arXiv subjects

Chalani Rajapakse

Publications and source records attributed to Chalani Rajapakse.

4 recordsLinked to original sources

arXiv2026

BaseCamp --- An Agentic AI Framework for Automating DNA Sequencing Data Pipelines

DNA sequencing pipelines, spanning quality control, alignment, variant calling, and annotation, are now reliably executed by workflow management systems that orchestrate established bioinformatics tools at scale. What remains manual is the decision layer surrounding that execution: selecting quality thresholds appropriate to a sample and platform, adjudicating borderline variant calls, diagnosing anomalies, and determining which findings warrant expert review. These decisions are repetitive, judgment-intensive, inconsistent across operators, and frequently undocumented. This paper introduces BaseCamp, a novel agentic AI framework for automating the decision layer of DNA sequencing pipelines. The framework decomposes the pipeline into six specialized AI agents, covering sample intake and quality control, alignment, variant calling, annotation, cross-stage monitoring, and reporting. Critically, BaseCamp agents do not perform sequence analysis: established tools execute alignment, calling, and annotation, while the agents select among them, configure them, interpret their output, and decide what follows. This confines language model reasoning to the judgment layer where it is reliable and preserves the reproducibility existing tooling guarantees. Agent reasoning is powered by a consortium of fine-tuned, domain-specialized large language models coordinated by a central reasoning LLM, executing locally so no sequencing data leaves the operating environment, under human-in-the-loop orchestration. Evaluation shows agent-generated configurations are concordant with expert practice, that an explicit filtering ledger renders inspectable what filtering otherwise removes without trace, and that cross-stage anomaly detection surfaces conditions execution monitoring misses. BaseCamp offers a generalizable blueprint for agentic automation of scientific data pipelines.

cs.AI↗

arXiv2026

Human-AI Agent Interaction as a Neuroplastic Training Environment

Interaction with AI agents has become one of the most frequent activities of everyday digital life. Whether conversing with an assistant, working with a coding copilot, or generating images, the interaction follows a common iterative loop: a request is issued, a result returned, appraised, and the request revised. We observe that this loop is a high-frequency stream of contact events -- moments at which a result meets a person and a conditioned response may fire before deliberate appraisal -- making everyday agent interaction an unrecognised neuroplastic training environment. When a result disappoints, reactive patterns of impatience, perfectionism, frustration, and self-criticism are repeatedly evoked, and under activity-dependent synaptic plasticity each uninterrupted cycle deepens the underlying pathway through long-term potentiation. Ordinary agent use may thus quietly strengthen the very patterns it provokes. We propose that the same training environment can be engaged to the opposite effect. Treating conditioned reactive patterns as physical neurone paths -- activated through a pre-cognitive feeling tone that opens a brief regulatory gap -- we develop a framework in which, at that gap, in place of the reactive re-prompt, a person performs behind-the-scenes observation: watching the neural process operate so the cascade does not complete and long-term depression weakens the path rather than potentiation strengthening it. We characterise this practice through three layers of observation and two modes of application: a user-guided mode requiring no change to existing tools, and an agent-assisted mode in which an ordinary agent is lightly configured to support observation at the gap. We illustrate the framework through generative image prompting, showing how a single frustrating session is behaviourally nearly identical whether or not it is observed, yet neurologically opposite.

cs.AI↗

arXiv2026

Towards an Agent-First Web: Redesigning the Web for AI Agents

The World Wide Web was built on an assumption held for three decades: the primary consumer of web content is a human being. This permeates every layer; its access model presumes human visitors, its economics rest on human attention, and its content targets human perception. The rapid emergence of AI agents as intermediaries between humans and web content invalidates this assumption. Yet the web resists agents through blanket blocking, CAPTCHA-based exclusion, and economic models that treat agent access as extraction rather than legitimate interaction. This paper proposes a principled redesign across three layers. At the access layer, agents acting for humans should inherit equivalent access rights, governed by rate limiting and agent identification metadata in HTTP requests, analogous to browser headers, alongside a dual-layer architecture serving human-readable and agent-optimized content from the same domain. At the economic layer, we propose an intent-based tier framework grounded in the agent-as-human-proxy principle: an agent's economic obligation mirrors that of the human it represents. A token-based subscription model meters content in tokens rather than pageviews, alongside a commissioned content economy anchoring AI content production in human intentionality. At the content layer, we identify epistemic recursion, the self-referential loop in which AI-generated content is consumed by agents to produce further content, progressively detaching web knowledge from human ground truth. We propose the Agent Text Markup Language (ATML), a four-level human supervision tier model, and a cryptographic provenance chain to counter this threat. Together these constitute ten design principles for an agent-first internet, one in which agents are first-class citizens whose integration requires renegotiating the web's foundational social contract across access, economics, and content.

cs.AI↗

arXiv2026

MindGap: A Conversational AI Framework for Upstream Neuroplastic Intervention in Post-Traumatic Stress Disorder

Post-Traumatic Stress Disorder (PTSD) is fundamentally a neuroplastic problem traumatic contact events encode over-reactive neural pathways through Hebbian long-term potentiation, producing hair-triggered amygdala-HPA stress cascades that fire before conscious awareness can intercept them. Existing therapeutic approaches, prolonged exposure, EMDR, cognitive behavioural therapy, operate predominantly downstream of the reactive cascade, teaching patients to tolerate or reframe distress after it has arisen. While clinically valuable, these suppression-based approaches do not produce the upstream pathway dissolution that constitutes lasting structural neural reorganisation. This paper proposes MindGap, a privacy-preserving on-device conversational AI framework that delivers structured neuroplastic rehabilitation for PTSD through the practice of dependent origination, a Buddhist psychological framework that identifies the precise moment between the pre-cognitive affective signal and the reactive elaboration that follows as the site of therapeutic intervention. MindGap guides patients through three progressive layers of observation at this feeling tone gap: noticing the bare affective signal before reactive elaboration, recognising it as self-arising rather than caused by the stimulus, and recognising the conditioned implicit belief beneath the feeling. Each layer corresponds to progressively deeper prefrontal regulatory engagement and progressively deeper long-term depression-mediated weakening of the reactive pathway, producing genuine upstream dissolution rather than downstream suppression. Running entirely on-device with no data egress, MindGap delivers daily calibrated exposure sessions through a fine-tuned lightweight large language model, making it deployable in sensitive clinical and military contexts where cloud-based solutions are not permitted.

cs.AI↗