Harvard Medical School Software Engineer Interview Guide

The 60-second brief

A Software Engineer at Harvard Medical School (HMS) occupies a unique and pivotal role at the intersection of cutting-edge technology and transformative biomedical research. Unlike traditional tech companies, engineering at HMS is often embedded within specific labs, core facilities, or specialized departments like the Department of Biomedical Informatics. Your work directly enables world-class scientists to process massive datasets, visualize complex biological structures, and accelerate the pace of medical discovery. The impact of this position is felt across a wide range of platforms, from clinical decision-support tools used in hospitals to high-performance computing pipelines that sequence genomes. As a Software Engineer, you are not just writing code; you are building the infrastructure that allows researchers to solve some of the most challenging problems in human health.

This guide is scoped to a Software Engineer candidate at Harvard Medical School.

Focus areas

• Python
• Take-Home Coding Assessments
• Phone Screen Interviewing

The Harvard Medical School interview process

Harvard Medical School candidates report 4 rounds over 3-5 weeks. The stages below are what candidates describe, not a published process.

Initial Outreach

The process begins with outreach to candidates, often involving administrative screening.

What to demonstrate

• The process begins with outreach to candidates, often involving administrative screening
• Depth in Python

How to prepare

• Answer aloud and timed: How do you handle large datasets in Python without exhausting system memory?
• Answer aloud and timed: Explain the difference between a list and a generator in Python and when you would use each in a data pipeline.

Technical Assessment

Candidates undergo evaluations focusing on Python proficiency and real-world research problems.

What to demonstrate

• Candidates undergo evaluations focusing on Python proficiency and real-world research problems
• Depth in Python

How to prepare

• Answer aloud and timed: Describe a time you had to debug a complex piece of code written by someone else. How did you approach it?
• Answer aloud and timed: What are your preferred libraries for data visualization, and why?

Behavioral Assessment

Final rounds involve meeting with researchers to assess cultural fit and collaboration skills.

What to demonstrate

• Final rounds involve meeting with researchers to assess cultural fit and collaboration skills
• Depth in Python

How to prepare

• Prepare three examples from your own work, each with a decision you made and an outcome you can quantify.
• Re-read the description of the behavioral assessment above and write down what you would ask to confirm before it.

Final Meeting with PI

Candidates meet with a Principal Investigator to discuss project alignment and expectations.

What to demonstrate

• Candidates meet with a Principal Investigator to discuss project alignment and expectations
• Depth in Python

How to prepare

• Answer aloud and timed: Give an example of a time you had to learn a new technology or domain (like a biological concept) quickly to complete a project.
• Answer aloud and timed: What is your approach to code reviews in a small team environment?

Where candidates lose points

Prioritize Documentation

In your technical assessments and take-home tests, treat documentation as a first-class citizen. At HMS, code that others cannot understand or replicate is considered a failure.

Showcase "Full-Stack" Thinking

Even if you are applying for a backend role, show that you understand how your work impacts the end-user (the researcher).

Be Patient with the Process

The academic hiring cycle is often slower than the corporate world. Stay engaged and use the time between rounds to learn more about the specific lab's research.

Some candidates report "ghosting" after technical rounds

If you haven't heard back, reach out politely. The delay is often due to the PI’s travel or grant deadlines rather than a lack of interest.

Questions & practice

Archive a resource graph without breaking live references or recursing

Medium · graph traversal · topological order · tenant isolation

Resources reference other resources within a tenant; for the largest tenant the reference table holds up to 2,000,000 nodes and 8,000,000 edges. Archiving a resource must archive everything reachable from it that nothing outside the set still references, refuse when a live external referrer exists, and terminate when references form cycles, which they legitimately do. Produce the archive order and the refusal list, targeting O(V+E). Say what stops the traversal crossing a tenant boundary, and why recursion is the wrong control structure at this size.

