Period ending 2026-09-21
2 new papers
A weekly snapshot of new work published in Model Activations.
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Period ending 2026-09-21
A weekly snapshot of new work published in Model Activations.
Period ending 2026-09-14
A weekly snapshot of new work published in Model Activations.
Period ending 2026-09-07
A weekly snapshot of new work published in Model Activations.
158 papers
concept'' inside a model is real rather than an artifact of sequence composition. We introduce a framework that combines sparse dictionary learning with causal intervention to extract, validate, and causally test interpretable features in genomic foundation models. Training top-$k$ sparse autoencoders on the hidden activations of two architecturally distinct models, Nucleotide Transformer ($6$-mer tokenization) and DNABERT-2 (byte-pair encoding), we recover thousands of monosemantic features that map to transcription-factor (TF) sequence motifs. We show that the naive validation of such features against position weight matrices is severely confounded by GC composition and repetitive elements, producing hundreds of spurious TF features'', and we develop a composition-matched, binding-resolved protocol that removes these confounds. Critically, we move beyond correlation: by ablating individual dictionary directions during the model's forward pass and measuring the induced shift in the model's own predictive distribution, we establish that specific features are \emph{causally} used to represent cell-type-specific TF binding, not merely motif presence. Across three transcription factors (CTCF, GATA1, REST) and both architectures, causally validated binding features emerge reproducibly (-- of tested features per condition), while two classes of negative control, scrambled binding labels and randomly selected features, yield no detectable signal. The framework is purely computational, uses only public data, and provides a reusable standard for interpretability claims in genomic deep learning.Can this object be found in the desert?'' or Is this prompt malicious?'' We measure how the instruction changes the model's internal representation using at a single readout point. We explore eight different MAGs. The extracted reasoning features predict the models' own world understanding and judgment, can be approximated into a single activation direction, we found that some features are more linearly represented and some less, this linear representation, which is vector steering, can change the LLMs' decisions through activation steering by injecting reasoning features. Finally, we use the same method to select the best training datasets for prompt-injection classifier probes: while similarity between ordinary activations is almost unrelated to downstream performance, RFD-based similarity achieves Top-1 and Top-2 accuracy.