Pavan Holur

Pavan Holur, Tianyi Wang, Shadi Shahsavari et al.

Social media is a breeding ground for threat narratives and related conspiracy theories. In these, an outside group threatens the integrity of an inside group, leading to the emergence of sharply defined group identities: Insiders -- agents with whom the authors identify and Outsiders -- agents who threaten the insiders. Inferring the members of these groups constitutes a challenging new NLP task: (i) Information is distributed over many poorly-constructed posts; (ii) Threats and threat agents are highly contextual, with the same post potentially having multiple agents assigned to membership in either group; (iii) An agent's identity is often implicit and transitive; and (iv) Phrases used to imply Outsider status often do not follow common negative sentiment patterns. To address these challenges, we define a novel Insider-Outsider classification task. Because we are not aware of any appropriate existing datasets or attendant models, we introduce a labeled dataset (CT5K) and design a model (NP2IO) to address this task. NP2IO leverages pretrained language modeling to classify Insiders and Outsiders. NP2IO is shown to be robust, generalizing to noun phrases not seen during training, and exceeding the performance of non-trivial baseline models by $20\%$.

Pavan Holur, K. C. Enevoldsen, Shreyas Rajesh et al.

DNA sequence alignment involves assigning short DNA reads to the most probable locations on an extensive reference genome. This process is crucial for various genomic analyses, including variant calling, transcriptomics, and epigenomics. Conventional methods, refined over decades, tackle this challenge in 2 steps: genome indexing followed by efficient search to locate likely positions for given reads. Building on the success of Large Language Models in encoding text into embeddings, where the distance metric captures semantic similarity, recent efforts have explored whether the same Transformer architecture can produce embeddings for DNA sequences. Such models have shown early promise in classifying short DNA sequences, such as detecting coding/non-coding regions, and enhancer, promoter sequences. However, performance at sequence classification tasks does not translate to sequence alignment, where it is necessary to search across the genome to align each read, a significantly longer-range task. We bridge this gap by framing the Sequence Alignment task for Transformer models as an "Embed-Search-Align" task. In this framework, a novel Reference-Free DNA Embedding model generates embeddings of reads and reference fragments, which are projected into a shared vector space where the read-fragment distance is used as a surrogate for alignment. Technical contributions include: (1) Contrastive loss for self-supervised training of DNA sequence representations, facilitating rich reference-free, sequence-level embeddings, and (2) a DNA vector store to enable search across fragments on a global scale. DNA-ESA is 99% accurate when aligning 250-length reads onto a human genome (3gb), rivaling conventional methods such as Bowtie and BWA-Mem. DNA-ESA exceeds the performance of 6 Transformer model baselines such as Nucleotide Transformer, Hyena-DNA, and shows task transfer across chromosomes and species.

Shreyas Rajesh, Pavan Holur, Mehmet Yigit Turali et al.

Language models are increasingly used to reason over content they were not trained on, such as new documents, evolving knowledge, and user-specific data. A common approach is retrieval-augmented generation (RAG), which stores verbatim documents externally (as chunks) and retrieves only a relevant subset at inference time for an LLM to reason over. However, this results in inefficient usage of test-time compute (LLM repeatedly reasons over the same documents); moreover, chunk retrieval can inject irrelevant context that increases unsupported generation. We propose a human-like non-parametric continual learning framework, where the base model remains fixed, and learning occurs by integrating each new experience into an external semantic memory state that accumulates and consolidates itself continually. We present Panini, which realizes this by representing documents as Generative Semantic Workspaces (GSW) -- an entity- and event-aware network of question-answer (QA) pairs, sufficient for an LLM to reconstruct the experienced situations and mine latent knowledge via reasoning-grounded inference chains on the network. Given a query, Panini only traverses the continually-updated GSW (not the verbatim documents or chunks), and retrieves the most likely inference chains. Across six QA benchmarks, Panini achieves the highest average performance, 5%-7% higher than other competitive baselines, while using 2-30x fewer answer-context tokens, supports fully open-source pipelines, and reduces unsupported answers on curated unanswerable queries. The results show that efficient and accurate structuring of experiences at write time -- as achieved by the GSW framework -- yields both efficiency and reliability gains at read time. Code is available at https://github.com/roychowdhuryresearch/gsw-memory.

Shreyas Rajesh, Pavan Holur, Chenda Duan et al.

