Deciphex today introduces CipherX, the AI engine behind its clinical diagnostic service, Diagnexia, and its pharmaceutical research business, Patholytix. CipherX has been in production since January 2026 and is launched publicly for the first time today.
A pathology foundation model is a large neural network trained on millions of tissue images to convert each image into a numerical representation of its morphological content. Every downstream tool works from that representation. The field has spent three years in a scale race, and performance at the tile level has now converged. Models built on larger datasets have not addressed the more challenging problems. A prediction from a foundation model cannot easily be traced to any structure on the slide. Replace the foundation model, and everything built on top has to be redone. Regulators are asking for auditable, model-invariant infrastructure that a raw foundation model does not provide. Deciphex's position is that further gains come from smarter data and smarter models, and that is why today, they are launching CipherX.
CipherX is a pathology AI engine built on two components. Its foundation model (FM) layer combines multiple encoders, including Deciphex's own DCX-3 fusion model, and selects an FM per task and per the rights attached to each dataset. Where CipherX differs is the proprietary ‘semantic layer’ that sits above its foundation models. It decomposes the foundation model's embeddings into ‘glyphs’, small recurring units of the model's representation corresponding to structural tissue elements that a subspecialist pathologist has confirmed and named. Signatures compose from glyphs into named histological structures a pathologist recognises. Spatial arrangement builds higher-order signatures without a new training run. Lymphocytes localised inside tumour give tumour-infiltrating lymphocytes. Organised lymphoid aggregates with germinal-centre architecture adjacent to tumour give tertiary lymphoid structures. Every output decomposes back to named structures a pathologist can inspect and reject. Replacing the foundation model beneath does not change the named vocabulary a customer has signed off on.
On the THUNDER and EVA public benchmark suites, DCX-3 places among the leading pathology foundation models, alongside Virchow2 , UNI2-H , H-Optimus-1 , RudolfV2 and Midnight.
In Diagnexia, three Assist tools built on CipherX run outside the diagnostic pathway, covering image quality assessment, complexity-based triage and post-authorisation review. Adenocarcinoma and melanoma detection tools built on CipherX signatures, in routine use reports 99.85% and 98.76% negative predictive value, respectively on routine casework.
Through Patholytix Research Services, Deciphex uses CipherX to power AI-enhanced histopathology analysis in translational research and clinical trial pathology, and to develop digital tissue biomarkers
and digital companion diagnostics. Any digital biomarker built on the engine inherits its architecture. Its output decomposes back to named tissue structures a reviewer can audit.
"There are strong pathology foundation models available today, and more coming from well-resourced teams,"
said Dr Donal O’Shea.
"What the field has been missing is a stable layer above the models that speaks in pathology terms, holds up as models change underneath, and lets a pathologist see how a conclusion was assembled. CipherX is that layer, and it has been running our clinical and research work for months."
CipherX is not currently offered as a licensed product. It reaches customers inside a Diagnexia clinical workflow or the Patholytix platform, applied to a sponsor's slides through Patholytix Research Services, or as a bespoke development programme delivered through Patholytix Research Services. CipherX does not replace pathologist judgement. Its production tools sit outside the direct diagnostic pathway.
About Deciphex
Deciphex is a computational pathology company headquartered in Dublin, Ireland. Diagnexia is Deciphex's clinical diagnostic service, delivering subspecialist reporting through a network of more than 250 pathologists across the United States and United Kingdom. Patholytix is Deciphex's pharmaceutical R&D business, comprising an image management platform used by nine of the ten largest global pharmaceutical companies, and Patholytix Research Services. Both businesses run on the CipherX AI engine.
Media Contact
Emily O’Brien
Marketing Operations Specialist
Deciphex
Email: emily.obrien@deciphex.com
Phone: +1 (206) 821-2383
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