Generative Art and Biology: Creating Life Through Computation

February 23, 2021 // Tom - art , julia , gpu

Computer graphics have been an interest of mine for as long as I’ve used a computer. The ability to create life like renderings has always held my captivation in one way or another. I grew up using open source graphics software like GIMP and later Blender3D. I fondly remember letting the family laptop run all night rendering frames for a 3D animation I had made in Blender for school. Being able to theoretically produce photorealistic images like Pixar or Lucasfilm made me feel like I could create my own reality, only given enough time and patience. Instead of going to school for animation, I hedged my bets on studying Computer Engineering, learning how the computer worked rather than learning how to use the suites of programs to their fullest. Throughout university I kept up with computer graphics by reading SIGGRAPH papers, watching the talks, and trying to implement some basic graphics programs myself.

Inherently, computation is often seen as uncreative. Systems are often purpose designed for a singular task: serve this web resource, convert this file, send this message. Certainly artists use computation to complement their vision, like a traditional artist would use with paint on canvas. This process still requires a large amount of input from the human artist: laying out compositions, selecting pallets, and tweaking lighting. What if a computer was solely responsible for the generation of the forms traditionally created by an artist? Writing code is a creative process, but can we design our code to be creative? Generative art puts the relationship between artist, programmer, and concept front and center. Manfred Mohr, one of the original generative artists, states succinctly in his interview in Computing Europe 1974:

THE MACHINE SEEN AS AN EXTENSION OF US.

His primary thesis being that the computer is a perfect tool for not only artists but everyone. This was a forward-looking view in 1974 as the computer is no longer a beige box sitting on a desk in our households, it has been integrated into nearly every facet of our lives, even so far as to be come a companion that we rely on constantly. We can extend ourselves reflexively into the digital realm, despite not understanding all the behind-the-scenes operations. Mohr envisions the artist’s relationship to computer systems as a dialectic one: we propose a thesis to a computational system, it responds with a generated anti-thesis and the cumulative outcome of this process many times over is the synthesis or final piece. A discourse, an iterative feedback loop revisited many times over in search of a common truth. Generative art is the combination of our messy, leaky, subjective outlook and the cold, meticulous computing of a machine.

THE IMITATION GAME

In some previous work where I modelled Reaction Diffusion systems with Julia, I explored the emergent organization of two simulated chemicals. Small variations in chemical feed and kill rates produce a large variation in overall structure and behavior at different scales. I use the term emergent here because structures emerge from random noise, the code is naively computing frame after frame, unaware that it’s producing such organic results. The term emergent gameplay refers to the complex situations that are produced from interactions with simple game mechanics. I’m simply programming a 0-player game, and letting the rules do the rest.

A couple of weeks after I finished up my Reaction Diffusion work, I found a post by Sage Jenson, in which they outlined a process for simulating slime molds (Physarum Polycephalum). They also did an exceptional job outlining the high level implementation with some nice drawings and animations. I was instantly mesmerized by the animated ebb and flows of slime. The structures that emerged were extremely intricate, and immediately invoked imagery of veins and roots. What stood out most to me was the the varied scale of certain features within the model. Small strands and loops combine and swirl to produce larger super structures which stabilize after 100 or so frames. I was astonished when I read the full paper containing the simple rules which produced these results.

In the real world, Physarum Polycephalum is a form of acellular slime mold hailing from the protist’s evolutionary tree. It typically lives on tree bark or stones in damp environments, feeding on basic food sources. Its life cycle contains many steps, however the most interesting behavior known as “Cytoplasmic Streaming”, happens during the organism’s plasmodium phase. This slime mold can can even solve the shortest path problem, with zero neurons.

Unfortunately, the authors of the slime mold paper weren’t able to get their virtual slime molds to solve complex pathing problems. They focused on reproducing the slim mold’s form with code, rather than precisely trying to simulate it down to the molecular scale. I was mainly interested in generating interesting forms, so I booted up a fresh Julia notebook and set out creating an implementation of my own.

AS WITH ALL THINGS, START SMALL

The paper Characteristics of pattern formation and evolution in approximations of physarum transport networks which Sage has based their work on, uses an agent based approach to approximate a slime mold’s behavior. We’ll start off with the concept of a model, which is essentially some data and rules. The data can be many things, including images, text, or numbers. The rules are the set of steps or computations needed to progress the model forward. In our case, each step represents a fixed interval of time. The model is initialized with some starting information, i.e. randomizing agents, defining parameters. We then run multiple steps, hundreds, thousands, sometimes millions of times, and observe how the data changes over time. These aren’t hard and fast definitions for a model, but are generalized within the context we’ll be using it.

