Digital Commons Network^™

Genomics And Bioinformatics Student Companion Workbook (First Edition), Na Xu, Tina Hu

Open Educational Resources

This Genomics and Bioinformatics Student Companion Workbook provides an integrated, hands-on introduction to the principles and applications of modern genomics and bioinformatics. Designed for undergraduate students, the workbook guides learners from foundational concepts of genome structure and sequencing technologies to advanced topics including variant analysis, comparative genomics, and multi-omics integration. Emphasizing the interplay between experimental biology and computational analysis, it introduces key analytical tools and biological databases that support genome interpretation and data-driven discovery.

Through a structured progression of chapters, students explore genome organization across diverse biological systems, from prokaryotes and viruses to complex eukaryotic genomes, and examine how genomic …

What Is The Skeleton Of Cognition? A Structural Account Of World Reconstruction Through Processing Axes, Griselda Poe

Publications and Research

This paper describes how the placement of a single processing axis reorganizes human cognition and generates a reconstructed world.

Most existing psychological and social theories begin from emotion, desire, morality, or social behavior. In doing so, they have discussed what forms on top of the cognitive skeleton without first fixing the skeleton itself. When the skeleton is not fixed, entirely different explanations of the same phenomenon can coexist, and it becomes difficult to identify which constitutes a foundational account.

This paper fixes the skeleton first. That skeleton is the processing axis.

The question is: when a single processing axis organizes …

Llms In Compiler Construction, Raffi Khatchadourian

Open Educational Resources

These lecture slides survey the use of large language models (LLMs) in compiler construction for a graduate compiler course (CSc 81010). They situate LLMs across the compiler pipeline and examine representative work: foundation models trained on LLVM IR and assembly (Meta's LLM Compiler), LLM-driven code optimization, binary decompilation (LLM4Decompile), and LLM-assisted automated refactoring—alongside the challenges of applying probabilistic models to tasks that demand correctness. The slides are a self-contained HTML (W3C Slidy) deck with editable Pandoc Markdown source. Part of a two-session unit on advanced compiler topics; see also "Deep Learning Compilers."

Deep Learning Compilers, Raffi Khatchadourian

Open Educational Resources

These lecture slides introduce deep learning compilers for a graduate compiler-construction course (CSc 81010). Building on the classical compiler pipeline, they show how modern machine-learning systems compile tensor programs: static tensor and type analysis (illustrated by a WALA/Ariadne-based refactoring of imperative TensorFlow code to graph mode), MLIR-based end-to-end compilation with IREE, and the PyTorch 2.x stack—TorchDynamo graph capture, AOTAutograd, PrimTorch operator decomposition, and TorchInductor lowering to Triton (GPU) and C++/OpenMP (CPU). The slides are a self-contained HTML (W3C Slidy) deck with editable Pandoc Markdown source. Part of a two-session unit on advanced compiler topics; see also "LLMs in Compiler Construction."

What History Shows: A Structural Account Of Fixed-Point Theory Formation, Griselda Poe

Publications and Research

Theory generation has long been subsumed under categories such as creativity, genius, and innovation. These categories do not distinguish assembly-based conceptual synthesis from fixed-point theory generation.

This paper makes that distinction explicit. The termination condition of assembly is external: data, citation, endorsement, usability. The termination condition of fixed-point theory generation is internal: consistency with internally held constraints, resolution of structural contradiction. The two operate under different processing conditions.

The historical record confirms this distinction. What Darwin, Einstein, Spinoza, and Kant produced was not assembly. Their processes involved unresolved branch retention and decomposition necessity, arriving at internally constrained fixed-point termination. Freud …

Propasafe-Hybrid: A Text-Based Hybrid Propaganda Detection Tool, Thomas Kimmeth, Avijit Roy, Vivek Sharma

