Eli Lilly and · Machine Learning Engineer
Updated · 2026-10-02

Eli Lilly and Machine Learning Engineer
Interview Questions & Guide 2026

THE 60-SECOND BRIEF

As a Machine Learning Engineer at Eli Lilly and, you will play a pivotal role in harnessing advanced machine learning techniques to drive innovation in pharmaceuticals. Your work will directly impact the development of therapies and solutions that improve patient outcomes. The integration of data science and machine learning within the company enables the transformation of vast datasets into actionable insights, ultimately enhancing the efficacy of drug discovery and development processes.

If the loop includes an asynchronous take-home, treat it as a code review of you rather than as a puzzle: structure, what you chose to test, and what you wrote down about the constraint you were working under. Hold the stated time box and say what you would have done with more of it.

Eli Lilly and candidates report 3 rounds · ≈ 3-5 weeks. The stages below are what candidates describe, not a published process.

Bound every outbound call with a timeoutDetect concurrent edits instead of losing writesTrace a symptom to a mechanism under load

36 min read

Browse Machine Learning Engineer questions

See the practice prompts

14Practice promptsAcross five skill areas
3With worked solutionsIncluded in the practice prompts

As a Machine Learning Engineer at Eli Lilly and, you will play a pivotal role in harnessing advanced machine learning techniques to drive innovation in pharmaceuticals. Your work will directly impact the development of therapies and solutions that improve patient outcomes. The integration of data science and machine learning within the company enables the transformation of vast datasets into actionable insights, ultimately enhancing the efficacy of drug discovery and development processes.

This role is critical as it not only contributes to the scientific and medical advancements at Eli Lilly and but also positions the company at the forefront of technological innovation in healthcare. You will collaborate with interdisciplinary teams to tackle complex challenges, leveraging your expertise to develop models that predict drug interactions, optimize clinical trials, and personalize treatment solutions. The complexity and scale of the projects you will engage with make this position both challenging and rewarding, offering a unique opportunity to make a significant difference in the lives of patients.

01

Initial Screening Call

reported

Half of this call is the part candidates treat as small talk: start date, notice period, work authorisation and its timing, location and time zone, on-call, and the number. Those are what kill offers late, after several engineers have each spent a day. Surfacing a hard constraint now costs you nothing and occasionally buys you something, since a loop compressed to fit a competing deadline can usually only be arranged if it is asked for early. The common failure is deflecting the compensation question twice, then discovering at offer stage that the band never reached your number.

What to demonstrate

  • Whether your hard constraints are compatible with the role before a loop gets booked: earliest start, notice period, what authorisation you hold and when it needs action, days on site, willingness to carry a pager
  • Whether you give a compensation range with something behind it, such as current total compensation or a competing timeline, rather than leaving the band untested
  • Whether your stated timeline is real, since a competing deadline raised now is something scheduling can sometimes work around and the same deadline raised at offer stage usually is not

How to prepare

  • Write each constraint down in one line before the call and state them as facts rather than negotiating them live under a question you were not expecting
  • Set your range from two or three current data points for that level and location, and name the structure you are quoting in, so the number is comparable to the one they are holding
  • If another process is running, say where it stands and by when, and ask directly whether this loop can be scheduled inside that window
PracHub interview research ↗
02

In-Depth Interviews

reported

You cannot drill a format you do not know, so put the preparation into material that travels. Three pieces of your own work, each rehearsed until you can take a follow-up you did not anticipate, will carry a conversation or a code walkthrough equally well. Specificity is what separates that from filler. A number needs its definition before it means anything: a p99 is over some window and measured at some hop, and a server-side figure excludes the queueing and network time a client would see. The number you cannot qualify is the one to leave out.