Approach

1. Load the subgraph with the tenant predicate on both endpoints of the edge, not only on the side you started from. Scoping the left table alone is the classic cross-tenant leak: one mis-entered edge then pulls another tenant's resources into the traversal and, worse, into the archive.
2. Traverse iteratively with an explicit stack. A 2,000,000-node graph can hold a chain deep enough to exhaust a native stack in the low tens of thousands of frames, and that failure is a process crash rather than an error you can return.
3. Treat cycles as data rather than corruption: compute strongly connected components with Tarjan in O(V+E) using its own explicit stack, then condense. The condensation is a DAG, so a topological order over it gives the archive order, and every member of a component archives in one transaction because no order within a cycle is valid.
4. Decide refusals with reverse edges. A candidate is archivable only if every in-edge originates inside the candidate set, so build the transpose or count in-degrees restricted to the visited set, and emit each blocked resource with the id of the external referrer, which is the only part of the answer an operator can act on.

Follow-up

• The graph is read in one query and the archive writes a minute later. What can change in between, and how do you make the write safe?
• The candidate set is 400,000 resources. Is that one transaction, and if not, what does a half-finished archive look like to a reader?

Canonicalise a request body into a stable idempotency fingerprint

Medium · parsing · canonicalisation · hashing

idempotency_key.request_fingerprint is a SHA-256 over the method, path and canonicalised body, and a retry whose fingerprint differs must be rejected with 422 rather than served the stored response. Write the canonicaliser. Bodies are JSON up to 256 KB nested at most 32 levels; clients vary key order, whitespace and unicode escaping, and some send 64-bit ids as JSON numbers. Produce a deterministic byte string such that semantically identical bodies match and any semantic difference does not. State your complexity and name two normalisations you refuse to perform.

Approach

1. Parse once into a tree, then re-serialise under fixed rules: object keys sorted, array order preserved, one escaping convention, no insignificant whitespace. Parsing is O(n) and sorting keys is O(k log k) per object, so O(n log n) overall with O(depth) stack, and the 32-level cap is enforced during parsing because hostile nesting is how a canonicaliser becomes a stack overflow.
2. Sort keys by their UTF-8 bytes and say why the obvious implementation is wrong in some runtimes: a default string comparison that orders by UTF-16 code units places surrogate pairs, meaning code points from U+10000 up, below U+E000 to U+FFFF, which is not UTF-8 byte order, so two services written in different languages disagree on the same document.
3. Do not re-encode numbers through a double. IEEE-754 binary64 represents integers exactly only up to 2^53, so normalising a 19-digit id through a float changes it, and 1 against 1.0 cannot be reconciled without deciding whether they are the same value. Preserve the literal token, and require ids as strings at the API boundary if you want them comparable.
4. Reject duplicate keys rather than picking one. JSON permits them and parsers disagree, most keeping the last, so any choice you make ties the fingerprint to a parser detail that the code handling the request does not necessarily share.

Follow-up

• A client sends the same logical request with an extra field your API ignores. Same key, different fingerprint, so you return 422. Is that the right answer?
• Where does the fingerprint get computed relative to request decompression and the body-size limit?

Identify the heaviest tenants in a five-minute window under memory pressure

Medium · top-k · heavy hitters · streaming

The edge service handles about 3,000 requests per second across roughly 50,000 tenants, peaking near 9,000. Expose the 50 heaviest tenants by request count over the trailing five minutes so limits can be tightened before one tenant's backfill starves the fleet. You may not retain five minutes of raw records. Give the exact solution and its memory, then the bounded-memory approximation with its error stated as a formula, and say which you would ship and at what tenant cardinality that choice changes.

Approach

1. Do the exact version first, because it is affordable at this cardinality: a ring of 300 one-second counters per tenant, advanced lazily, is 1,200 bytes of counters per tenant and roughly 60 to 90 MB for 50,000 tenants with overhead. Carry a running total and subtract the bucket you overwrite so a window read is O(1) rather than 300 adds.
2. Extract the top 50 with a size-k min-heap over the tenant sums: O(d log k) for d tenants, against O(d log d) to sort them all. Maintaining the heap continuously instead of on query requires a tenant-to-heap-index map, because incrementing a count already inside the heap means sifting from a known position, and without that map you rebuild the heap on every request.
3. State the approximation precisely rather than gesturing at sketches. Misra-Gries with m counters retains every item whose true count exceeds N/(m+1), and each retained count underestimates the truth by at most N/(m+1). With m = 1,000 and N = 900,000 requests in the window the error is roughly 900 requests, which is fine for spotting a tenant sending 50,000 and useless for ranking two tenants 200 apart.
4. Say what breaks when the window slides: Misra-Gries and Space-Saving are insert-only and cannot be decremented as records age out. The workable construction is one summary per sub-window, say ten seconds, with 30 summaries merged at query time, and the merged error is the sum of the per-summary errors, so the bound degrades linearly in the number of sub-windows.

