A Data Scientist’s Guide to Picking an Optimal Approximate Nearest-Neighbor Algorithm

Authors: Braden Riggs and George Williams

Choices are hard, let me help you with some recommendations. Photo by Anthony Martino on Unsplash

Whether you are new to the field of data science or a seasoned veteran, you have likely come into contact with the term, ‘nearest-neighbor search’, or, ‘similarity search’. In fact, if you have ever used a search engine, recommender, translation tool, or pretty much anything else on the internet then you have probably made use of some form of nearest-neighbor algorithm. These algorithms, the ones that permeate most modern software, solve a very simple yet incredibly common problem. Given a data point, what is the closest match from a large selection of data points, or rather what point is most like the given point? These problems are “nearest-neighbor” search problems and the solution is an Approximate Nearest Neighbor algorithm or ANN algorithm for short.

Approximate nearest-neighbor algorithms or ANN’s are a topic I have blogged about heavily, and with good reason. As we attempt to optimize and solve the nearest-neighbor challenge, ANN’s continue to be at the forefront of elegant and optimal solutions to these problems. Introductory Machine learning classes often include a segment about ANN’s older brother kNN, a conceptually simpler style of nearest-neighbor algorithm that is less efficient but easier to understand. If you aren’t familiar with kNN algorithms, they essentially work by classifying unseen points based on “k” number of nearby points, where the vicinity or distance of the nearby points are calculated by distance formulas such as euclidian distance.

ANN’s work similarly but with a few more techniques and strategies that ensure greater efficiency. I go into more depth about these techniques in an earlier blog here. In this blog, I describe an ANN as:

A faster classifier with a slight trade-off in accuracy, utilizing techniques such as locality sensitive hashing to better balance speed and precision.
– Braden Riggs, How to Benchmark ANN Algorithms

The problem with utilizing the power of ANNs for your own projects is the sheer quantity of different implementations open to the public, each having their own benefits and disadvantages. With so many choices available how can you pick which is right for your project?

Bernhardsson and ANN-Benchmarks to the Rescue

For this project, we need a little help from the experts. Photo by Tra Nguyen on Unsplash

We have established that there are a range of ANN implementations available for use. However, we need a way of picking out the best of the best, the cream of the crop. This is where Aumüller, Bernhardsson, and Faithfull’s paper ANN-Benchmarks: A Benchmarking Tool for Approximate Nearest Neighbor Algorithms and its corresponding GitHub repository comes to our rescue.

The project, which I have discussed in the past, is a great starting point for choosing the algorithm that is the best fit for your project. The paper uses some clever techniques to evaluate the performance of a number of ANN implementations on a selection of datasets. It has these ANN algorithms solve nearest-neighbor queries to determine the accuracy and efficiency of the algorithm at different parameter combinations. The algorithm uses these queries to locate the 10 nearest data points to the queried point and evaluates how close each point is to the true neighbor, which is a metric called Recall. This is then scaled against how quickly the algorithm was able to accomplish its goal, which it called Queries per Second. This metric provides a great reference for determining which algorithms may be most preferential for you and your project.

Screenshot from an earlier blog where I recreated Bernhardsson’s results benchmarking ANN algorithms on the Gloce-25-angular NLP dataset. Read more here. Image by Author.

Part of conducting this experiment requires picking the algorithms we want to test, and the dataset we want to perform the queries on. Based off of the experiments I have conducted on my previous blogs, narrowing down the selection of algorithms wasn’t difficult. In Bernhardsson’s original project he includes 18 algorithms. Given the performance I had seen in my first blog, using the glove-25 angular natural language dataset, there are 9 algorithms worth considering for our benchmark experiment. This is because some algorithms perform so slowly and so poorly that they aren’t even worth considering in this experiment. The algorithms selected are:

  • Annoy: Spotify’s “Approximate Nearest Neighbors Oh Yeah” ANN implementation.
  • Faiss: The suite of algorithms Facebook uses for large dataset similarity search including Faiss-lshFaiss-hnsw, and Faiss-ivf.
  • Flann: Fast Library for ANN.
  • HNSWlib: Hierarchical Navigable Small World graph ANN search library.
  • NGT-panng: Yahoo Japan’s Neighborhood Graph and Tree for Indexing High-dimensional Data.
  • Pynndescent: Python implementation of Nearest Neighbor Descent for k-neighbor-graph construction and ANN search.
  • SW-graph(nmslib): Small world graph ANN search as part of the non-metric space library.