For our specific model, we’ll start with the data. Since our model is agent-based, we’ll need some common environment or world for each agent to interact with. This provides a rudimentary way for agents to communicate. As outlined in the paper, they use a chemoattractant matrix, which I typically refer to as the grid. Functionally, this is just a greyscale image which each agent can “mark” to notify nearby agents. Below is a typical chemoattractant matrix after running the model for a 100 frames. Where the image is brighter, there is a higher density of agents.

Within the code, I’m using a CuArray{Float32, 3} to represent this information, I’ll get into why I’m using a 3D matrix instead of a 2D one later. Next, we’ll need some way to keep track of each agent’s position and it’s direction. Here’s a basic outline of how that’s stored per agent. Multiple SlimeAgents are appended to a list and each one is processed via the same set of rules. Each step, the agent’s internal data is updated to simulate it moving and rotating.

mutable struct SlimeAgent
x_position::Float32
y_position::Float32
end

In addition, we also need a few more global parameters to define where the agent senses, how much it rotates towards other agents, how far it moves, and how much chemoattractant it places when it’s finished moving. Since these are static parameters, we just define them at the model level, defining the agent structure to be only information that’s changing with respect to time. The finished agent looks something like this:

They consists of a body or anchor point, and three sensors which are projected in front of each agent for detecting chemoattractant. Next, we need a set of rules to move our data from one step to the next. I’ve outlined the pseudo-code below:

1. Motor Step
a. Check if agent can move forward.
b. if so: move and deposit "chemoattractant".
c. else: rotate in a random direction.
2. Sense Step
a. Sample the chemoattractant matrix in three directions
-> front, left, right.
b. if front sensor is the strongest: stay facing that direction.
c. else if front is the weakest: rotate randomly, left or right.
d. else if left is stronger than right: rotate left.
e. else if right is stronger than left: rotate right.

I’ve broken it down into three steps in my code motor, sense and swivel. First up, is the motor step:

Each agent will check whether it’s inbounds of the world, perform a basic obstacle detection check to see if any other walls are in front of it, then move forward, depositing a fixed amount of chemoattractant on the grid. If the agent is unable to move forward, we use a “dumb” motion planning algorithm. Just spin in place until you get unstuck! Next, the agent will sense its surroundings:

The agent samples the grid three times, once in front, to the left and to the right. In the initial parameters we give the model, we describe how far and wide each agent should sample. We do a basic linear transform to get each value, taking into account the agent’s heading, to find where each sensor should be. In the paper, the agent technically could sample more than one pixel of the grid but in my implementation I just round to the nearest pixel and take the value directly.

We then take the rules I outlined above and apply them to swivel the agent towards the direction of highest concentration. Letting this run over many steps with a couple of agents results in some interesting behavior.

Each agent follows each other’s trails, and tracing out new paths when they encounter the end of a specific path. I should also mention a fourth secret step: we also need to perform a gaussian blur to diffuse the chemoattractant around the map over time, this allows higher concentrations to spread out and fade overtime.

SCALING UP AND SCALING OUT

Now if you’ve read my blog before, you know what’s coming next… it’s time to scale up our simulation with GPUs. Unfortunately I don’t have much CPU based code to show, as I nearly immediately jumped to optimizing it with GPU. Although this time I’m using a new library called KernelAbstractions.jl. It’s a nice piece of kit, and allows generic kernels to be written, handling the routing between function and multiple parallel back-ends.

First on the list, we need a slightly more efficient way to store agent information. Since the GPU prefers vectorized data, I decompose the list of agents into each component x_position, y_position, and heading. Since the number of agents doesn’t change over time, we can make a couple static vectors in memory on the GPU and update them as needed. It ends up looking like this:

struct DecomposedGPUAgents
x::CuArray{Float32, 1}
y::CuArray{Float32, 1}
h::CuArray{Float32, 1}
v::CuArray{Int64, 1}
end

It’s passed to our kernel (shown below) by a helper function to route the data to the right place. Keep in mind, every piece of data is statically allocated within GPU memory on initialization, we’re just passing references around to each kernel. I also implemented a “variant” key which is used to look up an agent’s specific parameters for rotation, sensing, etc. This allows me to have multiple “species” interacting with one another. It’s also why I define the grid as a 3D matrix, each slice contains each variant’s chemoattractant maps.