What to demonstrate

  • Whether your examples carry detail only someone who did the work would hold, such as what the binding constraint actually was, which alternative you rejected and why it was worse, and what you measured on each side of the change
  • Whether a number survives one follow-up, meaning you can say what it was measured over and whether it moved because of your change or merely alongside it
  • Whether a failure is described with the specific change that followed it, rather than a lesson stated in general terms
  • Whether your part in a team effort is stated accurately, including what other people did

How to prepare

  • Write a page on each of three projects covering the constraint, the option you rejected, the measurement before and after, and what went wrong. Cut any line you cannot take a follow-up on, since you are writing the parts you will be pressed on rather than a summary.
  • Recover the real figures while you still have access: request volume, data size, latency with its percentile and window, team size, timeline. Note where each came from, whether a dashboard, a design document or memory, and mark the estimates so you can say which they are out loud.
  • Take your weakest project story to someone who works in a different area and have them ask why four times in succession. The point where you run out of answer is the part to go and re-read before the round.
PracHub interview research ↗
03

Team Interviews

reported

You cannot drill a format you do not know, so put the preparation into material that travels. Three pieces of your own work, each rehearsed until you can take a follow-up you did not anticipate, will carry a conversation or a code walkthrough equally well. Specificity is what separates that from filler. A number needs its definition before it means anything: a p99 is over some window and measured at some hop, and a server-side figure excludes the queueing and network time a client would see. The number you cannot qualify is the one to leave out.

What to demonstrate

  • Whether your examples carry detail only someone who did the work would hold, such as what the binding constraint actually was, which alternative you rejected and why it was worse, and what you measured on each side of the change
  • Whether a number survives one follow-up, meaning you can say what it was measured over and whether it moved because of your change or merely alongside it
  • Whether a failure is described with the specific change that followed it, rather than a lesson stated in general terms
  • Whether your part in a team effort is stated accurately, including what other people did

How to prepare

  • Write a page on each of three projects covering the constraint, the option you rejected, the measurement before and after, and what went wrong. Cut any line you cannot take a follow-up on, since you are writing the parts you will be pressed on rather than a summary.
  • Recover the real figures while you still have access: request volume, data size, latency with its percentile and window, team size, timeline. Note where each came from, whether a dashboard, a design document or memory, and mark the estimates so you can say which they are out loud.
  • Take your weakest project story to someone who works in a different area and have them ask why four times in succession. The point where you run out of answer is the part to go and re-read before the round.
PracHub interview research ↗

PracHub editorial advice for the preparation topics above.

01

Letting a slow dependency consume unbounded concurrency

The failure that takes a service down is usually not an error but a delay. A dependency answering in thirty seconds instead of fifty milliseconds holds each request's worker or connection six hundred times longer, and since required concurrency is arrival rate times latency, a fleet sized for sixty in-flight requests now needs thirty-six thousand to sustain the same rate - so it queues, and requests whose clients have already abandoned them still occupy resources. Retries make it precisely worse: a policy of three attempts triples the load on a dependency at the exact moment it is least able to serve, which is how one slow dependency becomes an outage of everything sharing that pool. Containment is four specific things - a timeout on every outbound call shorter than the caller's remaining budget, a bounded pool per dependency so one cannot starve the others, backoff with full jitter rather than a fixed delay so retries do not resynchronise, and a circuit that stops sending once the failure rate makes an attempt pointless.

02

Paginating with LIMIT/OFFSET over a set that changes while the client is reading it

OFFSET n makes the database produce and discard n rows before returning anything, so the cost of a page grows with its depth rather than with its size and page 500 costs five hundred pages of work. The correctness problem is worse than the cost: if a row is inserted or reordered between two page fetches, rows shift across the offset boundary and are either skipped entirely or returned twice, and neither outcome leaves any trace in the response for the client to detect. Keyset pagination - WHERE (sort_key, id) < ($last_sort_key, $last_id) ORDER BY sort_key DESC, id DESC LIMIT n, backed by an index in exactly that order - reads only the rows it returns and is stable against concurrent inserts. It requires the tie-break column: a timestamp is not unique, and duplicate sort keys straddling a page boundary reintroduce the skip it was adopted to remove.