Large Language Models (LLMs) face fundamental challenges in long-context reasoning: many documents exceed their finite context windows, while performance on texts that do fit degrades with sequence length, necessitating their augmentation with external memory frameworks. Current solutions, which have evolved from retrieval using semantic embeddings to more sophisticated structured knowledge graphs representations for improved sense-making and associativity, are tailored for fact-based retrieval and fail to build the space-time-anchored narrative representations required for tracking entities through episodic events. To bridge this gap, we propose the \textbf{Generative Semantic Workspace} (GSW), a neuro-inspired generative memory framework that builds structured, interpretable representations of evolving situations, enabling LLMs to reason over evolving roles, actions, and spatiotemporal contexts. Our framework comprises an \textit{Operator}, which maps incoming observations to intermediate semantic structures, and a \textit{Reconciler}, which integrates these into a persistent workspace that enforces temporal, spatial, and logical coherence. On the Episodic Memory Benchmark (EpBench) \cite{huet_episodic_2025} comprising corpora ranging from 100k to 1M tokens in length, GSW outperforms existing RAG based baselines by up to \textbf{20\%}. Furthermore, GSW is highly efficient, reducing query-time context tokens by \textbf{51\%} compared to the next most token-efficient baseline, reducing inference time costs considerably. More broadly, GSW offers a concrete blueprint for endowing LLMs with human-like episodic memory, paving the way for more capable agents that can reason over long horizons.

Zhe Fei, Mehmet Yigit Turali, Shreyas Rajesh et al.

Harmonizing medication data across Electronic Health Record (EHR) systems is a persistent barrier to monitoring medications for opioid use disorder (MOUD). In heterogeneous EHR systems, key prescription attributes are scattered across differently formatted fields and freetext notes. We present a practical framework that customizes open source large language models (LLMs), including Llama, Qwen, Gemma, and MedGemma, to extract a unified set of MOUD prescription attributes (prescription date, drug name, duration, total quantity, daily quantity, and refills) from heterogeneous, site specific data and compute a standardized metric of medication coverage, \emph{MOUD days}, per patient. Our pipeline processes records directly in a fixed JSON schema, followed by lightweight normalization and cross-field consistency checks. We evaluate the system on prescription level EHR data from five clinics in a national OUD study (25{,}605 records from 1{,}257 patients), using a previously annotated benchmark of 10{,}369 records (776 patients) as the ground truth. Performance is reported as coverage (share of records with a valid, matchable output) and record-level exact-match accuracy. Larger models perform best overall: Qwen2.5-32B achieves \textbf{93.4\%} coverage with \textbf{93.0\%} exact-match accuracy across clinics, and MedGemma-27B attains \textbf{93.1\%}/\textbf{92.2\%}. A brief error review highlights three common issues and fixes: imputing missing dosage fields using within-drug norms, handling monthly/weekly injectables (e.g., Vivitrol) by setting duration from the documented schedule, and adding unit checks to prevent mass units (e.g., ``250 g'') from being misread as daily counts. By removing brittle, site-specific ETL and supporting local, privacy-preserving deployment, this approach enables consistent cross-site analyses of MOUD exposure, adherence, and retention in real-world settings.

Pavan Holur, Shreyas Rajesh, David Chong et al.

An experienced human Observer reading a document -- such as a crime report -- creates a succinct plot-like $\textit{``Working Memory''}$ comprising different actors, their prototypical roles and states at any point, their evolution over time based on their interactions, and even a map of missing Semantic parts anticipating them in the future. $\textit{An equivalent AI Observer currently does not exist}$. We introduce the $\textbf{[G]}$enerative $\textbf{[S]}$emantic $\textbf{[W]}$orkspace (GSW) -- comprising an $\textit{``Operator''}$ and a $\textit{``Reconciler''}$ -- that leverages advancements in LLMs to create a generative-style Semantic framework, as opposed to a traditionally predefined set of lexicon labels. Given a text segment $C_n$ that describes an ongoing situation, the $\textit{Operator}$ instantiates actor-centric Semantic maps (termed ``Workspace instance'' $\mathcal{W}_n$). The $\textit{Reconciler}$ resolves differences between $\mathcal{W}_n$ and a ``Working memory'' $\mathcal{M}_n^*$ to generate the updated $\mathcal{M}_{n+1}^*$. GSW outperforms well-known baselines on several tasks ($\sim 94\%$ vs. FST, GLEN, BertSRL - multi-sentence Semantics extraction, $\sim 15\%$ vs. NLI-BERT, $\sim 35\%$ vs. QA). By mirroring the real Observer, GSW provides the first step towards Spatial Computing assistants capable of understanding individual intentions and predicting future behavior.