Publications and Research

Propagandistic content increasingly circulates through online news and social media, where readers often encounter it with limited scrutiny, highlighting the need for reliable and fine-grained detection. This paper introduces Propasafe-Hybrid, a sentence-level system that integrates a fine-tuned transformer classifier with LLM-based technique classification to identify, label, and explain specific propaganda strategies. The pipeline generates actionable outputs, including highlighted sentences, technique assignments, and concise rationales, so users can immediately understand why a sentence was flagged and how each label was determined. To control inference cost, Propasafe-Hybrid employs a cost-aware pre-filtering stage that forwards only high-likelihood sentences to LLMs, reducing token usage …

Radar Spoofing Attacks And Their Impact On Sensor Fusion-Based Perception For Autonomous Vehicles, Ahmad Mohammed Bara

Student Theses

Safe autonomous vehicle (AV) operation depends on robust perception of the surrounding environment. While multimodal sensing—integrating cameras, LiDAR, and radar—provides comprehensive environmental awareness, radar’s robustness under adverse conditions has made it a critical component of modern perception pipelines. However, the security vulnerabilities of radar within these fusion architectures remain largely unexplored. This work presents an end-to-end analysis of radar spoofing attacks on learning-based radar–camera fusion systems. Using a simulation framework grounded in reflect-array attack models, we inject physically plausible perturbations into radar measurements by altering depth by and velocity, while maintaining crossmodal consistency. Evaluation on the nuScenes dataset shows that …

Propasafe-Hybrid: A Text-Based Hybrid Propaganda Detection Tool (Ila 2026 Presentation), Thomas Kimmeth, Avijit Roy, Vivek Sharma

Publications and Research

This presentation introduces Propasafe-Hybrid, a hybrid system for sentence-level propaganda detection that combines offline transformer-based classification with selective large language model (LLM) explainability. The system employs a two-stage pipeline in which a local BERT-based classifier evaluates all input text and filters non-propagandistic content, while only high-confidence candidates are forwarded to an LLM for rhetorical technique labeling and explanation. This design enables cost-aware, privacy-conscious, and scalable analysis by reducing unnecessary reliance on external models.

Propasafe-Hybrid identifies propagandistic techniques such as loaded language, obfuscation, and appeal to fear, and generates concise natural language rationales that make these techniques interpretable to users. By …

Software Integration In Personal Healthcare Devices And The Patient User Experience, Yassine Chahid, Patrick Slattery

Publications and Research

This study examines the current landscape and future direction of medical device hardware and software integration, focusing on how each contributes to patient care. It begins by analyzing hardware focused medical devices, such as implantable tools patients may rely on to assist with their condition, alongside diagnostic and monitoring equipment used to treat conditions in a variety of medical areas (e.g. cardiovascular conditions). It then evaluates how software is currently integrated through embedded systems, data processing, and user interfaces that support real time monitoring and clinical decision making, and how this impacts quality of care for the patient whilst minimizing …

Processing Conditions In Narrative Interpretation: A Structural Account Of Cf/Ef Divergence In "The Clerk's Tale”, Griselda Poe

Publications and Research

This paper applies the framework established in Paper 19, "Cognition Is Not Content: A Structural Account of Processing Conditions," to re-describe Chaucer's "The Clerk's Tale" from The Canterbury Tales.

The same narrative produces two incompatible interpretations: a record of domestic violence, and a story of genuine love. This divergence does not arise from differences in ethical judgment or emotional response. It arises from structural differences in the conditions under which information is reconstructed.

This paper does three things. First, it analyzes the characters Walter and Griselda in terms of CF (Core-foregrounded) and EF (Modulation-foregrounded) processing conditions. Second, it describes …

Sentential Structures In Alexander Scriabin's Op. 8 Etudes, John Paul West

Theses and Dissertations

Historically, the sentence has proven to be one of the most versatile and pervasive forms in music, appearing since the mid-sixteenth century with occurrences too frequent to quantify. Sentential musical phrases emerged from music and poetry during the late-sixteenth and early-seventeenth centuries with the same short-short-long rhythmic impulse, originating from poetic and sing-song texts. Although the sentence is most often tied to the Classical period, it is not associated with any single era. Patterns of sentential phrases were already apparent and plentiful before the late eighteenth century, and composers used it as a device to expand musical form throughout the …

The Space In Between, Cailyn Dawson

Theses and Dissertations

This paper asks the question: is it possible for our bodies to hold contradicting identities at the same time?  Through monochromatic self- portraits, the artist creates a link between quantum mechanics and painting, using the principle of superposition to depict these multiple unformed states of being.