03

Finishing a solution without stating its complexity

Give time and space in the same breath as the code, and define n explicitly when there are two sizes, since n nodes and m edges are not interchangeable. Space is the half that gets skipped: count the auxiliary structures you allocate and the recursion stack at its deepest, not only the answer you hand back.

04

Check-then-act on shared state

Read, decide, write is not safe under concurrency unless the decision and the write are one atomic step: a unique constraint with conflict handling, a compare-and-set, or a row lock held for the whole transaction. Two requests can both pass the existence check before either inserts, which shows up as duplicate rows under load and never in a single-threaded test.

Choose a category, try a prompt, then open its approach, worked solution or follow-up when you need it.

11 technical prompts3 include a worked solution

Describe how you would improve an existing machine learning model's pe…

medium
machine learning fundamentals

Describe how you would improve an existing machine learning model's performance.

Approach
  1. State the learning problem: the label, the unit of prediction and how the model is used.
  2. Say how you would validate it, and where leakage could enter the split.
  3. Name the simplest model that could work and what would make you move past it.
Follow-up
  • Where could label leakage enter this setup?
  • How would you know the model is overfitting?

Describe a machine learning project you have worked on and the impact …

medium
machine learning fundamentals

Describe a machine learning project you have worked on and the impact it had.

Approach
  1. Say how you would validate it, and where leakage could enter the split.
  2. Name the simplest model that could work and what would make you move past it.
  3. Pick the metric from the cost of each error type, not from habit.
Follow-up
  • How would you know the model is overfitting?
  • Where could label leakage enter this setup?

How do you handle overfitting in a machine learning model?

medium
machine learning fundamentals

How do you handle overfitting in a machine learning model?

Approach
  1. Name the simplest model that could work and what would make you move past it.
  2. State the learning problem: the label, the unit of prediction and how the model is used.
  3. Pick the metric from the cost of each error type, not from habit.
Follow-up
  • How would you know the model is overfitting?
  • What changes if the classes are heavily imbalanced?

What metrics would you use to evaluate the success of a machine learni…

medium
machine learning fundamentals

What metrics would you use to evaluate the success of a machine learning model in a clinical setting?

Approach
  1. State the learning problem: the label, the unit of prediction and how the model is used.
  2. Pick the metric from the cost of each error type, not from habit.
  3. Name the simplest model that could work and what would make you move past it.
Follow-up
  • How would you know the model is overfitting?
  • What changes if the classes are heavily imbalanced?

Track a rolling failure rate per destination for circuit decisions

easyWorked solution
sliding windowring buffercircuit breaker

The egress service delivers about 1,500 webhooks per second across roughly 40,000 destinations, each call bounded by a 10 second timeout. Maintain, per destination, the failure rate over the trailing 60 seconds so a caller can ask before dispatch whether the circuit should open. Attempts arrive as (destination_id, finished_at_ms, outcome). Requirement: amortised O(1) per attempt, with total memory bounded by the destination count rather than by traffic. Give the structure, its exact memory, and the rule that stops a destination with three attempts from opening a circuit.