@kernel function motor_kernel!(x_a, y_a, h_a, v_a, obs, @Const(configs), @Const(rand_a), grids, @Const(w_s))
i = @index(Global)

v = v_a[i]
d, c = configs[1, v], configs[2, v]

# project future position, check world bounds, check obstacle map, etc.
x′ = x_a[i] + cos(h_a[i]) * d
y′ = y_a[i] + sin(h_a[i]) * d

# LOL float32 -> int32 in GPU land
w_idx = unsafe_trunc(Int32, clamp(ceil(x′), 1, w_s[1]))
w_idy = unsafe_trunc(Int32, clamp(ceil(y′), 1, w_s[2]))

if check_bounds(w_idx, w_idy, w_s) && obs[w_idx, w_idy] > 0.0f0
x_a[i] = x′
y_a[i] = y′
grids[v, w_idx, w_idy] += c
else
h_a[i] = rand_a[i] * 2π
end

nothing
end

Note the @kernel and @index macros, these are from KernelAbstractions.jl and they help to generalize kernel code. You’ll notice I’m using functions like clamp and ceil have no special incantations, because they are remapped by CUDA.jl to the appropriate GPU functions on the hardware. We perform all these calculations agent-wise, and going through our 3 steps: motor, sense, then swivel in a similar fashion.

For our fourth secret step, I wrote a simple box blur kernel, modifies the grid in place, then multiplies by a decay factor to lower the overall concentrations of chemoattractant.

@kernel function box3x3!(a, @Const(a_w), @Const(a_h), @Const(k_w), @Const(k_h))
""" Super basic box blur, fixed kernel """
g, i, j = @index(Global, NTuple)

kw_off = unsafe_trunc(Int32, floor(k_w/2))
kh_off = unsafe_trunc(Int32, floor(k_h/2))

nx, ny = (i - kw_off, i + kw_off), (j - kh_off, j + kh_off)

# Clamp the world neighborhood to our bounds
nx = clamp.(nx, 1, a_w)
ny = clamp.(ny, 1, a_h)

a_v = view(a, g, UnitRange(nx...), UnitRange(ny...))

a[g, i, j] = sum(a_v) / Float32(length(a_v))
end

VARIATION: THE SPICE OF LIFE

At this point I’ve worked out most of the bugs, I can throw a quick color ramp (magma is shown above.) to make things look presentable. By all accounts, I thought I was done until I saw Michael Fogleman’s post about slime molds. He implemented a method for different variants to interact via an attraction matrix. Basically, we keep a separate grid for each variant, and a lookup table which weighs each variant against itself and others. An attraction matrix for 3 variants might look like the following:

3×3 Array{Float32,2}:
1.08781   -0.795218  -1.31938
-0.958785   0.69557   -1.61444
-1.05305   -0.502094   0.96375

Cell [1,1] is how attracted variant 1 is to itself, cell [1,2] is how attracted (negatively in this case) to variant 2, and so on for variant 3. We generate a temporary “view” or chemoattractant map from each variants perspective, combining each individual map, taking into account each other variant’s weight.

function attract!(model)
# For each variant...
for variant in 1:size(model.grids)[1]
# Weigh each grid with it's respective variant weight.
for other_variant in 1:size(model.grids)[1]

factor = model.agent_attractors[variant, other_variant]
model.temp_grid[variant, :, :] += model.grids[other_variant, :, :] .* factor
end
end

# Double buffer our results.
copyto!(model.grids, model.temp_grid)
return nothing
end

Now, I must admit: I used Michael’s solution in Go as inspiration here. All that stuff about good artists copying and great artists stealing. What’s to say for an inspired artist? I spent way too much time trying to figure out a proper solution on my own, and his was quite clever. He’s single handedly responsible for pushing this project’s deadline because I really really wanted to get multiple variants working. Thanks again Michael! 😁

For the coloring: I just did a simple linear combination, and corrected the gamma by hand. Here’s some more multi-agent renders.

A bonus render, featuring an interesting orange sample from testing my CMYK like color combination code…

Anyways, I’ll most likely revisit this project in the future, as I accidentally wrote a great framework for visualizing agent based simulations. However, I’m quite burnt out from debugging, writing, and relearning Illustrator for those slick graphics earlier. Thanks again for reading and I hope you enjoyed coming with me on this little journey!