They Returned Fighting: World War I, Disillusionment, And The Remaking Of African-American Political Life In New York City, Michael Frank

Theses and Dissertations

They Returned Fighting examines how Black New Yorkers used World War I service, wartime activism, and postwar protest to press claims to citizenship and democracy, even as racial violence, discrimination, and contested public memory exposed the limits of that belonging in New York City and the United States.

Humanist Abstractions: Zilia Sánchez’S Forms Of Symbolism And The Reframing Of The Picture Plane, Sydney Srnka

Theses and Dissertations

This thesis examines the culturally specific visual language within the work of Zilia Sánchez through an analysis of her biography and semiotic strategies, arguing that meaning in her work emerges through the materiality of form, rather than through conventional stylistic categorization. It reconsiders how art-historical movements are used to organize artists, proposing a framework better suited to Sánchez’s practice. The issues of reception and legibility have shaped Sánchez’s career as an exile whose experience of displacement informed her shaped canvases. These works articulated a simultaneously unique and universal sense of experience. In researching Sánchez’s history, an alternative story for the …

The Effectiveness Of Utilizing An Arts-Integrated Approach With Students With Ieps In Grades K–5 Self-Contained Classrooms And Why An Arts-Integrated Approach Is Not Widely Implemented In The United States, Alexandra Leff

Theses and Dissertations

This thesis examines arts integration as an approach for K–5 students with IEPs. Drawing on research from Western and non-Western and data from two programs, it shows gains in academic achievement and social-emotional learning. Despite cultural and systemic barriers, findings support expanding arts integration through teacher training and policy reform.

Hanne Darboven: Bismarckzeit (Bismarck Time), Lindsey J. Poremba

Theses and Dissertations

This thesis examines post-war German artist Hanne Darboven’s 1978 work Bismarckzeit (Bismarck Time). Bismarckzeit is a significant work where images, quotations, and equations meet and explore history. This thesis studies the different visual languages in Darboven’s installation, comparing her work with that of Walter Benjamin’s Arcades Project.

Voyager, Ben K. Voss

Theses and Dissertations

This thesis explores painting as a site of meditation, time and (un)knowability.

Cognition Is Not Content: A Structural Account Of Processing Conditions, Griselda Poe

Publications and Research

Human cognition has been described in terms of content. This description becomes insufficient once artificial systems make output observable apart from subject attribution, intention, and relational context. Under this contrast condition, what becomes visible is a layered structure in which output, reconstruction, evaluation, and termination do not necessarily coincide. The same input may register as complete under one processing condition while remaining unresolved under another. This separability means that content-based description does not merely omit an additional variable: it can mislocate a processing difference as a difference in meaning, personality, intention, ability, or attitude. This is not a proposal for …

Reading The Room: A Structural Account Of Constraint-Based Processing And Its Limits In Artificial Systems, Griselda Poe

Publications and Research

This paper does not introduce a new structure.

It makes explicit a structural relation implied but not directly stated in prior work.

Human interpersonal processing is grounded in the co-presence of internal constraint and dependency.

These do not exist as separable components.

They form a single structural condition.

This paper shows that what is commonly described as “reading the room” is not a unitary function.

It differs across configurations in how this condition is processed.

In EF configurations, the effect of this condition is expressed through translation into self-return: outputs are evaluated in terms of how they return to the …

Extreme Cf: A Structural Account Of Processing Absence And Category Absence In Cf-Foregrounded Configurations, Griselda Poe

Publications and Research

Existing frameworks of cognition and intervention assume that processing occurs, meaning is available, and evaluation can be applied.

This paper describes a configuration in which this assumption does not hold.

In CF-foregrounded processing where modulation is absent, processing occurs only when coherence is satisfied. When coherence is not satisfied, processing does not occur. Under this condition, no representation is generated, no evaluation applies, and no action selection is produced.