Follow-up

• The heaviest tenant is heavy because of one export job rather than user traffic. Should the limiter treat those as the same tenant?
• Two tenants sit tied at the boundary of the top 50. Does your answer flap, and does the flapping matter?

Keep soft-deleted accounts from blocking re-registration

Easy · soft delete · unique constraints · engine differences

app_user holds user_id, tenant_id, email CITEXT, password_hash (NULL for SSO principals), email_verified_at, auth_version, status ('invited','active','suspended','deactivated'), created_at, updated_at, deleted_at. Two live accounts for one address inside a tenant must be impossible, but an address freed by a soft delete must be reusable, and the same tenant may delete and re-register it repeatedly. Write the uniqueness DDL for PostgreSQL 16, then the equivalent for MySQL 8 where partial indexes do not exist, and say what each permits once three deleted rows already hold that address.

Approach

1. Start from what is actually unique: not (tenant_id, email), but (tenant_id, email) among live rows. PostgreSQL says that directly — CREATE UNIQUE INDEX app_user_live_email ON app_user (tenant_id, email) WHERE deleted_at IS NULL. A full constraint over the same two columns burns the address permanently the first time someone deletes an account.
2. Keep case-insensitivity in the type or the index, never in the application: CITEXT as given, or UNIQUE (tenant_id, lower(email)) as an expression index where the extension is unavailable. A case-sensitive unique column is exactly how two accounts for one human appear.
3. For MySQL 8 the predicate has to move inside the key: add a discriminator column that is a constant 0 while the row is live and is set to user_id on delete, with UNIQUE (tenant_id, email, deleted_marker). Live rows share the constant and still collide; deleted rows differ from each other and stop colliding.
4. State the NULL variant and its dependency: leaving the marker NULL for deleted rows also works, because a unique index treats NULLs as distinct — true in MySQL, and true in PostgreSQL only under the default NULLS DISTINCT, which PostgreSQL 15 lets you reverse. Check the polarity against the three existing deleted rows: constant-on-live is what preserves the collision you want, and reversing it silently admits duplicate live accounts.

Follow-up

• A deleted account re-registers with the same address the next day. Do the old resource rows follow the new user_id, and how does the API keep the two principals apart?
• How do you honour an erasure request while resource_revision.actor_user_id still references this table?

Write the update path that detects a concurrent edit

Medium · optimistic concurrency · transactional outbox · audit history

resource carries version INT NOT NULL DEFAULT 1. resource_revision holds revision_id, resource_id, version, actor_user_id, change_kind, patch JSONB, request_id, created_at with UNIQUE (resource_id, version). outbox_event holds aggregate_type, aggregate_id, aggregate_version, event_type, payload, status. A PUT carries the version the client read. Write the exact statements for the single transaction that applies the edit, records the revision and enqueues 'resource.updated', and give the handler's branch on zero affected rows. Then say what PostgreSQL 16 does under READ COMMITTED when two of these updates hit one row at once.

