Pillar I · The scientific learner

Design how scientific learning systems work

Foundational Scientific Learning-System Design

We design scientific representations, model architectures and information flow, learning signals and objectives, and the ways models learn and adapt. These choices determine which distinctions a system can preserve, which relationships it can express, and how it can use limited evidence.

We also study how models, data, simulation, experiments, tools, and scientific judgment work together as a complete system. Research infrastructure and scientific evaluation are part of this design: they shape what can be tested, compared, and reused, and how progress toward scientific understanding and reliable design is assessed.

Core question
How should a scientific system learn?
Research focus
Design scientific learning systems, their research infrastructure, and scientific evaluation.
Intended contribution
Learning components whose structure can be understood, tested and reused across scientific settings.

Try changing the connections

Explore the learner

Same information. Different connections.

Keep the four input values fixed. Change which units interact and see what each calculation can preserve.

Illustrative arithmetic, not measured data, a trained model or a physical interaction.

Compare all three calculations

Pairing A

1–2 and 3–4

Mean of raw features: 2.5

(1 × 2) + (3 × 4) = 14

Pairing B

1–3 and 2–4

Mean of raw features: 2.5

(1 × 3) + (2 × 4) = 11

Pairing C

1–4 and 2–3

Mean of raw features: 2.5

(1 × 4) + (2 × 3) = 10

What a learner can distinguish depends on which information its representation and computations retain. The inputs alone do not specify the relationships.

What does this example establish?

This calculation preserves the distinction between these three pairings. It does not distinguish every possible graph or establish a physical mechanism. Pooling after an interaction-aware update can retain information that averaging raw inputs loses. A useful scientific learner also needs appropriate representations, guiding signals and learning dynamics.

View the original worked diagram

Same units. Different relationships.

A representation must preserve the distinctions the scientific question depends on. In this small example, the feature values stay fixed while the connections change.

Both graphs contain feature values 1, 2, 3 and 4, with mean 2.5. Graph A connects 1 to 2 and 3 to 4; Graph B connects 1 to 3 and 2 to 4. Adding the products along their connections gives 14 for A and 11 for B.
Illustrative calculation, not measured data or a proposed model. Averaging these input features ignores the connections. A relation-dependent calculation can retain this particular distinction; it does not by itself establish a physical interaction or a mechanism.
Read the calculation and its limits

Each numbered node is an information unit carrying one scalar feature. Lines specify pairs in the example; their position and length have no physical meaning.

  • Feature mean, both graphs: (1 + 2 + 3 + 4) / 4 = 2.5.
  • Graph A, sum of connected-pair products: (1 × 2) + (3 × 4) = 14.
  • Graph B, sum of connected-pair products: (1 × 3) + (2 × 4) = 11.

The example motivates designing which units interact and how their information is combined. It does not show that every graph can be distinguished this way, or that pooling after an interaction-aware update necessarily loses this information.

View full-size diagram: Wide layout Vertical layout

Left: a blue sphere, a teal cube and a navy faceted form occupy coordinate planes. Centre: recurring forms connect in a sparse network. Right: an adjusted network sits beside amber reference tiles, with faint outlines suggesting previous positions.

Representations organise scientific states; interactions connect them; learning revises the system using evidence and guiding signals. These choices are designed together. This conceptual illustration does not specify a model architecture; the worked example on this page makes one interaction choice explicit.

Space
Represent what matters
Interaction
Expose meaningful relations
Learning
Update from evidence

Conceptual framework

From a scientific question to a testable mechanism

A scientific question frames the joint design of representation space, interaction structure and learning dynamics, leading to a testable mechanism. The middle dimensions influence one another.

View full-size framework: Wide layout Vertical layout

Read the framework step by step
  1. 01

    Scientific question

    Define the distinction, mechanism, or decision the learner must support.

  2. 02

    Representation space

    Encode states so scientifically relevant structure can be preserved.

  3. 03

    Interaction structure

    Make the relations that may drive behaviour explicit and inspectable.

  4. 04

    Learning dynamics

    Update structure from evidence while tracking stability and uncertainty.

  5. 05

    Testable mechanism

    Return an explanation, control, or design implication to evidence.

This diagram illustrates representation and learning within Pillar I. It is a conceptual framework, not an experimental result.

Scope

Design the model, the system, and its evaluation.

These choices determine which distinctions a system can preserve, which relationships it can express, and how it can use limited evidence.

01

Representation space

Organise molecular, sequence, material, or multimodal states around distinctions that matter to the scientific question.

02

Model architecture and information flow

Design model architectures and information flow to preserve scientific distinctions and express relevant relationships.

03

Learning signals and objectives

Use labels, constraints, perturbations, and learning objectives that reflect the intended scientific question.

04

Learning dynamics

Study how representations and interactions stabilise, transfer, fail, and change as new evidence arrives.

05

Systems and research infrastructure

Study how models, data, simulation, experiments, tools, and scientific judgment work together, and what can be tested, compared, and reused.

06

Scientific evaluation

Assess progress toward scientific understanding and reliable design.

Research contributions

Methods that make scientific structure accessible.

We develop representations, interaction models and evaluation methods that connect learning architecture to scientific questions.

Method families under study

  • Structured and geometric representation learning
  • Interaction-aware and pair-specific modelling
  • Contrastive, weakly guided, and multi-view learning
  • Stability, sensitivity, and uncertainty analysis
  • Perturbation-centred interpretation and controls
  • Research infrastructure and scientific evaluation

What we aim to develop

Representation specification
A clear description of states, invariances, limits and scientific meaning.
Interaction map
A description of the relations a model captures and how alternative explanations can be tested.
Evaluation framework
Comparisons, controls and uncertainty tests that reveal where a learning method succeeds and fails.
Reusable learning component
A documented primitive, operator, or module that can be challenged in more than one testbed.

Representative testbeds

The learner must survive more than one scientific setting.

Testbeds are used to challenge transfer, identifiability, and evidence requirements. They do not redefine the Pillar as an applications category.

  • 01Molecular interactions and drug discovery
  • 02Proteins, peptides, and sequences
  • 03Biomaterials and delivery systems
  • 04Complex scientific data and mechanisms

Research horizon

Separate present work from future synthesis.

These are planning windows. Expansion will follow research progress and validation.

  1. Now

    Mechanistic questions in molecular and materials science

    We develop and test AI methods for mechanism understanding, discovery, and design through scientific questions and feedback from experiments and simulation.

  2. Over approximately five years

    Building reusable scientific capabilities

    We aim to develop reusable representation and model methods, scientific system architectures, research infrastructure, evidence-acquisition strategies, and evaluation systems that support mechanism understanding and reliable design.

  3. Over approximately five to ten years

    Testing principles across systems

    We aim to extract mathematical, computational, and system-design principles and test how these methods and capabilities transfer and combine across broader scientific fields.

Scientific principles

A learning system is credible only when it can be challenged.

Separate structure from shortcuts

Use strict splits, matched controls, and null tests that challenge easier alternative explanations.

Report stability and failure

Treat sensitivity, uncertainty, negative evidence, and boundary conditions as part of the scientific result.

Require a testable consequence

Interpretation should imply a perturbation, control, observation, or design decision that could be wrong.

Make results reproducible

Connect conclusions to the data, methods and analyses that support them.