Approach
  1. Name the exact-deque version and then reject it as the default. Holding timestamps and advancing a tail pointer past anything older than now minus 60 seconds is a correct two-pointer window at amortised O(1) per attempt, but its memory tracks in-window traffic, so one destination in a retry storm holds hundreds of thousands of entries while thousands of quiet destinations hold none.
  2. Use a ring of 60 one-second buckets per destination, each bucket a pair of counters for attempts and failures. On an attempt, advance the ring by the elapsed whole seconds, zeroing at most min(elapsed, 60) buckets, then increment the head. That is amortised O(1) with a fixed footprint per destination.
  3. State the footprint: 60 buckets times two 4-byte counters is 480 bytes of payload per destination, so 40,000 destinations is roughly 20 to 25 MB with per-entry overhead, bounded by the catalogue rather than by the rate. The cost is granularity, since the oldest bucket ages out in whole seconds, which is far tighter than the decision needs.
  4. Require a minimum sample before the circuit may open. A destination with three attempts and three failures reads as 100 percent and is not evidence; a floor of roughly 20 attempts in the window makes the ratio meaningful, and below that floor use a run of consecutive failures as the trigger instead.
  5. Expire idle destinations, or memory grows with every destination ever seen rather than with the live set. Hold the rings in a bounded LRU keyed on destination_id and treat a miss as no history, which is the correct default for an endpoint that has been silent for a minute.
  6. Keep the half-open probe out of the window arithmetic. After the circuit opens, one probe per interval decides whether to close it, and folding that single success into a window that still holds a 100 percent failure history would reopen the destination on one data point.
Worked solution 20 min
  1. Define the bucket struct and the advance step: take floor(finished_at_ms / 1000), compare with the ring's current second, zero min(delta, 60) buckets forward, then write into the new head.
  2. Trace a destination that receives 5 attempts, goes silent for 90 seconds, then receives one more, and confirm the rate is computed from one attempt rather than six.
  3. Compute total memory for 40,000 destinations at 60 buckets of two 4-byte counters, and state what changes if the window widens to 300 seconds.
  4. Write the open rule as a single predicate combining the minimum-attempt floor with the rate threshold.
EXPECTED RESULTA per-destination ring of 60 one-second (attempts, failures) buckets advanced lazily for amortised O(1) cost, roughly 480 bytes of counters per destination and about 20 to 25 MB for 40,000 of them, an LRU bound on live rings, and an open rule requiring both a minimum attempt count in the window and a rate above threshold.
Follow-up
  • The fleet is 30 instances and each sees roughly a thirtieth of a destination's traffic. Where does the rate actually live, and what does a per-instance answer get wrong?
  • A destination answers in 9.5 seconds and succeeds. It is not failing but it is consuming your per-destination concurrency. What signal should open the circuit here?
  • How would you make the window survive a process restart, and is it worth the cost?

For a candidate senior enough that the loop turns on design and judgement rather than on whether the coding round gets finished. Five days build one system properly and then stress it; coding gets a single maintenance day, on the assumption that the risk at this level is an unexamined tradeoff rather than a missed algorithm.

Small steps. Visible outcomes.0 / 7 completed
ONE WEEK · YOUR PACE

Prepare, practise & reflect

One practical outcome each day. Spend longer where you need it.

0 / 7 done
01Numbers before diagrams
  • Build your own reference card of the figures you will re-derive all week: bytes for a realistic record, requests per second implied by a given daily active count, and the storage that a year at a given write rate produces. Derive each one rather than copying it, because the derivation is what survives a follow-up.
  • Turn one product statement into capacity requirements. From ten million daily users at four writes and forty reads each, state the peak-to-average factor you are assuming and why, then produce peak write QPS, peak read QPS and a year of storage.
  • Write the two numbers whose order of magnitude changes the design, the read-to-write ratio and the working-set size against memory per node, and state the threshold at which each one flips your answer.

Deliverable: A one-page numbers card and one worked capacity estimate with every assumption written down.

Practice prompt ↗Practice prompt ↗Worked solution ↗
02One system, from requirements to schema
  • Spend the first ten minutes producing only functional requirements, non-functional targets with numbers attached, a p99 latency, a durability expectation, a consistency requirement, and an explicit out-of-scope list.
  • Define the interface before the boxes: the three or four endpoints, their parameters, what each returns, and which of them are idempotent.
  • Write the data model, then write the single access pattern that justifies it, and state what the schema would have to become if the dominant access pattern were the other one.

Deliverable: One design carried to endpoint-and-schema depth, with non-functional targets expressed as numbers and a written out-of-scope list.