Pavan Holur, Shadi Shahsavari, Ehsan Ebrahimzadeh et al.

Readers' responses to literature have received scant attention in computational literary studies. The rise of social media offers an opportunity to capture a segment of these responses while data-driven analysis of these responses can provide new critical insight into how people "read". Posts discussing an individual book on Goodreads, a social media platform that hosts user discussions of popular literature, are referred to as "reviews", and consist of plot summaries, opinions, quotes, or some mixture of these. Since these reviews are written by readers, computationally modeling them allows one to discover the overall non-professional discussion space about a work, including an aggregated summary of the work's plot, an implicit ranking of the importance of events, and the readers' impressions of main characters. We develop a pipeline of interlocking computational tools to extract a representation of this reader generated shared narrative model. Using a corpus of reviews of five popular novels, we discover the readers' distillation of the main storylines in a novel, their understanding of the relative importance of characters, as well as the readers' varying impressions of these characters. In so doing, we make three important contributions to the study of infinite vocabulary networks: (i) an automatically derived narrative network that includes meta-actants; (ii) a new sequencing algorithm, REV2SEQ, that generates a consensus sequence of events based on partial trajectories aggregated from the reviews; and (iii) a new "impressions" algorithm, SENT2IMP, that provides finer, non-trivial and multi-modal insight into readers' opinions of characters.

Shadi Shahsavari, Pavan Holur, Timothy R. Tangherlini et al.

Rumors and conspiracy theories thrive in environments of low confidence and low trust. Consequently, it is not surprising that ones related to the Covid-19 pandemic are proliferating given the lack of any authoritative scientific consensus on the virus, its spread and containment, or on the long term social and economic ramifications of the pandemic. Among the stories currently circulating are ones suggesting that the 5G network activates the virus, that the pandemic is a hoax perpetrated by a global cabal, that the virus is a bio-weapon released deliberately by the Chinese, or that Bill Gates is using it as cover to launch a global surveillance regime. While some may be quick to dismiss these stories as having little impact on real-world behavior, recent events including the destruction of property, racially fueled attacks against Asian Americans, and demonstrations espousing resistance to public health orders countermand such conclusions. Inspired by narrative theory, we crawl social media sites and news reports and, through the application of automated machine-learning methods, discover the underlying narrative frameworks supporting the generation of these stories. We show how the various narrative frameworks fueling rumors and conspiracy theories rely on the alignment of otherwise disparate domains of knowledge, and consider how they attach to the broader reporting on the pandemic. These alignments and attachments, which can be monitored in near real-time, may be useful for identifying areas in the news that are particularly vulnerable to reinterpretation by conspiracy theorists. Understanding the dynamics of storytelling on social media and the narrative frameworks that provide the generative basis for these stories may also be helpful for devising methods to disrupt their spread.

Shadi Shahsavari, Ehsan Ebrahimzadeh, Behnam Shahbazi et al.

Reader reviews of literary fiction on social media, especially those in persistent, dedicated forums, create and are in turn driven by underlying narrative frameworks. In their comments about a novel, readers generally include only a subset of characters and their relationships, thus offering a limited perspective on that work. Yet in aggregate, these reviews capture an underlying narrative framework comprised of different actants (people, places, things), their roles, and interactions that we label the "consensus narrative framework". We represent this framework in the form of an actant-relationship story graph. Extracting this graph is a challenging computational problem, which we pose as a latent graphical model estimation problem. Posts and reviews are viewed as samples of sub graphs/networks of the hidden narrative framework. Inspired by the qualitative narrative theory of Greimas, we formulate a graphical generative Machine Learning (ML) model where nodes represent actants, and multi-edges and self-loops among nodes capture context-specific relationships. We develop a pipeline of interlocking automated methods to extract key actants and their relationships, and apply it to thousands of reviews and comments posted on Goodreads.com. We manually derive the ground truth narrative framework from SparkNotes, and then use word embedding tools to compare relationships in ground truth networks with our extracted networks. We find that our automated methodology generates highly accurate consensus narrative frameworks: for our four target novels, with approximately 2900 reviews per novel, we report average coverage/recall of important relationships of > 80% and an average edge detection rate of >89\%. These extracted narrative frameworks can generate insight into how people (or classes of people) read and how they recount what they have read to others.