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Cookbook

End-to-end recipes from real Silico experiments — each pairs the research workflow with the science, and forks into your own workspace so you can pick up where it left off.

Getting startedGuided tutorials and faithful paper replications to get oriented.3 recipesLife sciencesGenomic and protein foundation models put to work.4 recipesSafety & alignmentReading, steering, and training model behavior toward safer, more reliable outputs.4 recipes

All recipes

19 recipes
Build a tool-call safety guardrail from a model's activations

A live monitor that flags an unsafe tool call before it runs, powered by a linear probe that reads the model's own activations rather than its words

Language modelsLinear probesSafety & guardrails
What DPO changes inside a language model

A reader-driven tour of the features alignment amplifies and suppresses, and how much of it is visible in the preference data before training starts

Language modelsSparse autoencodersPost-training & RLSafety & guardrails
Reward shaping: trading off safety and compliance

Reward shaping is a tunable safety dose for DPO — a small α-sweep maps how much over-refusal each unit of added safety costs

Language modelsPost-training & RLSafety & guardrails
Driving novelty in protein generation models

A generation-time nudge that recovers novelty from a copy-prone design model

Life sciencesSteeringMemorization
Probe the copy-number axis in Evo 2 7B

a linear probe + steering vector for tandem-repeat copy number

Life sciencesLinear probesSteering
Train hallucinations out of a model using a probe of its own activations

A hallucination probe, then RL that uses it as a reward to cut the hallucination rate

Language modelsLinear probesPost-training & RLSafety & guardrails
Discovering the geometry of emotions

A map of emotion inside a language model — a polar readout plus a steering dial

Language modelsNeural geometrySteering
Train an agent with reinforcement learning in Silico

A GRPO run that trains a 4B agent to GPT-4.1 level

Language modelsPost-training & RLEvaluation & benchmarking
Building an AI Cancer Case Reviewer

Reproducing a molecular-tumor-board agent, then swapping out one subsystem at a time to find which design choices actually move the score

Language modelsEvaluation & benchmarkingAblationLLM Guardrails
Decoding your genome with EVEE

A reading of one human genome with a genomic foundation model: what its DNA carries, and why carrying a disease variant is almost never the same as having the disease.

Life sciencesLinear probes
Finding the Tree of Life in Evo 2

A faithful replication that reads bacterial phylogeny out of a genomic model's embeddings

Life sciencesNeural geometryEvaluation & benchmarking
Getting Started with Neural Geometry

A worked tutorial: find a structured concept hiding in a model's activations, prove it is real, and steer the model along it — on the seven days of the week in Llama-3.1-8B.

Language modelsNeural geometrySteeringCircuits & causal tracing
How LMs mix mechanisms to retrieve bound entities

Figure 2 of Mixing Mechanisms, rebuilt from scratch on causalab and verified against the raw interventions, then replicated across two model families — from a single Silico prompt

Language modelsCircuits & causal tracing
Reading and steering emotion inside a speaking AI

An autoregressive speech model carries a moving, frame-by-frame emotion signal as it talks. Reading that signal shows arousal is the trustworthy axis, and a single direction added during generation steers the prosody.

MultimodalAudio & speechNeural geometrySteeringLinear probes
Replicating Interpretability in the Wild

Recovering the IOI circuit from Wang et al. (2022) with a native path-patching primitive and no original-paper code, then a preliminary look at the same circuit in an 8B model

Language modelsCircuits & causal tracing
Replicating ROME's Causal Tracing

Recovering the causal-tracing sites from Meng et al. (2022) with a native activation-restoration primitive and no original-paper code, then testing whether the same structure appears in an 8B model

Language modelsCircuits & causal tracing
Steer a VLM's gaze over images

A ten-head gaze-steering handle that overrides a VLM's text prompt — a click-to-steer demo plus a prompt-conflict sweep

MultimodalVisionSteeringCircuits & causal tracing
Training a discovery SAE on Qwen3-4B

A general-purpose sparse autoencoder that turns Qwen3-4B into a browsable atlas of 40,960 labeled concepts

Language modelsSparse autoencodersAutointerpretability
Verbalizing the weekday manifold

A SelfIE read-out of a model's weekday geometry — a nameable ring plus a causal-subspace test

Language modelsNeural geometryCircuits & causal tracing