Practice prompt ↗Practice prompt ↗
03The consistency you are actually buying
  • Write out what a client sees under asynchronous replication when its write commits on the leader and its next read is served by a lagging follower, then write the two fixes, pinning that session's reads to the leader for a bounded window or carrying a version token the replica must reach, and the cost of each.
  • Work the quorum arithmetic on paper for N of three with W and R of two, and separate what R + W > N does guarantee, that any read set intersects any write set, from what it does not: on its own it is not linearizability, and a sloppy quorum that accepts writes on nodes outside the preference list breaks even the intersection.
  • Take two storage choices with different defaults, a single-leader relational store committing synchronously and a quorum-replicated store that converges eventually, and write the specific product behaviour that would be wrong under each, rather than a general statement about which is stronger.

Deliverable: A page separating what quorum overlap guarantees from what it does not, with one concrete product misbehaviour attached to each gap.

Practice prompt ↗Practice prompt ↗
04Failure is the design
  • For one write path, work through the case where the client times out after the server has already committed, then design the idempotency key: who generates it, how long it is retained, and what the duplicate request returns.
  • Express the retry policy as parameters rather than as a word: maximum attempts, base delay, backoff factor, jitter, and which error classes are retried at all. Then state why retrying a non-idempotent write without a key is a correctness bug and not merely waste.
  • Compute the fan-out effect on tail latency. If a request waits on ten backends and each independently exceeds its p99 one percent of the time, the chance at least one is slow is 1 - 0.99^10, about ten percent. Then write why independence is the optimistic assumption and what correlates them in practice.
  • Name the backpressure mechanism for one queue or one dependency in the design, a bounded queue with shedding or a concurrency limit, and write what the caller is told when it engages.

Deliverable: One write path with an idempotency design, a parameterised retry policy, and a written tail-latency calculation with its assumption named.

Practice prompt ↗Practice prompt ↗Worked solution ↗
05Scaling the hot path
  • Choose cache-aside or write-through for one read path and write the staleness window each produces, then name the invalidation event and what the system does when that event is lost.
  • Design against the stampede: either coalesce requests so only one recomputes a missing key, or refresh early with jittered expiry, and write why identical TTLs on keys populated in the same moment produce a synchronised expiry and a thundering herd.
  • Shard one table by a key you choose, then answer the two questions that break the choice: which queries now require a scatter-gather, and what happens to the distribution when one tenant is a hundred times larger than the median.
  • Write the cost of adding a node under plain modulo placement, where nearly every key moves, against consistent hashing, where roughly one key in n+1 moves, and state what virtual nodes are for.

Deliverable: A caching and sharding decision for one path, each with its failure mode and its rebalancing cost written beside it.

Practice prompt ↗Practice prompt ↗
06Keep the coding hand in, at the bar that applies to you
  • Solve one medium problem in thirty minutes, then spend twenty more making it production-shaped: named invariants, validation at the boundary, and errors that distinguish a caller mistake from an internal fault.
  • Write the tests you would require of a colleague's version of that function: one for empty input, one for the boundary, and one for the case the implementation is most likely to get wrong.
  • Read a piece of your own code from six months ago and write the change you would ask for, phrased as you would actually phrase it in review.

Deliverable: One problem hardened to review standard, with its test list and one written review comment.

Practice prompt ↗Practice prompt ↗
07Defend it while being interrupted
  • Run a forty-five-minute design mock with an interviewer briefed to change a requirement halfway, a tenfold traffic increase or a new strict consistency requirement, and to push on one number you estimated.
  • Rehearse the two sentences a senior loop is listening for: naming the tradeoff you are choosing against and why, and saying what you would measure to learn that the choice was wrong.
  • Prepare the design you regret: a real decision, the constraint that produced it, what it cost, and what you changed afterwards.

Deliverable: Mock notes recording how the design changed under the new requirement, plus a written account of one regretted decision.

Practice prompt ↗Practice prompt ↗Worked solution ↗

Expand any day for tasks and deliverables. Your progress is saved on this device.

Counting review comments or mentees proves nothing. The useful version is a specific change you approved with a reservation you stated, or one you blocked and the delay that cost. Say which standard you were holding and why it was worth the friction. A mentoring story needs the thing the other person can now do without you.

What motivates you in your work, particularly in a healthcare setting?

medium
behavioural and collaboration

What motivates you in your work, particularly in a healthcare setting?