In addition to the algorithms, it was important to pick a dataset that would help distinguish the optimal ANN implementations from the not so optimal ANN implementations. For this task, we chose 1% — or a 10 million vector slice — of the gargantuan Deep-1-billion dataset, a 96 dimension computer vision training dataset. This dataset is large enough for inefficiencies in the algorithms to be accentuated and provide a relevant challenge for each one. Because of the size of the dataset and the limited specification of our hardware, namely the 64GBs of memory, some algorithms were unable to fully run to an accuracy of 100%. To help account for this, and to ensure that background processes on our machine didn’t interfere with our results, each algorithm and all of the parameter combinations were run twice. By doubling the number of benchmarks conducted, we were able to average between the two runs, helping account for any interruptions on our hardware.

This experiment took roughly 11 days to complete but yielded some helpful and insightful results.

What did we find?

After the exceptionally long runtime, the experiment completed with only three algorithms failing to fully reach an accuracy of 100%. These algorithms were Faiss-lshFlann, and NGT-panng. Despite these algorithms not reaching perfect accuracy, their results are useful and indicate where the algorithm may have been heading if we had experimented with more parameter combinations and didn’t exceed memory usage on our hardware.

Before showing off the results, let’s quickly discuss how we are presenting these results and what terminology you need to understand. On the y-axis, we have Queries per Second or QPS. QPS quantifies the number of nearest-neighbor searches that can be conducted in a second. This is sometimes referred to as the inverse ‘latency’ of the algorithm. More precisely QPS is a bandwidth measure and is inversely proportional to the latency. As the query time goes down, the bandwidth will increase. On the x-axis, we have Recall. In this case, Recall essentially represents the accuracy of the function. Because we are finding the 10 nearest-neighbors of a selected point, the Recall score takes the distances of the 10 nearest-neighbors our algorithms computed and compares them to the distance of the 10 true nearest-neighbors. If the algorithm selects the correct 10 points it will have a distance of zero from the true values and hence a Recall of 1. When using ANN algorithms we are constantly trying to maximize both of these metrics. However, they often improve at each other’s expense. When you speed up your algorithm, thereby improving latency, it becomes less accurate. On the other hand, when you prioritize its accuracy, thereby improving Recall, the algorithm slows down.

Pictured below is the plot of Queries Performed per Second, over the Recall of the algorithm:

The effectiveness of each algorithm as evaluated by Queries per Second which is scaled logarithmically and Recall (accuracy). The further up and to the right the algorithm’s line is, the better said algorithm performed. Image by Author.

As evident by the graph above there were some clear winners and some clear losers. Focusing on the winners, we can see a few algorithms that really stand out, namely HNSWlib (yellow) and NGT-panng (red) both of which performed at a high accuracy and a high speed. Even though NGT never finished, the results do indicate it was performing exceptionally well prior to a memory-related failure.

So given these results, we now know which algorithms to pick for our next project right?

Unfortunately, this graph doesn’t depict the full story when it comes to the efficiency and accuracy of these ANN implementations. Whilst HNSWlib and NGT-panng can perform quickly and accurately, that is only after they have been built. “Build time” refers to the length of time that is required for the algorithm to construct its index and begin querying neighbors. Depending on the implementation of the algorithm, build time can be a few minutes or a few hours. Graphed below is the average algorithm build time for our benchmark excluding Faiss-HNSW which took 1491 minutes to build (about 24 hours):

Average build time, in minutes, for each algorithm tested excluding Faiss-HNSW which took 24 hours to build. Note how some of the algorithms that ran quickly took longer to build. Image by Author.

As we can see the picture changes substantially when we account for the time spend “building” the algorithm’s indexes. This index is essentially a roadmap for the algorithm to follow on its journey to find the nearest-neighbor. It allows the algorithm to take shortcuts, accelerating the time taken to find a solution. Depending on the size of the dataset and how intricate and comprehensive this roadmap is, build-time can be between a matter of seconds and a number of days. Although accuracy is always a top priority, depending on the circumstances it may be advantageous to choose between algorithms that build quickly or algorithms that run quickly:

  • Scenario #1: You have a dataset that updates regularly but isn’t queried often, such as a school’s student attendance record or a government’s record of birth certificates. In this case, you wouldn’t want an algorithm that builds slowly because each time more data is added to the set, the algorithm must rebuild it’s index to maintain a high accuracy. If your algorithm builds slowly this could waste valuable time and energy. Algorithms such as Faiss-IVF are perfect here because they build fast and are still very accurate.
  • Scenario #2: You have a static dataset that doesn’t change often but is regularly queried, like a list of words in a dictionary. In this case, it is more preferential to use an algorithm that is able to perform more queries per second, at the expense of built time. This is because we aren’t adding new data regularly and hence don’t need to rebuild the index regularly. Algorithms such as HNSWlib or NGT-panng are perfect for this because they are accurate and fast, once the build is completed.

