regimes, our approach reduces long-horizon RMSE by 15-35%, improves peak timing error by 1-3 weeks, and lowers peak magnitude bias by up to 30% relative to strong time-series, neural ODE, and hybrid baselines, without relying on auxiliary covariates.

RAG without Forgetting: Continual Query-Infused Key Memory

Retrieval-augmented generation (RAG) systems commonly improve robustness via query-time adaptations such as query expansion and iterative retrieval. While effective, these approaches are inherently stateless: adaptations are recomputed for each query and discarded thereafter, precluding cumulative learning and repeatedly incurring inference-time cost. Index-side approaches like key expansion introduce persistence but rely on offline preprocessing or heuristic updates that are weakly aligned with downstream task utility, leading to semantic drift and noise accumulation. We propose Evolving Retrieval Memory (ERM), a training-free framework that transforms transient query-time gains into persistent retrieval improvements. ERM updates the retrieval index through correctness-gated feedback, selectively attributes atomic expansion signals to the document keys they benefit, and progressively evolves keys via stable, norm-bounded updates. We show that query and key expansion are theoretically equivalent under standard similarity functions and prove convergence of ERM's selective updates, amortizing optimal query expansion into a stable index with zero inference-time overhead. Experiments on BEIR and BRIGHT across 13 domains demonstrate consistent gains in retrieval and generation, particularly on reasoning-intensive tasks, at native retrieval speed.

Agentic Framework for Epidemiological Modeling

Epidemic modeling is essential for public health planning, yet traditional approaches rely on fixed model classes that require manual redesign as pathogens, policies, and scenario assumptions evolve. We introduce EPIAGENT, an agentic framework that automatically synthesizes, calibrates, verifies, and refines epidemiological simulators by modeling disease progression as an iterative program synthesis problem. A central design choice is an explicit epidemiological flow graph intermediate representation that links scenario specifications to model structure and enables strong, modular correctness checks before code is generated. Verified flow graphs are then compiled into mechanistic models supporting interpretable parameter learning under physical and epidemiological constraints. Evaluation on epidemiological scenario case studies demonstrates that EPIAGENT captures complex growth dynamics and produces epidemiologically consistent counterfactual projections across varying vaccination and immune escape assumptions. Our results show that the agentic feedback loop prevents degeneration and significantly accelerates convergence toward valid models by mimicking professional expert workflows.

Utilizing Metadata for Better Retrieval-Augmented Generation

Retrieval-Augmented Generation systems depend on retrieving semantically relevant document chunks to support accurate, grounded outputs from large language models. In structured and repetitive corpora such as regulatory filings, chunk similarity alone often fails to distinguish between documents with overlapping language. Practitioners often flatten metadata into input text as a heuristic, but the impact and trade-offs of this practice remain poorly understood. We present a systematic study of metadata-aware retrieval strategies, comparing plain-text baselines with approaches that embed metadata directly. Our evaluation spans metadata-as-text (prefix and suffix), a dual-encoder unified embedding that fuses metadata and content in a single index, dual-encoder late-fusion retrieval, and metadata-aware query reformulation. Across multiple retrieval metrics and question types, we find that prefixing and unified embeddings consistently outperform plain-text baselines, with the unified at times exceeding prefixing while being easier to maintain. Beyond empirical comparisons, we analyze embedding space, showing that metadata integration improves effectiveness by increasing intra-document cohesion, reducing inter-document confusion, and widening the separation between relevant and irrelevant chunks. Field-level ablations show that structural cues provide strong disambiguating signals. Our code, evaluation framework, and the RAGMATE-10K dataset are publicly hosted.

Hindsight is 20/20: Building Agent Memory that Retains, Recalls, and Reflects

Agent memory has been touted as a dimension of growth for LLM-based applications, enabling agents that can accumulate experience, adapt across sessions, and move beyond single-shot question answering. The current generation of agent memory systems treats memory as an external layer that extracts salient snippets from conversations, stores them in vector or graph-based stores, and retrieves top-k items into the prompt of an otherwise stateless model. While these systems improve personalization and context carry-over, they still blur the line between evidence and inference, struggle to organize information over long horizons, and offer limited support for agents that must explain their reasoning. We present Hindsight, a memory architecture that treats agent memory as a structured, first-class substrate for reasoning by organizing it into four logical networks that distinguish world facts, agent experiences, synthesized entity summaries, and evolving beliefs. This framework supports three core operations -- retain, recall, and reflect -- that govern how information is added, accessed, and updated. Under this abstraction, a temporal, entity aware memory layer incrementally turns conversational streams into a structured, queryable memory bank, while a reflection layer reasons over this bank to produce answers and to update information in a traceable way. On key long-horizon conversational memory benchmarks like LongMemEval and LoCoMo, Hindsight with an open-source 20B model lifts overall accuracy from 39% to 83.6% over a full-context baseline with the same backbone and outperforms full context GPT-4o. Scaling the backbone further pushes Hindsight to 91.4% on LongMemEval and up to 89.61% on LoCoMo (vs. 75.78% for the strongest prior open system), consistently outperforming existing memory architectures on multi-session and open-domain questions.

Exploring LLMs for Scientific Information Extraction Using The SciEx Framework

Large language models (LLMs) are increasingly touted as powerful tools for automating scientific information extraction. However, existing methods and tools often struggle with the realities of scientific literature: long-context documents, multi-modal content, and reconciling varied and inconsistent fine-grained information across multiple publications into standardized formats. These challenges are further compounded when the desired data schema or extraction ontology changes rapidly, making it difficult to re-architect or fine-tune existing systems. We present SciEx, a modular and composable framework that decouples key components including PDF parsing, multi-modal retrieval, extraction, and aggregation. This design streamlines on-demand data extraction while enabling extensibility and flexible integration of new models, prompting strategies, and reasoning mechanisms. We evaluate SciEx on datasets spanning three scientific topics for its ability to extract fine-grained information accurately and consistently. Our findings provide practical insights into both the strengths and limitations of current LLM-based pipelines.

Demystify, Use, Reflect: Preparing students to be informed LLM-users

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.

When can isotropy help adapt LLMs' next word prediction to numerical domains?

Recent studies have shown that vector representations of contextual embeddings learned by pre-trained large language models (LLMs) are effective in various downstream tasks in numerical domains. Despite their significant benefits, the tendency of LLMs to hallucinate in such domains can have severe consequences in applications such as energy, nature, finance, healthcare, retail and transportation, among others. To guarantee prediction reliability and accuracy in numerical domains, it is necessary to open the black-box and provide performance guarantees through explanation. However, there is little theoretical understanding of when pre-trained language models help solve numeric downstream tasks. This paper seeks to bridge this gap by understanding when the next-word prediction capability of LLMs can be adapted to numerical domains through a novel analysis based on the concept of isotropy in the contextual embedding space. Specifically, we consider a log-linear model for LLMs in which numeric data can be predicted from its context through a network with softmax in the output layer of LLMs (i.e., language model head in self-attention). We demonstrate that, in order to achieve state-of-the-art performance in numerical domains, the hidden representations of the LLM embeddings must possess a structure that accounts for the shift-invariance of the softmax function. By formulating a gradient structure of self-attention in pre-trained models, we show how the isotropic property of LLM embeddings in contextual embedding space preserves the underlying structure of representations, thereby resolving the shift-invariance problem and providing a performance guarantee. Experiments show that different characteristics of numeric data and model architecture could have different impacts on isotropy.