Approach
  1. Pick a story where you made the decision, not one where you watched it.
  2. State the situation in two sentences and spend the rest on the reasoning.
  3. Close with what you would do differently, concretely.
Follow-up
  • How did you know your change caused the improvement?
  • What did you decide not to do, and why?

How do you handle feedback and criticism of your work?

medium
behavioural and collaboration

How do you handle feedback and criticism of your work?

Approach
  1. Give the blast radius: what could have broken, and what you measured.
  2. State the situation in two sentences and spend the rest on the reasoning.
  3. Close with what you would do differently, concretely.
Follow-up
  • What would you do differently if you ran that again?
  • What did you decide not to do, and why?

Reverse your own decision and price the reversal

medium
reversibilitymeasurementmigrations

Describe a technical decision you made and later reversed. Pick one that cost something: a service you split and merged back, a cache you added and removed, an index you created that pushed the planner onto a worse plan, a projection you rebuilt from scratch. State what you believed when you decided, the measurement that changed your mind, how long the wrong version ran in production, and what the reversal cost in migrations, dual writes, and a deprecation window for callers you did not own.

Approach
  1. State the original rationale without irony, in the version you would still defend given what was known then. If it is not defensible, the story is about carelessness rather than judgement, and a different example serves you better.
  2. Give the measurement that moved with a before and after: the p99 that did not improve, the cache hit rate that sat at 40%, the plan that flipped to a sequential scan once the table passed a size you can name.
  3. Cost the reversal in steps, not adjectives: expand-and-contract deploys, the dual-write window, the callers who had to be notified, the rows already written in the wrong shape that had to be backfilled or abandoned.
  4. Distinguish reversal from rewrite by naming what you kept. Most good reversals preserve the schema or the interface and undo one decision inside it, which is also why they were affordable.
  5. Finish on the process change: the smallest experiment that would have produced the same measurement in a day, and why you did not run it the first time.
Follow-up
  • What in that decision was irreversible, and did you know it was irreversible when you made it?
  • How did you tell the people who had already built on top of the original decision?
  • What do you now measure before committing to a change of this size?
  • 01

    What motivates you in your work, particularly in a healthcare setting?

  • 02

    How do you handle feedback and criticism of your work?

  • 03

    Describe a technical decision you made and later reversed. Pick one that cost something: a service you split and merged back, a cache you added and removed, an index you created that pushed the planner onto a worse plan, a projection you rebuilt from scratch. State what you believed when you decided, the measurement that changed your mind, how long the wrong version ran in production, and what the reversal cost in migrations, dual writes, and a deprecation window for callers you did not own.

PracHub interview preparation framework ↗
Is this an official Eli Lilly and interview guide?

No. It is PracHub's own research and practice material for the Machine Learning Engineer role at Eli Lilly and. Rounds and questions reflect what candidates have reported, not a process Eli Lilly and has published, and they change over time. Confirm the current format and scope with your recruiter.

PracHub interview research ↗
How difficult are the interviews?

The interviews can be challenging, focusing both on technical and behavioral aspects. Candidates should prepare thoroughly, as interviewers will assess both your expertise and cultural fit.

PracHub interview research ↗
What differentiates successful candidates?

Successful candidates often demonstrate a strong blend of technical skills, problem-solving ability, and a collaborative mindset. They align well with Eli Lilly and's values and show a genuine interest in advancing healthcare.

PracHub interview research ↗
What is the typical timeline from the initial screen to an offer?

The timeline can vary, but candidates may expect the process to take several weeks, depending on the number of interview rounds and the coordination of schedules.

PracHub interview research ↗
Is remote work an option for this role?

While the specifics may vary by team and project, Eli Lilly and supports a hybrid work model, allowing for flexibility in working arrangements.

PracHub interview research ↗
Sources & methodology 3 sources ↗

No official company page is cited. Rounds and questions come from candidate reports and PracHub editorial material; each source shows the date it was read.