Within single-layer cognitive models, EF and CF are not distinguished. Within such models, CF does not exist as a condition.

This configuration has not been represented as a category within existing …

Climate Change And Transportation, Paul J. Marchese

Open Educational Resources

This module examines how climate change is affecting transportation systems across multiple sectors, including roads, rail, air, maritime, and active transportation. It highlights key climate trends such as rising temperatures, sea level rise, and extreme weather, and explains how these factors disrupt infrastructure, operations, and safety. The module also explores the economic, operational, and policy challenges associated with maintaining resilient transportation systems under changing environmental conditions. Finally, it presents a range of adaptation and mitigation strategies, emphasizing engineering solutions, sustainable technologies, and data-driven decision-making.

Pre-Experiential Constraint Reconstruction: A Structural Account Of The Prior Layer In Dialogue With Jung, Griselda Poe

Publications and Research

Experiences commonly described as pre-experiential memory—such as immediate recognition, familiarity without prior exposure, and the sense of "already knowing"—are typically interpreted as the retrieval of stored content. However, this storage-based account does not provide a structurally consistent explanation of how such content is preserved prior to experience or reactivated in a form that aligns with present input.

This paper extends the three-layer cognitive architecture developed in prior work in this series (Poe, 2026n), in which cognition operates across Core processing, Modulation, and an operationally inaccessible Prior layer that supplies constraints to all processing.

This paper proposes an alternative account in …

The Core-Modulation Architecture (Cma): A Structural Overview Of Hallucination As Structural Mismatch, Griselda Poe

Publications and Research

Hallucination is defined not as factual error but as a structural failure of alignment across target, layer, and constraint.

Within the Core-Modulation Architecture (CMA), cognition proceeds through layered processing and requires layer-specific termination conditions. Hallucination arises when Modulation-level termination is registered as completion while Core-level resolution has not occurred, producing structurally ungrounded but locally coherent outputs.

Detection is therefore structural rather than content-based, focusing on layer mismatch and termination failure.

This document presents a minimal structural account of hallucination within the CMA framework.

Ai Method For Classification Of Diagnosis Of Near-Infrared Breast Lesion Images, Kaiquan Chen, Fangyang Shen, Honggang Wang, Zhengchao Dong, Jizhong Xiao, Ming Ma, Afroza Aktar, Christopher Chow, Wenxiong Zhang

Publications and Research

In near-infrared optical breast lesion screening and diagnosis systems, high-speed four-dimensional scanners can dynamically acquire tens of thousands of lesion images within a five-minute period. Currently, manual computer annotation is required to generate standard samples from these scanned breast lesion images, a process that depends heavily on physicians with clinical expertise. On average, a single physician can annotate only approximately ten samples per working day. As a result, this process is time-consuming and labor-intensive, and the collected samples often suffer from low accuracy, large variability, and limited diagnostic reliability. Several AI-based annotation tools, such as QuPath, HALO AI™, and X-AnyLabeling, …

Searching Within Galaxies For The Earliest Signs Of Quenching With Spatially Resolved Star Formation Histories In Uvcandels Galaxies At Z < 0.3, Charlotte Olsen, Eric Gawiser, Charlotte Welker, Harry Teplitz, Kartheik Iyer, Xin Wang, Marc Rafelski, Rogier A. Windhorst, Anton Koekemoer, Anahita Alavi, Ben Sunnquist, Norman Grogin, Yicheng Guo, Christopher J. Conselice, L. Y. Aaron Yung, Kalina Nedkova, Bahram Mobasher, Ray A. Lucas, Vihang Mehta, Y. Sophia Dai, Jonathan P. Gardner

