Analyzing the spikes to understand their statistics.

<p>(<b>A</b>) 10 identified transistors and (<b>B</b>) their spiking (rising edge) behavior over a short time window during behavior DK.</p

Understanding the processor.

<p>(<b>A</b>) For the processor we understand its hierarchical organization as well as which part of the silicon implements which function. For each of these “functional modules” we know how the outputs depend on the inputs. (<b>B</b>) For the brain, it is harder to be sure. The primate visual system is often depicted in a similar way, such as this diagram adapted from the classic Felleman and vanEssen [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005268#pcbi.1005268.ref066" target="_blank">66</a>] diagram. These areas are primarially divided according to anatomy, but there is extensive debate about the ideal way of dividing the brain into functional areas. Moreover, we currently have little of an understanding how each area’s outputs depend on its inputs.</p

Optical reconstruction of the microprocessor to obtain its connectome.

<p>In [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005268#pcbi.1005268.ref011" target="_blank">11</a>], the (<b>A</b>) MOS 6502 silicon die was examined under a visible light microscope (<b>B</b>) to build up an image mosaic (<b>C</b>) of the chip surface. Computer vision algorithms were used to identify metal and silicon regions (<b>E</b>) to detect transistors (<b>F</b>), (<b>G</b>) ultimately producing a complete accurate netlist of the processor (<b>D</b>).</p

Examining local field potentials to understand network properties.

<p>We recorded from the processor during behavior DK. (<b>A</b>) Transistor switching is integrated and low-pass filtered over the indicated region. (<b>B</b>) local-field potential measurements from the indicated areas. (<b>C</b>) Spectral analysis of the indicated LFP regions identifies varying region-specific oscillations or “rhythms”.</p

Dimensionality Reduction to understand the roles of transistors.

<p>We apply non-negative matrix factorization (NMF) to the space invaders (SI) task. (<b>A</b>) shows the six reduced dimensions as a function of time showing clear stereotyped activity. (<b>B</b>) the learned transistor state vectors for each dimension (<b>C</b>) Map of total activity—color indicates the dimension where the transistor has maximum value, and both saturation and point size indicate the magnitude of that value.</p

Quantifying tuning curves to understand function.

<p>Mean transistor response as a function of output pixel luminance. (<b>A</b>) Some transistors exhibit simple unimodal tuning curves. (<b>B</b>) More complex tuning curves. (<b>C</b>) Transistor location on chip.</p

Spike-word analysis to understand synchronous states.

<p>(<b>A</b>) Pairs of transistors show very weak pairwise correlations during behavior SI, suggesting independence. (<b>B</b>) If transistors were independent, shuffling transistor labels (blue) would have no impact on the distribution of spikes per word, which is not the case (red).</p

Lesioning every single transistor to identify function.

<p>We identify transistors whose elimination disrupts behavior analogous to lethal alleles or lesioned brain areas. These are transistors whose elimination results in the processor failing to render the game. (<b>A</b>) Transistors which impact only one behavior, colored by behavior. (<b>B</b>) Breakdown of the impact of transistor lesion by behavioral state. The elimination of 1565 transistors have no impact, and 1560 inhibit all behaviors.</p

Discovering connectivity and cell type.

<p>Reproduced from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1005268#pcbi.1005268.ref031" target="_blank">31</a>]. (<b>A</b>) The spatial distribution of the transistors in each cluster show a clear pattern (<b>B</b>) The clusters and connectivity versus distance for connections between Gate and C1, Gate and C2, and C1 and C2 terminals on a transistor. Purple and yellow types have a terminal pulled down to ground and mostly function as inverters. The blue types are clocked, stateful transistors, green control the ALU and orange control the special data bus (SDB).</p

The processor activity map.

<p>For each of three behavioral states we plotted all the activities. Each transistor’s activity is normalized to zero-mean and unit variance and plotted as a function of time.</p