Approach

1. One transaction, three writes, no network call inside it: UPDATE resource SET title = $3, version = version + 1, updated_at = now() WHERE resource_id = $1 AND tenant_id = $4 AND version = $2; then INSERT the resource_revision row at version $2 + 1; then INSERT the outbox_event row at the same aggregate_version. The event goes to a table rather than a broker because no transaction spans both.
2. Branch on the affected-row count before doing anything else. Zero has three causes — stale version, wrong tenant, row gone — so re-read once and map to 409 carrying the current version, or 404 for an id outside the caller's tenant, which also stops the endpoint confirming that another tenant's id exists.
3. State the engine behaviour instead of assuming it. Under READ COMMITTED the second UPDATE blocks on the row lock, and when the first commits PostgreSQL re-evaluates the WHERE clause against the newly committed row, so the version predicate now fails and the statement reports zero rows. Under REPEATABLE READ the identical collision raises SQLSTATE 40001 instead, so the handler must fold both shapes into one conflict response.
4. Keep UNIQUE (resource_id, version) even though the predicate already serialises writers. It is what makes a lost update unwritable if any other path ever reaches the revision table, and it converts a logic bug into 23505 rather than into a silently missing history row.

Follow-up

• A client sends the version it read ten minutes ago and the resource has moved three versions. What is in your 409 so it can resolve the conflict without a full re-fetch?
• Two editors, two disjoint fields, no overlap. Does your answer still refuse the second write, and should it?

Explain the difference between a list and a generator in Python and when you would use each in a data pipeline

Medium · Python & Technical Logic

Explain the difference between a list and a generator in Python and when you would use each in a data pipeline.

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

What are your preferred libraries for data visualization, and why?

Medium · Python & Technical Logic

Approach

1. Clarify what is being asked and what a complete answer contains.
2. State your assumptions explicitly before working the problem.
3. Say what you would check first and why it is the highest-information step.
4. Work from the requirement backwards to the design.

Follow-up

• What assumption would you test first?
• How would you know your answer was wrong?

How would you design a system to store and retrieve large amounts of metadata associated with clinical samples

Medium · System Design & Architecture

How would you design a system to store and retrieve large amounts of metadata associated with clinical samples?

Approach

1. Fix the scope first: who calls this, how often, and what they do when it fails.
2. Name the read and write paths separately; they rarely have the same bottleneck.
3. Choose a partition key and say what query it makes expensive.
4. State the consistency you need, and where you are willing to be stale.

Follow-up

• What breaks first when traffic grows ten times?
• How does this behave when that dependency is down for an hour?

Walk us through the architecture of a web application you built from scratch.

Medium · System Design & Architecture

Approach

1. Fix the scope first: who calls this, how often, and what they do when it fails.
2. Name the read and write paths separately; they rarely have the same bottleneck.
3. Choose a partition key and say what query it makes expensive.
4. State the consistency you need, and where you are willing to be stale.

Follow-up

• What breaks first when traffic grows ten times?
• How does this behave when that dependency is down for an hour?

How do you ensure that your software is reproducible across different computing environments?

Medium · System Design & Architecture

Approach

1. Fix the scope first: who calls this, how often, and what they do when it fails.
2. Name the read and write paths separately; they rarely have the same bottleneck.
3. Choose a partition key and say what query it makes expensive.
4. State the consistency you need, and where you are willing to be stale.

Follow-up

• What breaks first when traffic grows ten times?
• How does this behave when that dependency is down for an hour?

Exports duplicate a row range about once a week

Hard · leases · clock skew · idempotency

Roughly once a week an export writes a file containing a duplicated range of rows. The affected job_run rows show attempt = 1, status = succeeded, one started_at, and a lease_owner naming a different host from the one whose logs show the job starting. Leases last 30 seconds and are heartbeated every 10 from inside the handler; lease_expires_at is computed on the worker and compared against the database's now(). Find the mechanism, and give a fix that holds even if you cannot fix the clocks.

Approach

1. Start from the fact that eliminates the obvious answer. attempt = 1 means no retry was recorded, so this is not a re-run after failure; two workers ran the same row concurrently and the takeover path never touched the counter. lease_owner naming a host other than the one that started the job is the same statement from the other side.
2. Enumerate the mechanisms that cause a premature takeover, then find the signal that separates them. Either the lease genuinely expired because the heartbeat did not fire, which is what happens when the heartbeat runs on the handler's own thread and the handler makes a long blocking call, or it only appeared expired because two clocks disagree, since lease_expires_at is written from the worker's clock and evaluated against the database's. The discriminator is the distribution: incidents clustered on the longest exports indict the heartbeat, incidents clustered on one host indict skew. Measure both, and measure each host's offset against the database directly.
3. Read the reclaim query precisely. In PostgreSQL now() is transaction start time, not statement time, so a reclaimer holding a long transaction compares against an older timestamp than expected; clock_timestamp() is the statement-time function. This is worth ruling in or out before you redesign anything, because it changes which rows look expired.
4. Remove the second clock rather than trying to synchronise it. Issue and extend the lease in the database, with lease_expires_at = now() + interval '30 seconds' in both the claim and the heartbeat, so exactly one clock is ever compared and worker skew stops mattering to this predicate.