Publications and Research

Understanding the complicated processes that regulate star formation and cause a galaxy to become quiescent is key to our comprehension of galaxy evolution. We used eight well-resolved star-forming z < 0.3 galaxies from the UVCANDELS survey, where a total of 10 Hubble Space Telescope bands, including UV follow-up in UVIS/F275W, allow us to reconstruct the star formation histories (SFHs) of regions across each galaxy. This approach provides a powerful tool to explore the spatiotemporal connection between star formation and galaxy evolution. The spatial and temporal profiles of stellar mass and star formation rate (SFR) surface density were obtained from the SFHs of these regions. We measure scaling relations and projected radial profiles of regions within each galaxy at the time of observation and at 1 Gyr lookback time, noting possible trends in the evolution. By comparing the change in star formation over time, we can infer the timing and location of star formation and see early signs of star formation shutting off before quenching occurs. We compared the SFR density–stellar mass density scaling relations for individual galaxies as they evolve from 1 Gyr lookback time. The correlation lines pivot around a log-stellar mass surface density of 7.25 [M⊙ kpc−2], which may be evidence of a self-regulating process on these scales. Radial profiles of the galaxy logarithmic specific SFR (sSFR) show an overall decrease over 1 Gyr, but five galaxies show a greater change in log(sSFR) at the outskirts than the center, indicating a possible early onset of quenching in these galaxies.

Cuny Oer Initiative Catalog (Ay 2024-2025), Jahanara Alamgir, Yujin Lee-Hwang, Rachael Nevins, Elliot Galvis, Rebecca Morofsky, Andrew Mckinney, Jojo Karlin

Open Educational Resources

This circulating catalog inventories the reusable teaching objects produced by CUNY campuses in AY 2024-2025! You’ll find textbooks, assignments, syllabi, videos, and more, organized by discipline and with brief descriptions of the resource. This publication (which links to all the resources) is supplemented by a by our online, filterable CUNY OER Initiative Catalog.

The CUNY OLS Research and Publishing Strategy team gathered, described and indexed the work of the campuses. OLS Fellow Hwang-Lee Yujin designed the publication.

Development And Evaluation Of An Mpas-Based Urban Modeling System For The New York City Region, Marco S. Yu, Kristian Rice

Publications and Research

Complex geometry and varying land cover make urban environments difficult to simulate accurately. This research presents a performance evaluation of the newly developed urban modeling system in the Model for Prediction Across Scales (MPAS). Weather over the New York metropolitan area during June 2018 was simulated using supercomputing resources and the new urban modeling system. Modeled 2-m air temperature was compared with historical hourly observations from five NYC Mesonet stations, one located in each of the five boroughs. Comparison showed that the model follows the timing of warming and cooling well, but overestimates the magnitude of temperature swings at peaks …

Msh 115 - World Music Writing Intensive, Margaret Farrell

Open Educational Resources

This syllabus guided our exploration of music around the globe. In this writing intensive section, music served as a means to internalize information through writing as well as inspiration for developing a clear and persuasive writing style. Our investigations included consideration the forms of the music as well as their cultural and historical contexts.

Structural Silence: When Ai Infrastructure Fails Speakers Of Underrepresented Languages, Avijit Roy, Proma Roy

Publications and Research

Artificial intelligence tools for education and language support are increasingly framed as scalable responses to access gaps in under-resourced communities. Yet the infrastructure underlying these tools—training corpora, tokenization schemes, evaluation benchmarks, and deployment architectures—encodes a set of assumptions that systematically disadvantages speakers of underrepresented languages before a single model is trained. This paper examines those assumptions through the lens of Bengali, one of the world’s most widely spoken languages with roughly 285 million speakers (Ethnologue, 2025; International Communication and Leadership School, 2026), and the structural barriers that emerge when attempting to build AI-assisted educational tools for Bengali-speaking learners in low-connectivity …

The Core-Modulation Architecture (Cma): A Structural Overview Of A 14-Paper Research Program (Preprint), Griselda Poe

Publications and Research

This document provides a structural overview of the Core-Modulation Architecture (CMA), a 14-paper research program on cognition, communication, and AI interaction.

The series specifies the conditions under which cognition operates, terminates, fails, and generates structure. Rather than describing cognition by its contents (beliefs, emotions, decisions), it defines cognition through its underlying architecture: constraint-governed processing across layers with distinct termination conditions.

The framework introduces a layered model consisting of Core processing (constraint preservation and structural coherence) and Modulation (affective calibration and social interface adjustment), extended by a Prior layer as the source of constraints. Across the series, phenomena such as miscommunication, …