There is a third scenario worth mentioning. In my experiments attempting to benchmark ANN algorithms on larger and larger portions of the deep1b dataset, available memory started to become a major limiting factor. Hence, picking an algorithm with efficient use of memory can be a major advantage. In this case, I would highly recommend the Faiss suite of algorithms which have been engineered to perform under some of the most memory starved conditions.

Regardless of the scenario, we almost always want high accuracy. In our case accuracy, or recall, is evaluated based on the algorithm’s ability to correctly determine the 10 nearest-neighbors of a given point. Hence the algorithm’s performance could change if we consider its 100 nearest-neighbors or its single nearest-neighbor.

The Summary

What will you pick for your next project? Photo by Franck V. on Unsplash

Based on our findings from this benchmark experiment there are clear benefits to using some algorithms as opposed to others. The key to picking an optimal ANN algorithm is understanding what about the algorithm you want to prioritize and what engineering tradeoffs you are comfortable with. I recommend you prioritize what fits your circumstances, be that speed (QPS), accuracy (Recall), or pre-processing (Build time). It is worth noting algorithms that perform with less than 90% Recall aren’t worth discussing. This is because 90% is considered to be the minimum level of performance when conducting nearest-neighbor search. Anything less than 90% is underperforming and likely not useful.

With that said my recommendations are as follows:

  • For projects where speed is a priority, our results suggest that algorithms such as HNSWlib and NGT-panng perform accurately with a greater number of queries per second than alternative choices.
  • For Projects where accuracy is a priority, our results suggest that algorithms such as Faiss-IVF and SW-graph prioritize higher Recall scores, whilst still performing quickly.
  • For projects where pre-processing is a priority, our results suggest that algorithms such as Faiss-IVF and Annoy exhibit exceptionally fast build times whilst still balancing accuracy and speed.

Considering the circumstances of our experiment, there are a variety of different scenarios where some algorithms may perform better than others. In our case, we have tried to perform in the most generic and common of circumstances. We used a large dataset with high, but not excessively high, dimensionality to help indicate how these algorithms may perform on sets with similar specifications. For some of these algorithms, more tweaking and experimentation may lead to marginal improvements in runtime and accuracy. However, given the scope of this project it would be excessive to attempt to accomplish this with each algorithm.

If you are interested in learning more about Bernhardsson’s project I recommend reading some of my other blogs on the topic. If you are interested in looking at the full CSV file of results from this benchmark, it is available on my GitHub here.

Future Work

Whilst this is a good starting point for picking ANN algorithms there are still a number of alternative conditions to consider. Going forward I would like to explore how batch performance impacts our results and whether different algorithms perform better when batching is included. Additionally, I suspect that some algorithms will perform better when querying for different numbers of nearest-neighbors. In this project, we chose 10 nearest neighbors, however, our results could shift when querying for 100 neighbors or just the top 1 nearest-neighbor.


  1. Computer specifications: 1U GPU Server 1 2 Intel CD8067303535601 Xeon® Gold 5115 2 3 Kingston KSM26RD8/16HAI 16GB 2666MHz DDR4 ECC Reg CL19 DIMM 2Rx8 Hynix A IDT 4 4 Intel SSDSC2KG960G801 S4610 960GB 2.5″ SSD.
  2. Link to How to Benchmark ANN Algorithms: https://medium.com/gsi-technology/how-to-benchmark-ann-algorithms-a9f1cef6be08
  3. Link to ANN Benchmarks: A Data Scientist’s Journey to Billion Scale Performance: https://medium.com/gsi-technology/ann-benchmarks-a-data-scientists-journey-to-billion-scale-performance-db191f043a27
  4. Link to CSV file that includes benchmark results: https://github.com/Briggs599/Deep1b-benchmark-results


  1. Aumüller, Martin, Erik Bernhardsson, and Alexander Faithfull. “ANN-benchmarks: A benchmarking tool for approximate nearest neighbor algorithms.” International Conference on Similarity Search and Applications. Springer, Cham, 2017.
  2. Deep billion-scale indexing. (n.d.). Retrieved July 21, 2020, from http://sites.skoltech.ru/compvision/noimi/
  3. Liu, Ting, et al. “An investigation of practical approximate nearest neighbor algorithms.” Advances in neural information processing systems. 2005.

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