Follow-up

• The displaced worker has already streamed half the file to object storage. What makes that side effect safe to repeat?
• You now count takeovers. What alert fires on that counter, and at what threshold?

Suggested practice checklist

Built from the rounds and topics Harvard Medical School candidates report.

Day 1 — Map the Harvard Medical School loop

• Write out the reported sequence: Initial Outreach, Technical Assessment, Behavioral Assessment, Final Meeting with PI.
• For each round, write one sentence on what it is judging, from the description above, and mark the one you are least ready for.

Deliverable: A one-page map of the 4 reported rounds, with the weakest marked.

Day 2 — Work Python

• Spend the session on Python, which Harvard Medical School candidates report being tested on.
• Write one worked example in Python and time yourself on it.

Deliverable: One timed worked example in Python.

Day 3 — Work Take-Home Coding Assessments

• Spend the session on Take-Home Coding Assessments, which Harvard Medical School candidates report being tested on.
• Write one worked example in Take-Home Coding Assessments and time yourself on it.

Deliverable: One timed worked example in Take-Home Coding Assessments.

Day 4 — Work Phone Screen Interviewing

• Spend the session on Phone Screen Interviewing, which Harvard Medical School candidates report being tested on.
• Write one worked example in Phone Screen Interviewing and time yourself on it.

Deliverable: One timed worked example in Phone Screen Interviewing.

Day 5 — Answer out loud: Python & Technical Logic

• Answer aloud, timed: How do you handle large datasets in Python without exhausting system memory?
• Answer aloud, timed: Explain the difference between a list and a generator in Python and when you would use each in a data pipeline.

Deliverable: Spoken answers to 2 reported Python & Technical Logic question(s), under time.

Day 6 — Answer out loud: Behavioral & Lab Collaboration

• Answer aloud, timed: Describe a situation where you had to explain a technical limitation to a non-technical stakeholder.
• Answer aloud, timed: How do you prioritize tasks when multiple researchers are asking for your help on different projects?

Deliverable: Spoken answers to 2 reported Behavioral & Lab Collaboration question(s), under time.

Day 7 — Answer out loud: System Design & Architecture

• Answer aloud, timed: How would you design a system to store and retrieve large amounts of metadata associated with clinical samples?
• Answer aloud, timed: Walk us through the architecture of a web application you built from scratch.

Deliverable: Spoken answers to 2 reported System Design & Architecture question(s), under time.

Behavioural preparation

Behavioural rounds judge the decision you made and what it cost.

How do you handle large datasets in Python without exhausting system memory?

Medium · Python & Technical Logic

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. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

Describe a time you had to debug a complex piece of code written by someone else. How did you approach it?

Medium · Python & Technical Logic

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. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

Describe a situation where you had to explain a technical limitation to a non-technical stakeholder.

Medium · Behavioral & Lab Collaboration

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. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

How do you prioritize tasks when multiple researchers are asking for your help on different projects?

Medium · Behavioral & Lab Collaboration

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. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

Give an example of a time you had to learn a new technology or domain (like a biological concept) quickly to c

Medium · Behavioral & Lab Collaboration

Give an example of a time you had to learn a new technology or domain (like a biological concept) quickly to complete a project.

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. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?

What is your approach to code reviews in a small team environment?

Medium · Behavioral & Lab Collaboration

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. Give the blast radius: what could have broken, and what you measured.
4. Name the disagreement and how you resolved it with evidence.

Follow-up

• What would you do differently if you ran that again?
• How did you know your change caused the improvement?